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Kajala Arabidopsis
Kajala Arabidopsis
Kajala Arabidopsis
doi: 10.1111/j.1365-313X.2011.04769.x
SUMMARY
C4 photosynthesis occurs in the most productive crops and vegetation on the planet, and has become
widespread because it allows increased rates of photosynthesis compared with the ancestral C3 pathway.
Leaves of C4 plants typically possess complicated alterations to photosynthesis, such that its reactions are
compartmented between mesophyll and bundle sheath cells. Despite its complexity, the C4 pathway has
arisen independently in 62 separate lineages of land plants, and so represents one of the most striking
examples of convergent evolution known. We demonstrate that elements in untranslated regions (UTRs) of
multiple genes important for C4 photosynthesis contribute to the metabolic compartmentalization characteristic of a C4 leaf. Either the 5 or the 3 UTR is sufficient for cell specificity, indicating that functional
redundancy underlies this key aspect of C4 gene expression. Furthermore, we show that orthologous PPDK and
CA genes from the C3 plant Arabidopsis thaliana are primed for recruitment into the C4 pathway. Elements
sufficient for M-cell specificity in C4 leaves are also present in both the 5 and 3 UTRs of these C3 A. thaliana
genes. These data indicate functional latency within the UTRs of genes from C3 species that have been
recruited into the C4 pathway. The repeated recruitment of pre-existing cis-elements in C3 genes may have
facilitated the evolution of C4 photosynthesis. These data also highlight the importance of alterations in trans
in producing a functional C4 leaf, and so provide insight into both the evolution and molecular basis of this
important type of photosynthesis.
Keywords: C4 photosynthesis, untranslated regions, pyruvate,orthophosphate dikinase, carbonic anhydrase,
Cleome gynandra, Arabidopsis.
INTRODUCTION
Having evolved in at least 62 separate lineages of land
plants, C4 photosynthesis is considered one of the most
remarkable examples of convergent evolution (Sage et al.,
2011). Current estimates are that land plants first started to
use C4 photosynthesis around 3032 million years ago, and
that it evolved in response to high temperatures and
reductions in atmospheric CO2 content (Christin et al.,
2008; Edwards et al., 2010; Vicentini et al., 2008). The C4
pathway allows CO2 to be concentrated around the central
photosynthesis enzyme Ribulose-1,5-Bisphosphate Carboxylase Oxygenase (RuBisCO). Because RuBisCO does not
completely distinguish between CO2 and O2 (Bowes et al.,
1971), the increased supply of CO2 to RuBisCO in C4 plants
reduces the oxygenation reaction, and in turn limits the
wasteful reactions of photorespiration (Hatch, 1987). In all
cases, C4 plants use a biochemical pump to increase the
amount of CO2 in compartments within which RuBisCO is
limited. Although photosynthesis reactions are compart 2011 The Authors
The Plant Journal 2011 Blackwell Publishing Ltd
regulation of both the PEPC and PPDK genes being important for M-cell specificity in maize and Flaveria.
It is known that genes encoding NAD-dependent malic
enzyme (NAD-ME) and NADP-dependent malic enzyme
(NADP-ME) from C3 species contain cis-elements sufficient
for BS specificity in C4 leaves, and thus cell specificity in the
C4 leaf can be mediated by changes in trans (Brown et al.,
2011). The location of cis-elements within the coding region
of these ME genes and the requirement for transcription
implies post-transcriptional regulation (Brown et al., 2011).
To determine the importance of regulation of C4 genes by
elements within their transcripts, and the extent to which
these elements are present in C3 orthologs, we used the
Cleome genus, which is closely related to Arabidopsis
thaliana and contains C3 and C4 plants (Brown et al., 2005;
Marshall et al., 2007; Voznesenskaya et al., 2007). The phylogenetic proximity to A. thaliana facilitates annotation of
likely gene function, and also provides relatively simple
resources for functional analysis of orthologous genes in a C3
species. To investigate mechanisms underlying M-cell specificity in Cleome gynandra, we isolated cDNAs and genomic
sequences encoding PPDK and CA4, and investigated
regions of each gene that were sufficient for accumulation
in M cells. By comparison with regulation of the orthologous
PPDK and b-CA4 genes from C3 A. thaliana, we were also able
to investigate the extent to which mechanisms have evolved
de novo in the C4 PPDK and CA4 genes from C. gynandra.
RESULTS
Cloning PPDK from C. gynandra
Compartmentation of photosynthesis proteins between M
and BS cells in C4 species can be generated by both transcriptional and post-transcriptional mechanisms, and in
most cases alterations in cis-elements have been linked to
this compartmentation (Akyildiz et al., 2007; Hibberd and
Covshoff, 2010; Westhoff and Gowik, 2004). To investigate
mechanisms underlying the accumulation of proteins in M
cells, we used a combination of degenerate PCR, 5 and 3
RACE, 454 sequencing and genome walking to isolate the
gene encoding PPDK from C. gynandra, the most closely
related C4 plant to the C3 model Arabidopsis thaliana (Brown
et al., 2005; Marshall et al., 2007). This allowed us to
assemble the sequence of the PPDK gene from C. gynandra
(Figure 1a). To confirm that the CgPPDK gene is highly
expressed, targeted to chloroplasts and therefore probably
important for C4 photosynthesis, we used two approaches.
First we created a fusion between the promoter sequence
(including the 5 UTR) isolated from C. gynandra and the
uidA gene encoding b-glucuronidase (GUS) and investigated whether it contained enhancer elements compared
with the orthologous promoter from the closely related C3
species A. thaliana (Figure S1A,B). This promoter drives
expression of transcripts that encode the longer form of the
C4 evolution 49
(a)
(b)
(c)
(e)
(f)
(d)
(g)
Figure 1. The PPDK promoter from C4 C. gynandra contains enhancer elements that are recognized in C3 A. thaliana.
(a) Structure of the C4 PPDK gene from C. gynandra. Exons are numbered and indicated by boxes, with black representing those that encode the mature protein, gray
representing the chloroplast transit peptide, and white indicating 5 or 3 untranslated regions. The translational start and stop codons are annotated. The promoter
directing expression of the chloroplastic protein is upstream of the first exon, while intron 2 contains a promoter that generates transcripts encoding the cytosolic
PPDK.
(b, c) GUS staining of stable transformants of A. thaliana containing either the endogenous A. thaliana (b) or C. gynandra (c) chloroplastic PPDK promoter fused to
the uidA gene. Scale bars are 0.5 cm.
(d) Quantitative analysis of GUS activity shows a 20-fold enhancement when the C. gynandra promoter was used. Boxes indicates upper and lower quartiles,
median values are represented by horizontal lines within the boxes, and minimum and maximum MUG activities for each construct are indicated by black dots and
whiskers.
(eg) Confocal laser scanning microscopy after microprojectile bombardment of Arabidopsis thaliana leaves shows that the PPDK::GFP fusion protein localizes to
chloroplasts. (e) Chlorophyll channel, (f) GFP channel, and (g) chlorophyll and GFP images merged. Scale bars = 10 lm.
(a)
(c)
(b)
(e)
CaMV 35S promoter, when the CgPPDK cDNA including 5
and 3 UTRs (Figure S1D) was incorporated into this construct, GUS accumulated preferentially in M cells (Figure 2f
and Table S1). This indicates that neither the endogenous
promoter nor the introns of CgPPDK are necessary for
preferential accumulation in M cells of C. gynandra, and that
elements contained within the transcript are sufficient for
M-cell specificity.
To investigate regions of the CgPPDK transcript that are
sufficient for preferential accumulation in M cells, we
produced a series of truncations fused to uidA
(Figure S1EG). The results showed that the CgPPDK coding
region was not necessary for preferential accumulation in M
cells, and that either the 5 UTR or 3 UTR alone was
sufficient (Figure 2f and Table S1). Compared with each UTR
alone, the presence of both 5 and 3 UTRs slightly increased
the proportion of M cells accumulating GUS.
(d)
(f)
(g)
C4 evolution 51
(a)
(b)
(c)
(d)
(e)
(a)
2 3
4 5 67
8 9
CgCA4
TAA
ATG
2
5 6 7 8
AtCA4
TAA
ATG
1
3 45 6
7 8
10 11
12 13
CgBASS2
TGA
ATG
1 2 3 4 5 6
7 8 9 10 11 12
13
AtBASS2
1 kb
TAA
ATG
(b)
(c)
(d)
(e)
(f)
(g)
(h)
(i)
C4 evolution 53
important. However, we cannot rule out the possibility that
transcriptional mechanisms contribute to cell specificity.
The fact that the BS specificity of NAD-ME proteins important for C4 photosynthesis in C. gynandra is mediated by
elements that are present in their coding regions, together
with the data on CgPPDK and CgCA4, suggests that
transcript sequence is important for M-cell and BS-cell
specificity in this species.
Genes recruited into M- or BS-specific function in the C4
pathway are present in C3 plants, but prior to recruitment
into C4 photosynthesis, tend to be expressed at relatively
constitutive and low levels (Aubry et al., 2011; Brown et al.,
2010; Taylor et al., 2010). When we expressed the uidA gene
under the control of the CgPPDK promoter in A. thaliana,
accumulation of GUS was increased in mature leaves
compared with use of the endogenous AtPPDK promoter.
This indicates that the C4 PPDK promoter has acquired
strong enhancer elements that extend expression from
senescent leaves in the C3 species A. thaliana (Taylor et al.,
2010) into mature photosynthetic leaves of C. gynandra.
Furthermore, our data indicate that these enhancer elements
are recognized by factors in A. thaliana, and thus trans
factors responsible for enhanced expression in the C4 plant
C. gynandra are already present in A. thaliana. The increased accumulation of GUS when fused to the 5 UTR of
CgPPDK alone indicates that at least part of this increased
expression may be due to elements within the 5 UTR. Our
data are also consistent with the PPDK gene recruited into
the C4 pathway from C. gynandra possessing the same dual
promoter system that produces either cytosolic of chloroplastic isoforms of PPDK as reported for other species
(Parsley and Hibberd, 2006; Rosche and Westhoff, 1995;
Sheen, 1991).
Mechanisms underlying cell specificity in C4 leaves
Because a large number of genes in multiple plant lineages
are co-opted into the pathway, it is not surprising that a
number of mechanisms, ranging from transcriptional
through post-transcriptional to translational, are known to
control accumulation of proteins in either M or BS cells
(Berry et al., 1987; Hibberd and Covshoff, 2010; Sheen,
1999). However, although post-transcriptional regulation
(Patel et al., 2004, 2006) and translational elongation (Berry
et al., 1986) have been implicated in the accumulation of
protein in BS cells, there have been no reports that these
mechanisms result in accumulation of proteins in M cells of
C4 leaves. The regulation of CgPPDK and CgCA4 is therefore
more similar to that of RbcS in the BS cells of F. bidentis
(Patel et al., 2004, 2006) and NAD-ME in C. gynandra (Brown
et al., 2011) than to that of PPDK or other M-cell-specific
proteins studied to date (Akyildiz et al., 2007; Gowik et al.,
2004; Kausch et al., 2001; Matsuoka and Numazawa, 1991).
The 5 or 3 UTR of CgPPDK or equivalent regions of
CgCA4 are sufficient to generate M-cell specificity in
ACKNOWLEDGEMENTS
We thank the Frank Smart fund for a studentship to K.K., the Biotechnology and Biology Sciences Research Council for funding, and
Samart Wanchana (C4 Rice Centre, International Rice Research
Institute) for advice.
SUPPORTING INFORMATION
Confocal laser scanning microscopy
The subcellular localization of translational fusions of coding
sequences of PPDK and CA4 to GFP was visualized by laser scanning confocal microscopy. Sections of transformed leaves were
placed on microscope slides adaxial side up, a drop of water was
added, and a cover slip was placed on top. The cells were viewed
using a Leica TCS SP5 confocal microscope (http://www.leica.com/)
with an excitation wavelength of 488 nm and a 63 water-immer-
C4 evolution 55
Figure S3. Alignment of the 5 UTRs and 3 UTRs of C. gynandra and
A. thaliana PPDK genes.
Figure S4. Quantitative assessment of CA4 and BASS2 transcripts
from mesophyll and bundle sheath cells of C. gynandra.
Figure S5. Alignment of the 5 UTRs and 3 UTRs of C. gynandra and
A. thaliana CA4 genes.
Table S1. Number of cells showing GUS staining after microprojectile bombardment.
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