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Chapter 5. Regulation of Neuronal
Gene Expression and Protein
Synthesis
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.1 The central dogma of molecular biology.
The three main steps of information decoding within eukaryotic cells are depicted. Genetic information encoded within DNA
is duplicated by the process of DNA replication, or the information within DNA is converted to RNA via the process of
transcription. The information encoded within the RNA sequence is converted into protein via the process of translation.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.2 The structure of deoxyribonucleic acid (DNA).
(A) Structure of a right-handed DNA showing the four nucleotide bases paired and arranged in a double helix configuration. (B)
Chemical structure of DNA showing the hydrogen bonds between the bases as red dotted lines.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.3 The structure of ribonucleic acid (RNA).
(A) Chemical structure of a short stretch of single-stranded RNA showing the ribonucleosides linked by phosphodiester
bonds. (B) Secondary structure of a transfer RNA (tRNA) molecule showing its anticodon pairing with the codon within an
mRNA molecule.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.4 Sequence of events in transcription.
(A) Step-wise assembly of the transcriptional complex. (B) Representative model of a transcriptional complex with
activators, repressors and the basal transcriptional machinery.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.5 The initiation of eukaryotic transcription.
The four main steps in transcription initiation are shown: Following relaxation of chromatin to make the DNA accessible via
chromatin remodeling, there is the association of trans acting proteins aided by cis and trans activating and enhancing
sequences and finally by the recruitment of RNA polymerase to the promoter and formation of the basal transcription complex.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.6 The structure of messenger RNA (mRNA).
The figure shows a typical mRNA molecule with the 5-methyl cytosine CAP at the 5′ end, the open reading frame with the
start/stop codons and the poly-A tail. Also illustrated flanking the open reading frame are 5′ and 3′ UTRs (untranslated regions)
that contribute to translational regulation and transport.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.7 The mechanism of mRNA splicing.
The figure depicts the steps in mRNA splicing showing the various proteins and small RNAs involved as well as the cis
sequences encoded within the pre-mRNA that direct the removal of introns.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.8 The packaging of DNA within chromatin.
(A) Depiction of chromatin from the higher order structures to the basic unit called a nucleosome. The figure shows the various
covalent modifications on histone “tails” that stick out of the nucleosome. (B) Details of the structure of an individual nucleosome
particle showing the core histone octamer (H2A, H2B, H3 and H4), the DNA wrapped around the core in grey and the linker histone
H1 as a rod.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.9 Mechanisms of neuronal activity-induced transcription of Fos.
This figure represents the steps of activity-induced transcription of the Fos gene by various transcription factors. (A) Initially, the Fos
promoter is occupied by sequence-specific transcription factors that bind to their respective response elements (REs) along with RNA
polymerase II, which primes the gene for an immediate response to neuronal activity. Transcription is silenced by the association of
HDACs that prevents chromatin relaxation. (B) Neuronal activity leads to an increase in calcium, which in turn leads to the
recruitment of CBP and other activating cofactors and the removal of HDACs from the promoter. (C) Enhancer elements distant from
the promoter also recruit CREB and SRF to enhance transcription. (D) Steps of transcription elongation involve the phosphorylation of
the polymerase on two sites, pSer2 and pSer5. Phosphorylation on pSer5 leads to stalled elongation. Phosphorylation on both sites is
necessary for uninterrupted elongation.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.10 Mechanisms of CREB-mediated transcription.
(A) A schematic model showing various second messenger pathways that control CREB mediated transcription. (B) A model of the
structure of the bZIP dimer (orange and green helical segments) bound across the grooves formed in the DNA double helix. (C) The
current model of CREB-mediated transcription. Under basal conditions, unphosphorylated CREB is bound to the CRE element in the
promoter of its target genes. Upon neural activity, CREB is phosphorylated at Ser-133 by various kinases within the KID domain. The
KIX domain of CBP can then bind to CREB and recruit RNA polymerase II and other factors that activate transcription. (D) CREB has
distinct domains that interact with different cofactors including TAFII130, CBP and CRTC, which can also promote CREB-mediated
transcription by a mechanism independent from the phosphorylation of Ser 133.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.11 Steps involved in translation initiation.
Eukaryotic translation initiation factor 2 (eIF2) and GTP bind to methionyl–transfer RNA (Met–tRNAiMet), and the ternary complex
associates with the 40S ribosomal subunit. The association of eIF3 and eIF1A, additional initiation factors, with the 40S subunit promotes
ternary complex binding and generates the 43S pre-initiation complex. The cap-binding complex, which consists of eIF4E (4E), eIF4G and
eIF4A (4A), binds to 5' methylated cap of the mRNA (m7GTP). eIF4G also binds to the poly(A)-binding protein (PABP), which links the 5'
and 3' ends of the mRNA. This mRNA circularization and the helicase activity of eIF4A promote the binding of the 43S pre-initiation
complex to the mRNA to generate the 48S pre-initiation complex. The ribosome then scans the mRNA to find the AUG start codon.
Subsequently, GTP is hydrolyzed by eIF2, which triggers the dissociation of the initiation factors from the 48S complex, thereby
permitting binding of the large 60S ribosomal subunit, which requires eIF5B and GTP. This results in the formation of the 80S ribosome
that is competent for translation elongation and protein synthesis.
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Figure 5.12 Translational control by the phosphorylation of eIF2α.
The eukaryotic translation initiation factor 2 (eIF2) binds to methionyl–transfer RNA (Met–tRNAiMet) when it is bound to GTP and
then associates with the 40S ribosomal subunit. After the ribosome finds the start codon, GTP is hydrolyzed by eIF2 and eIF2
bound to GDP is released. The guanine nucleotide-exchange factor (GEF) eIF2B converts inactive eIF2–GDP back to eIF2–GTP. This
step is inhibited by the phosphorylation of the α subunit of eIF2 on serine 51 by one of the four known eIF2 kinases (HRI, PKR,
GCN2, and PERK). Phosphorylation of eIF2α converts eIF2 to a competitive inhibitor of eIF2B, which results in more eIF2 bound to
GDP, thereby reducing general translation but increasing translation of specific mRNAs with upstream open reading frames
(uORFs).
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Figure 5.13 Cap-dependent translational control by the mTORC1 and ERK signaling pathways.
Sequential activation of PI3K, PDK, Akt, and mammalian target of rapamycin complex 1 (mTORC1) results in activation of p70 S6 kinase 1
(S6K1). Phosphorylation of eIF4E-binding protein 2 (4E-BP2) by mTORC1 induces its release from eIF4E, which results in the association of
eIF4E with eIF4G and the formation of the active eIF4F initiation complex (eIF4E+eIF4A+eIF4G). eIF4F promotes the binding of mRNA to the
43S pre-initiation complex to form the 48S initiation complex. The ERK-dependent phosphorylation of Mnk1, which can phosphorylate eIF4E,
and S6K1, which can phosphorylate ribosomal protein S6, is correlated with enhanced translation initiation.
Copyright © 2014 Elsevier Inc. All rights reserved
Figure 5.14 CPE-dependent translational control by CPEB.
CPE-binding protein (CPEB) binds to the mRNA cytoplasmic polyadenylation element (CPE) to control polyadenylation. CPEB also
associates with symplekin, a scaffold-like protein that also binds Gld2 (a poly(A) polymerase), PARN (a deadenylating enzyme), and
PABP (not shown); together this complex of proteins is known as the cleavage and polyadenylation specificity factor (CPSF).
Phosphorylation of CPEB by either Aurora A or αCaMKII, enhances its affinity for the CPSF, and also releases PARN. Because CPEB is also
bound to an active Gld2, the poly(A) tail of the mRNA is extended, and translation of the CPE-containing mRNA is promoted.
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