Chapter 3
Genes, Gene Expression and
Development
© 2012 by John Wiley & Sons, Ltd.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.1 Structure of chromatin. (a) Simplified diagram illustrating nucleosome
structure. The core particle consists of two molecules each of histones H2A, H2B,
H3 and H4. Histone H1 is on the outside of the particle. This is based on a diagram
in Raven et al. (2003). (b) DNA is wrapped round nucleosomes to form the ‘beads
on a string’ structure (note: histone H1 is omitted from this diagram for the sake of
clarity). The beads on a string structure is further coiled to make the 30 nm ‘solenoid’
fibre.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.2 General structure of a plant gene.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.3 Diagram of the processing of ribosomal RNA. Note that in the mature
rRNA, the 5.8S molecule is hydrogen-bonded (base-paired) to the 25S molecule
(indicated in the diagram by upright lines between the two).
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.4 Protein targeting to the ER. Proteins destined for the lumen of the ER
have, at their N-terminus, a signal peptide. This is recognized and bound by the
signal-recognition particle (SRP), temporarily halting synthesis of the protein. The
SRP docks onto the SRP receptor in the ER membrane and protein synthesis is
resumed. As it is being synthesized, the protein is threaded through the translocation
complex into the lumen of the ER. During this process, the signal peptide is removed
by signal peptidase. From Buchanan B. et al. (2002) Biochemistry and Molecular
Biology of Plants, ASPB, Rockville, MD, p 181.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.5 Two N-terminally located plant bi-partite nuclear localization signals. The
basic amino acids arginine (R), histidine (K) and lysine (L) are shown in red*. Note
that both these NLSs also have basic amino acids in the spacer region. * The full list
of single letter abbreviations for amino acids is given in the Glossary.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.6 Diagram illustrating transport of proteins through the nuclear pore complex. A protein carrying a
nuclear localization signal (NLS) is recognized by importin-a (which binds to the NLS) and importin-b (which
docks at the nuclear pore complex (NPC)). Transport through the pore can only occur in the presence of the
Ran-GTPase, which hydrolyses its bound GTP to GDP and Pi. In this form, the Ran facilitates the transport
of the transport complex through the pore. Inside the nucleus, Ran swaps its bound GDP for a GTP. This
enables it to bind directly to importin-b, leading to the dissociation of the transport complex. Note: the exact
mode of association of Ran with the transport complex prior to transit of the NPC is not clear. In this diagram,
its positioning is for the sake of clarity, not a specific indication of actual in vivo position.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.7 Computer-generated model of phosphoglycerate kinase (PGK) from pea.
PGK is a ‘moonlighting’ protein with a primary role in the cytosol and a secondary
role in the nucleus. The protein possesses a nuclear localization signal, shown in
red on the computer model. Photograph by Kirsty Line, Richard Kaschula, Jennifer
Littlechild and JAB.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.8 Targeting proteins to the chloroplast. All proteins destined for the chloroplast have an N-terminal
chloroplast stroma targeting domain. The newly synthesized proteins are bound by the chaperone Hsp70
and ‘escorted’ to the proteinaceous pore complexes (which bring the outer and inner envelopes into contact).
Once inside, the stromal targeting domain is removed. On the left side of the diagram, the protein possesses
no further targeting domains and either folds to assume its active configuration or is inserted into the
thylakoid membrane. The right side of the diagram illustrates a protein that has a second targeting sequence
for insertion into the thylakoid lumen. These are escorted by Hsp70 to the thylakoid surface and then
imported into the lumen by an import complex. The second targeting domain is removed when the protein
reaches the lumen. Note: more details may be found in the text. From Buchanan, B. et al (2002)
Biochemistry and Molecular Biology of Plants, ASPB, Rockville, MD, p 167.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.9 Diagram of an RNA silencing mechanism. Doublestranded RNA is a
target for Dicer ribonuclease, which cuts the RNA into 21 bp pieces. The pieces
associate with the AGO protein (not shown) in the RNA-induced silencing complex
(RISC). Denaturation of the small dsRNAs releases the small inhibitory RNA
molecules to base-pair with the target RNA (which, in the example shown here, will
be the same as the first strand of the original dsRNA at the top of the diagram) to
form a partially double-stranded molecule. This is a target for Slicer ribonuclease
and is thus degraded.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.10 Diagram of the ubiquitin-proteasome system for protein degradation. Proteins that are destined
for degradation are ‘marked’ by ubiquitin, a small (76 amino acids) protein. Ubiquitin is transferred by a
ubiquitination complex to lysine residues in the target protein by a five-step process. Further ubiquitin
residues may then be added in the same way. The marked protein is then delivered to the proteasome for
degradation and the ubiquitin is recycled. Key E1 = ubiquitin-activating enzyme; E2 = ubiquitin-conjugating
enzyme; E3 = ubiquitin-ligating enzyme. These are the main members of the ubiquitination complex. From
Buchanan B. et al. (2002) Biochemistry and Molecular Biology of Plants, ASPB, Rockville, MD. p 451.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.11 (a) Phototropism: Clover seedlings bend towards a unilateral source of light. Photograph by Brad
Bowman (b) In 1919, Paál showed that asymmetric replacement of a coleoptiles tip caused bending similar
to that seen in phototropism. This suggested that phototropic bending was caused by the asymmetric
distribution of a diffusible substance. In 1926, Went collected that substance, namely auxin, in gelatine
blocks; placing blocks asymmetrically on decapitated coleoptiles also induced bending. From Taiz, L and
Zeiger, E (2002) Plant Physiology, Sinauer, Sunderland, MA.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.12 Auxin signalling pathway. In the absence of auxin, the SCFTIR
ubiquitination complex is inactive. AUX and IAA proteins which are transcriptional
repressors prevent ARFs (auxin-response factors) from transcribing auxinresponsive genes. When auxin is bound to its receptor TIR, AUX/IAA proteins are
ubiquitinated by the SCFTIR complex and degraded by the proteasome. ARFs are
then able to transcribe the auxin-response genes.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.13 Cytokinin signalling pathway. Cytokinin receptors span the plasma
membrane. They have an external receptor domain and an internal histidine kinase
domain. Binding of cytokinin (CK) causes dimerization of the receptor, followed by
autophosphorylation and phosphate transfer. The histidine kinase domain also
phosphorylates AHP, a histidine phospho-transfer protein. This enters the nucleus
and transfers the phosphate group to a response-regulator protein (ARR), leading to
the transcription of cytokinin-responsive genes.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.14 GA signalling pathway. GA signalling is very similar to IAA signalling. In
the absence of GA, DELLA proteins inhibit the up-regulation by the GA-transcription
factors (GA-TFs) of the GA-responsive genes. When GA is present, it is bound by
GID1, which then interacts with the DELLA protein (or proteins), bringing them into
contact with GID2, which is part of the SCFGID2 ubiquitination complex. The DELLA
protein(s) is/are ubiquitinated and then degraded by the proteasome. This allows
transcription of the GA-responsive genes. Note: different DELLA proteins are
involved in different situations. In control of rice stem elongation, the relevant DELLA
protein is SLR1.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.15 ABA signalling pathways. Proteins with ABA receptor properties occur in four different locations.
At the plasma membrane, ABA binds to and activates a membrane-spanning G-protein. The downstream
effects of this are not yet clear. In the cytoplasm, ABA binds to the PYR family of receptors. This leads to
inhibition of the protein phosphatases AB1 and AB2, allowing phosphorylation of the regulatory protein
snRK2. Downstream of this are the effects of ABA on stomatal closure, ion channels, NADPH oxidase
activity and transcription of some ABA responsive genes. In the chloroplast, ABA binds to ABAR, leading to
effects on chlorophyll synthesis and plastid-nuclear signalling. In the nucleus, ABA binds to FCA (an RNAbinding protein), dissociating it from its partner, FY. This, in turn, prevents FCA-FY from inhibiting the floral
repressor protein FLC. When FLC is not inhibited, the activity of genes leading to flowering, including FT and
SOC1, is inhibited. ABA thus prevents, or at least delays, flowering.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.16 Ethylene synthesis. Ethylene is synthesized from the amino acid,
methionine via the cell’s methyl donor, S-adenosyl methionine. Control over ethylene
synthesis is exerted at the last two steps.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.17 Ethylene signalling pathway. Ethylene receptors such as ETR1 are membrane-spanning
proteins with an external receptor and an internal histidine kinase. In the absence of ethylene, a signalling
cascade from CTR inhibits the action of EIN2. This, in turn, permits the degradation of EIN3 and thus
ethylene-responsive genes are not transcribed. In the presence of ethylene, the receptor dimerizes and the
internal domains undergo autophosphorylation and phosphate transfer. In this state, the receptor inhibits
CTR, thus releasing EIN2, which is able to enter the nucleus and inhibit the degradation of EIN3. Ethyleneresponsive genes are transcribed. Note: CTR is also located in the ER but, for the sake of clarity in the
diagram, this is not shown.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.18 Structure of brassinolide.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.19 Brassinosteroid signalling pathway. Brassinosteroid receptors such as
BRI1 are large, complex proteins that span the plasma membrane. Also required for
activity is another membrane-spanning protein, BAK1, and the two form a heterodimer. In the absence of brassinosteroid (BL), a protein kinase, BIN2 phosphorylates
two transcription factors, preventing them from entering the nucleus and marking
them for degradation by the ubiquitin-proteasome system. When BL binds to BRI1,
its internal domain and that of BAK1 are phosphorylated. This leads to the inhibition
of BIN2, preventing the destruction of BES1 and BZR1. These enter the nucleus.
BES1 combines with BIM to up-regulate the BL-responsive genes, while BZR1
inhibits the transcription of genes involved in BL biosynthesis.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.20 Salicylic acid structure.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.21 Structure of jasmonic acid and its close derivative, methyl jasmonate.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.22 (a) General structure of strigolactones. (b) Two naturally occurring
strigolactones: on the left, (+)-strigol; and on the right, orobanchol.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.23 Phytochrome spectra. The inactive form of phytochrome, PR, is
converted to the active form, PFR, by exposure to red light (peak absorbance at 666
nm). PFR is converted back to PR by exposure to far-red light (peak absorbance at
730 nm).
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.24 Phytochrome chromophore structure. The chromophore is joined to the
phytochrome protein via a thio-ether linkage (S-S bridge) between the chromophore
and a cysteine residue. The red/far-red reversibility lies in the ‘flipping’ of a double
bond in the pyrrole ring nearest to the protein attachment point.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.25 Transverse sections of leaves of sugar maple (Acer saccharum): (a)
leaf from sunny side of the tree; (b) leaf from centre of the canopy. From Fig. 6.16 of
Hart JW (1988) Light and Plant Growth, reproduced by permission of Springer,
Heidelberg.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.26 Phytochrome signalling pathways: (a) COP (and DET & FUS) proteins inhibit phytochromeresponsive transcription factors. These proteins are inactivated by the active form of phytochrome (PFR),
probably acting as a dimer. The inactivated proteins leave the nucleus and the transcription factors are freed
to interact with the relevant genes. (b) Dimers of the phytochrome-interacting factors (PIFs) bind to
promoters of phytochrome-responsive genes. Active phytochrome dimers bring about phosphorylation of the
PIFs. This leads to their degradation by the ubiquitin-proteasome system. The gene promoters are then
available for binding by positive transcription factors.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.27 (a) Action spectrum for phototropism.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.27 (b) LOV domains are the domains in phototropin proteins that bind the FMN photoreceptors.
Absorption spectra (left) and fluorescence spectra (right) for LOV domain proteins from Arabidopsis (top four
panels in each column; the bottom panels show data from a phytochrome-related protein associated with two
LOV domains). Part of Figure 1 in Christie et al. (1999), Proceedings of the National Academy of Sciences,
USA 96, 8779–8783, © National Academy of Sciences, USA; reproduced with permission.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.
Figure 3.28 FMN – flavin mononucleotide, the phototropin photoreceptor.
Functional Biology of Plants
Martin J. Hodson and John A. Bryant
© 2012 by John Wiley & Sons, Ltd.