2 Convergent GRN evolution at the spatial-temporal level: Carbon
Concentrating Mechanisms
Dry habitats are often also sunny, placing further specific restraints
on plant physiology and specifically photosynthesis: high light
intensity and high temperature. As plants acclimate to drought by
restricting their water loss through closing their stomata, they also
restrict CO2 uptake, reducing the available
CO2 for photosynthesis. High light becomes damaging if
the energy obtained from light absorption is not used by the
photosynthetic electron transport chain due to the absence of
CO2. Simultaneously, high temperature reduces the
solubility of gases so that RuBisCO activity shifts away from
carboxylation towards more oxygenation, increasing photorespiration and
leading to wasted energy (Edwards, 2019). To adapt to these constraints,
carbon concentrating mechanisms (CCMs) have evolved in numerous lineages
to enable efficient photosynthesis in dry, hot, and high light
environments while improving water use efficiency.
CCMs work by separating the initial carbon fixing away from the
photosynthetic carbon fixing (Calvin cycle) either temporally across the
diurnal cycle, or spatially across different cell types or compartments.
Both the temporal separation, as seen in Crassulacean Acid Metabolism
(CAM), and spatial separation, as seen in C4photosynthesis, have evolved independently in over 60 lineages (Edwards
& Ogburn, 2012). The evolutionary paths to both CAM and
C4 photosynthesis have been recently reviewed and
discussed in great detail (Bräutigam, Schlüter, Eisenhut, & Gowik,
2017; Chen, Xin, Wai, Liu, & Ming, 2020; Edwards, 2019; Heyduk,
Moreno-Villena, Gilman, Christin, & Edwards, 2019; Niklaus & Kelly,
2019; Schlüter & Weber, 2020; Sedelnikova, Hughes, & Langdale, 2018)
and in short, both require two main aspects: 1) an anatomical adaptation
and 2) co-option of the carbon concentrating metabolic pathway to the
correct spatiotemporal location. The main anatomical adaptation for CAM
is enlarged storage vacuole to store the malate synthesized during the
night and enable the day-night CCM (Luttge, 1987). In many
C4 plants, the spatial separation is across two cell
types, mesophyll and bundle sheath, and to achieve this,
C4 leaves adapt with so-called Kranz anatomy with
enlarged bundle sheath cells with increased plastid numbers and
increased vein density (Haberlandt, 1904). The regulation of Kranz
anatomy is proving to be a complex process (Sedelnikova et al., 2018),
and although it has readily evolved convergently in some plant clades,
it is starting to appear that not all plant clades are pre-conditioned
for the C4 photosynthesis to evolve (Edwards & Ogburn,
2012). Conversely to complex leaf anatomy and its regulation, all the
enzymes required for both the CAM and C4 metabolic
pathways, such as phosphoenolpyruvate (PEP) carboxylase and malate
dehydrogenase, are present in all plants serving other functions. To
co-opt these enzymes for CCMs, the expression and regulatory patterns
have evolved to be spatially and temporally specific
(Brown et al., 2011; Burgess
et al., 2016; Christin et al., 2013; Dunning, Moreno-Villena, et al.,
2019; Gowik et al., 2004; Heyduk, Ray, et al., 2019; Kajala et al.,
2012; Ming et al., 2015; Rondeau et al., 2005; Schulze et al., 2013;
Williams et al., 2016; Yang et al., 2017). Whole genome sequencing has
enabled a level of understanding of how these CCMs evolved in plants.
The first C4 (Sorghum bicolor ) (Paterson et al.,
2009) and CAM (Phalaenopsis equestris ) (Cai et al., 2015) genomes
provided insights about redirection of genes involved in
C3 photosynthesis and expansion of ancient and recent
gene families. Transcriptomic approaches are also offering new evidence
about convergent evolution of genes and regulatory pathways underlying
these CCMs. For example, the genome and temporal transcriptome
sequencing of the CAM species Kalanchoë fedtschenkoi revealed
that the independent emergences of CAM from C3 have been
based on rewiring of diel gene expression patterns along with protein
sequence mutations (Yang et al., 2017). Furthermore, the pineapple
genome (Ananas comosus (L.) Merr.), another CAM species,
indicated that the transition from C3 to CAM was based
on regulatory neofunctionalization of pre-existing genes and regulation
of circadian clock components through evolution of novelcis -regulatory elements (Ming et al., 2015).
To resolve how gene expression patterns and GRNs have evolved in
convergent C4 lineages, comparative leaf transcriptomics
have been utilized, including comparisons of C3,
C4 and intermediate
C3-C4 leaves, developmental gradients,
specific cell types and environmental cues (Aubry, Kelly, Kümpers,
Smith-Unna, & Hibberd, 2014; Bräutigam et al., 2011; Burgess et al.,
2016; Dunning et al., 2017; Gowik et al., 2004; Li et al., 2010). From
these comparisons shared routes to C4 are starting to
emerge. Transcriptomic comparison across the monocot-dicot divide
revealed deep evolutionary conservation of C4 leaf
development pathways and that certain homologous cell type-specific
regulators were co-opted during the independent evolutions of
C4 photosynthesis (Aubry et al., 2014). Not only is it
possible to co-opt the same orthologs as another species, but it is also
possible to co-opt the very gene from another species. Transcriptomics
of closely related Alloteropsis grasses revealed that recurrent
evolution of C4 among the group was enabled by co-opting
genes across species boundaries, specifically by introgressions of the
C4 components (Dunning et al., 2017). Subsequently, it
was discovered that grasses have utilized lateral gene transfer also to
speed up C4 evolution (Dunning, Olofsson, et al., 2019;
Phansopa, Dunning, Reid, & Christin, 2020). Furthermore, the
understanding of C4 enzymes’ regulatory networks in
ancestral C3 state was elucidated also by a
transcriptomics approach: comparison of how light and chloroplasts
regulate C4 enzymes in closely related
C3 and C4 plants. This linked the
C4 enzymes into a pre-existing C3regulatory network, explaining the readiness of C4 to
evolve at the molecular level (Burgess et al., 2016). Regardless of
these examples of GRN readiness for C4 evolution, or
“genetic potentiation”, the C4 lineages are not evenly
distributed across the angiosperms (Edwards, Osborne, Strömberg, Smith,
& Consortium, 2010). This can be due either to the different lineages
facing different evolutionary pressures, or differences in either
genetic or anatomic potentiation (Heyduk, Moreno-Villena, et al., 2019),
and remains a question to be addressed in the future.
Counter-intuitively, C4 and CAM can exist in the same
leaf. A recent transcriptomic approach was taken to dissect the
behaviour of both C4 and drought-induced CAM in the same
plant, Portulaca oleracea , offering insight on how the regulatory
networks of shared enzymes might be able to coexist while responding to
different environmental and temporal cues (Ferrari et al., 2020). With
more C4 and CAM genomes and transcriptomes becoming
recently available (Phytozome v.12.1, Goodstein et al. (2012)), the door
is open for better understanding of convergent evolution of CCMs and
other parallel drought adaptations in these species.