Subdivision of light signalling networks contributes to partitioning … · In all two-cell C 4 species, these two specialised cell 84 types are arranged concentrically in an outer

Short title 1

Cell specific light response in C4 photosynthesis 2

Corresponding Author 3

Email stevenkellyplantsoxacuk Telephone +44 (0)1865 275123 4

Title 5

Subdivision of light signalling networks contributes to partitioning of C4 photosynthesis 6

Author names and affiliations 7

Ross-W Hendron1 and Steven Kelly1 8

1Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 9

3RB UK 10

One sentence summary 11

Cell-specific activation of photosynthetic machinery is mediated by differences in light 12 signalling networks between photosynthetic cell types these differences indicate that the 13 regulatory system that facilitates C4 photosynthesis may have evolved to reinforce 14 differences in within-leaf light availability 15

Author Contributions 16

SK and RWH conceived the experiments RWH conducted the analysis SK and RWH 17

wrote the paper 18

Abstract 19

Plants coordinate the expression of photosynthesis-related genes in response to growth 20

and environmental changes In species that conduct two-cell C4 photosynthesis 21

expression of photosynthesis genes is partitioned such that leaf mesophyll and bundle 22

sheath cells accumulate different components of the photosynthetic pathway The 23

identities of the regulatory networks that facilitate this partitioning are unknown Here we 24

Plant Physiology Preview Published on December 20 2019 as DOI101104pp1901053

show that differences in light perception between mesophyll and bundle sheath cells 25

facilitate differential regulation and accumulation of photosynthesis gene transcripts in the 26

C4 crop maize (Zea mays) Key components of the photosynthesis gene regulatory 27

network differentially accumulated between mesophyll and bundle sheath cells indicative 28

of differential network activity across cell types We further show that blue light (but not 29

red) is necessary and sufficient to activate Photosystem II assembly in mesophyll cells in 30

etiolated maize Finally we demonstrate that 61 of all light-induced mesophyll and 31

bundle sheath genes were induced only by blue light or only by red light but not both 32

These findings provide evidence that subdivision of light signalling networks is a 33

component of cellular partitioning of C4 photosynthesis in maize 34

Introduction 35

Light is of fundamental importance to photoautotrophs who harness energy from photons 36

to synthesise sugars Given the central role that light plays in the growth of plants it is 37

fitting that they have evolved sophisticated methods to sense it and use this environmental 38

cue to optimise their photosynthetic capabilities In the model plant Arabidopsis thaliana 39

five families of photoreceptors of varying spectral sensitivities allow discrimination 40

between different wavelengths of light These families comprise the phytochromes 41

cryptochromes phototropins UVRs and Zeitlupe proteins (Christie et al 2015 Lin 2000 42

Rizzini et al 2011 Schepens et al 2004 Smith 2000) In brief red light stimulates 43

phytochrome signalling blue light stimulates cryptochromes phototropins and Zeitlupes 44

while UV-B stimulates UVR8 Once stimulated photoreceptors either activate signalling 45

cascades (Petroutsos et al 2016) bind DNA directly (Yang et al 2018) andor bind to 46

and affect the DNA binding properties of many transcription factors that serve as light 47

signalling intermediates such as PHYTOCHROME INTERACTING FACTORS (PIFs) and 48

CRYPTOCHROME INTERACTING BASIC-HELIX-LOOP-HELIX (CIBs) genes (Li et al 49

2011 Yu et al 2010) Thus expression of nucleus-encoded photosynthesis genes is 50

modulated both by photoreceptor activity and by a network of light-responsive transcription 51

factors Different wavelengths of light also influence post-transcriptional regulation of gene 52

expression modulating translational efficiency through light-induced alternate start codon 53

usage (Kurihara et al 2018) and protein degradation through ubiquitination pathways (Xu 54

et al 2015) By linking light cues to the regulation of photosynthesis genes plants are 55

able to coordinate development of chloroplasts and optimise photosynthetic rates in 56

mature leaf tissue under changing environmental conditions (Ohashi-Kaneko et al 2006 57

Ort et al 2011 Waters and Langdale 2009) 58

In most angiosperm species photosynthesis occurs in the leaf mesophyll In 59

dicotyledonous species this cell layer contains at least two distinct cell-types the palisade 60

cells that are located adjacent to the upper leaf epidermis and the spongy mesophyll cells 61

located beneath them All light that strikes a leaf surface is filtered as it penetrates through 62

these cell layers such that light availability in the spongy mesophyll is reduced by as much 63

as 90 in comparison to the palisade (Cui et al 1991 Terashima and Hikosaka 1995) 64

This biophysical light filtration is responsible for a decreasing gradient in chlorophyll and 65

photosynthetic capacity through the mesophyll such that upper palisade cells carry out the 66

vast majority of photosynthesis in a dicot leaf (Evans and Vogelmann 2003 Tholen et al 67

2012) In addition different wavelengths of photosynthetically active light vary in their 68

ability to penetrate leaf tissues with longer wavelength red light penetrating significantly 69

deeper than shorter wavelength blue light (Slattery et al 2016 Vogelmann and Evans 70

2002) Modelling light penetration through the leaf suggests that just 4 of incoming 71

diffuse blue light reaches the second layer of cells In contrast 12 of red light reaches 72

these deeper cells and thus both the intensity and spectrum of light change as light 73

passes through the leaf (Xiao et al 2016) Although monocotyledonous leaves contain 74

more uniformly shaped mesophyll cells analogous light filtration is thought to occur 75

(Kume 2017 Takahashi et al 1994) 76

While most plant species conduct all the reactions required to carry out photosynthesis in 77

a single cell some species have evolved a way to split the process between two 78

specialized cell types This spatial division of photosynthesis is known as C4 79

photosynthesis and it has evolved independently at least 61 times in both eudicots and 80

monocots (Sage 2016) The result of this spatial partitioning is a depletion of O2 and an 81

increase in CO2 around rubisco that together reduce energy loss through photorespiration 82

(von Caemmerer and Furbank 2016) In all two-cell C4 species these two specialised cell 83

types are arranged concentrically in an outer layer of photosynthetic carbon assimilation 84

tissue (PCA) surrounding an inner layer of photosynthetic carbon reduction tissue (PCR) 85

which in turn surrounds the vascular tissue in a concentric wreath-like arrangement is 86

known as Kranz anatomy (Muhaidat et al 2007 Nelson and Langdale 1989) Thus in 87

two-cell C4 species all light reaching the PCR cell layer must first pass through an outer 88

PCA cell layer This means that in two-cell C4 species with Kranz anatomy light reaching 89

the PCR layer is ~10-fold dimmer and depleted in blue relative to red wavelengths 90

compared to light that reaches the PCA layer This light filtering is thought to be one 91

reason why photosynthetic rates are lower under blue light than red in C4 species such as 92

maize (Zea mays) and miscanthus (Miscanthus x giganteus) (Sun et al 2014 2012) 93

During maize leaf development early transcriptional changes give rise to vasculature and 94

determination of mesophyll and bundle sheath cell identities (Sedelnikova et al 2018) 95

After this cell determination stage cells at the base of the leaf blade are primed to respond 96

to light cues to promote photosynthetic maturation in expanding leaf blades (Wang et al 97

2013b) The leaf blade emerges vertically and the leaf is exposed to light on both the 98

adaxial and abaxial surfaces during this greening phase Since bundle sheath cells are 99

always shrouded in a layer of mesophyll cells the light stimulus is inherently asymmetrical 100

between these cell types during photosynthetic activation Given the integration of light 101

signals with the transcriptional control of photosynthesis (Wang et al 2017a) it was 102

hypothesised that the gene regulatory networks that control photosynthesis gene 103

expression may differentially accumulate between PCA and PCR cells in a manner that is 104

consistent with biophysical light filtration and may therefore facilitate partitioning of 105

photosynthetic reactions in C4 species Although the regulators that facilitate this 106

partitioning are unknown two lines of evidence concerning the light dependent regulation 107

of cell specific gene expression support this hypothesis First the photosystem II (PSII) 108

complex is expressed only in mesophyll cells in maize (Drozak and Romanowska 2006) 109

and the expression of the gene encoding photosystem II D2 protein (psbD) is blue light 110

responsive and under the control of sigma factor 5 (SIG5) which in maize only 111

accumulates under blue light (Tsunoyama et al 2002) Second rubisco is only found in 112

the bundle sheath of maize and the gene encoding rubisco small subunit (rbcS-m3) is 113

expressed in maize bundle sheath cells in response to red light induction and is not 114

expressed in mesophyll cells due to blue light repression (Markelz et al 2003 Purcell et 115

al 1995) However the extent to which blue light and red light facilitate partitioning of 116

photosynthetic gene expression between bundle sheath and mesophyll cells is unknown 117

Here we tested the hypothesis that the gene regulatory networks for photosynthesis are 118

partitioned between bundle sheath and mesophyll cells in the C4 plant maize in a manner 119

that is consistent with biophysical light filtration within the leaf That is that the expression 120

of genes whose transcripts preferentially accumulate in mesophyll cells will be responsive 121

to both blue and red light stimulation while expression of genes whose transcripts 122

preferentially accumulate in bundle sheath cells will be responsive only to red light 123

stimulation We show that transcription factors and photoreceptors that are known to 124

regulate photosynthesis differentially accumulated between mesophyll and bundle sheath 125

cells in maize leaves Through spectrum specific de-etiolation experiments we show that 126

blue light but not red resulted in rapid accumulation of chlorophyll fluorescence from 127

functional PSII assembly Furthermore we demonstrate that transcripts encoding 128

mesophyll specific genes increased in abundance in response to either red or blue light 129

while transcripts encoding bundle sheath specific genes increased in abundance in 130

response to red light Together these findings provide evidence that subdivision of light 131

signalling networks contributes to cellular partitioning of C4 photosynthesis in maize 132

Results 133

The photosynthesis gene regulatory network shows extensive partitioning between 134

bundle sheath and mesophyll cells in maize 135

Much of what is known about the regulation of photosynthesis gene expression has been 136

determined in Arabidopsis (Arabidopsis thaliana) (Wang et al 2017a) To date few 137

regulators of photosynthesis gene expression have been characterised in other species 138

and little is known about how these genes are regulated in grasses (Wang et al 2017a) 139

However it is likely that maize orthologs of known photosynthesis regulatory genes in 140

Arabidopsis provide some of this regulatory function To estimate the extent to which the 141

gene regulatory network for photosynthesis was partitioned between bundle sheath and 142

mesophyll cells in maize the complete set of maize genes that are orthologous to 143

Arabidopsis genes that encode known photoreceptors or light-modulated transcription 144

factors were identified and analysed (accession numbers for all genes are detailed in 145

Supplemental File S1) 146

Of the 58 known photosynthesis regulatory genes in Arabidopsis 49 had at least one 147

ortholog in maize Multiple gene duplication events have occurred in the lineage leading to 148

maize since Arabidopsis and maize last shared a common ancestor (Lee et al 2013) and 149

as a consequence most of these regulatory genes in Arabidopsis have more than one 150

ortholog in maize Specifically the 49 Arabidopsis genes had 97 orthologs in maize The 151

differential accumulation of transcripts corresponding to these 97 maize genes was 152

assessed in two transcriptome datasets in which the transcriptomes of mesophyll and 153

bundle cells were separately sequenced one taken from mature maize leaves (Chang et 154

al 2012) and one from developing maize leaves (Tausta et al 2014) 155

Of the 6210 genes differentially regulated between bundle sheath and mesophyll cells in 156

the developing leaf dataset (Tausta et al 2014) 3741 were also differentially regulated in 157

the same way in the mature dataset (agreement = 60) Of these genes 1370 encoded 158

transcription factors Transcription factors were therefore more likely to be differentially 159

expressed between cell types than randomly sampled genes (p le 0001 n = 1000 Monte 160

Carlo simulations) Indeed the transcription factors that are orthologous to known 161

photosynthesis regulating transcription factors in Arabidopsis thaliana (n = 67) were also 162

more likely to be differentially expressed between bundle sheath and mesophyll cells than 163

randomly sampled genes (p le 0002 n = 1000 Monte Carlo simulations) Thus 164

transcriptional regulators including those which can be inferred to regulate photosynthesis 165

in maize show evidence of partitioning between bundle sheath and mesophyll cells A 166

complete list of all differentially regulated photosynthesis related transcription factors 167

between bundle sheath and mesophyll cells of the two relevant datasets is provided in 168

Supplemental File S2 169

To investigate the evolutionary relationships between these transcription factors a set of 170

orthogroups were defined at the most recent common ancestor of the dicots and 171

monocots An orthogroup is the complete set of genes descended from a single gene that 172

was present in the most recent common ancestor of a set of species under consideration 173

Thus the orthogroups defined here grouped together all maize genes that were 174

descended from a single copy gene in the most recent common ancestor of the monocots 175

and dicots under consideration (species are detailed in Supplemental File S3) This 176

analysis revealed that many of the differentially accumulating transcription factors 177

identified above were related to each other having arisen through gene duplication events 178

since the monocot-dicot ancestor Figure 1 shows the maize genes (within the nine 179

orthogroups that contained more than one differentially expressed maize gene) that were 180

differentially expressed in either dataset Figure 1A displays orthogroups where the maize 181

paralogs differentially accumulated in opposite cell types This list includes well 182

characterised photosynthetic regulators such as the GOLDEN-2 LIKE genes (GLKs) PIFs 183

and CIBs This subfunctionalisation of paralogous genes extends previous studies that 184

have suggested a role for such subfunctionalisation for generating cell-specific dimorphic 185

chloroplasts (Wang et al 2013a) 186

In addition to subfunctionalisation three orthogroups were detected within which all 187

paralogs were preferentially expressed in the same cell type (ie ZIM-LIKE genes (ZML1 188

and ZML2) and SIG2 expressed in the mesophyll and OBF-BINDING PROTEIN 3 (OBP3) 189

expressed in the bundle sheath Figure 1B) As these duplication events precede the origin 190

of C4 photosynthesis in maize it is perhaps more likely that these expression patterns 191

represent the ancestral expression state in the C3 ancestor of maize rather than 192

independent evolution of cell type specificity Of particular note was that the maize 193

phytochrome genes were all preferentially expressed in bundle sheath cells (Figure 1C) 194

Hence of the photosynthetic regulators whose maize paralogs were preferentially 195

expressed in the same cell types blue light signalling intermediate ZMLs (Shaikhali et al 196

2012) were associated with the mesophyll and red light photoreceptors (ie PHYs) were 197

associated with bundle sheath cells Thus we hypothesised that the partitioning of 198

photosynthetic regulators between cell types may be due to cellular differences in light 199

perception Specifically we hypothesised that photosynthetic machinery in bundle sheath 200

cells would be more sensitive to red light than blue and that the photosynthetic machinery 201

in mesophyll cells would be more responsive to blue light than red 202

Blue light but not red stimulates assembly of photosystem II in etiolated maize 203

seedlings 204

To test our hypothesis we exploited the fact that many C4 monocots and dicots exhibit 205

preferential accumulation of PSII in mesophyll cells (Houmlfer et al 1992 Meierhoff and 206

Westhoff 1993 Schuster et al 1985 Sheen and Bogorad 1988) If the hypothesis is 207

correct mesophyll cells should be responsive to blue light and bundle sheath cells should 208

be more responsive to red light and thus it should be possible to trigger mesophyll cell 209

specific gene regulatory networks using blue light but not red Moreover given that PSII 210

accumulates only in the mesophyll cells of maize it should be possible to trigger PSII 211

expression specifically with blue light stimulation but not with red light 212

Maize seedlings were de-etiolated by illumination with either blue or red light and 213

functional PSII assembly was monitored by measuring photosystem II efficiency (фPSII) 214

after three hours using fluorescence Significantly more PSII fluorescence was observed 215

following de-etiolation under blue light than under red light irrespective of leaf number or 216

plant age (Figure 2A) Time course analysis of the PSII induction kinetics revealed that 217

significant induction of PSII fluorescence was detectable within 90 minutes of exposure to 218

blue light (Figure 2B) with only a minor increase in фPSII detected after three hours of 219

stimulation with red light (Figure 2B) Despite differences in experimental set up relating to 220

light administration environmental conditions and fluorescence measurement devices that 221

generated data for Figures 2A and 2B (detailed in Methods) it is clear that the mesophyll 222

regulatory network governing фPSII development exhibited reduced red light sensitivity 223

but was strongly activated by blue light 224

Moreover we tested whether this preferential induction of PSII under blue light was also 225

observed in barley (Hordeum vulgare) a C3 monocot When de-etiolated barley leaves 226

were subjected to the same time course experimental procedure as maize leaves either 227

blue or red light was individually sufficient to induce PSII development (Figure 2C) Thus 228

the light signalling network governing фPSII development in barley was stimulated by both 229

blue and red light In contrast the maize mesophyll regulatory network for PSII activation 230

was induced specifically by blue light whereas red light was not a sufficient stimulus 231

Activation of blue light signalling networks promotes the transcription of PSII 232

assembly components 233

While the rapid increase in PSII activation under blue light was likely predominantly due to 234

post-translational assembly of PSII monomers already in the etioplast (Forger and 235

Bogorad 1973 Muumlller and Eichacker 1999) it was also expected to be driven by 236

spectrum specific transcriptional responses To determine which genes were responsible 237

for the differences in photosystem II assembly total RNA was isolated from leaves at the 238

end of the red or blue light induction period described above and subjected to 239

transcriptome sequencing Samples were also taken from etiolated leaves that received no 240

light treatment and were sampled at the same time of day as de-etiolated plants and 241

mRNA transcript abundance quantified (Supplemental File S4) Transcripts that 242

preferentially accumulated under blue light or under red light were detected using 243

differential expression analysis These cohorts of blue light-preferential transcripts and red-244

light preferential transcripts were tested for enrichment of functional terms (detailed in 245

Supplemental File S5-6) This analysis revealed 13 significantly enriched categories within 246

the red light-preferential transcripts which included sugar transporters plasma membrane 247

intrinsic proteins (PIP) and photosynthesis (PS) genes (Figure 3A) By contrast blue light 248

preferentially induced the expression of transcripts that were enriched for 25 functional 249

categories These encompassed regulatory functions (RNA processing translation 250

proteins and proteins associated with chloroplast targeting) in addition to Nitrogen 251

metabolism tetrapyrrole synthesis and amino acid metabolism (Figure 3B) 252

Many of these genes differentially induced by red or blue light were also known transcripts 253

that accumulated differentially between mesophyll and bundle sheath cells (called 254

mesophyll or bundle sheath genes) Figure 3C indicates the proportion of differentially light 255

induced mesophyll and bundle sheath genes in each category and which were also 256

induced preferentially by blue or red light This analysis revealed that across the vast 257

majority of categories in which at least one mesophyll or bundle sheath gene was 258

differentially induced by light (2328) mesophyll genes were more likely than bundle 259

sheath genes to be induced by blue light and bundle sheath genes were more likely 260

induced by red light This pattern was especially clear for large MapMan categories (eg 261

Protein RNA Cell) This result indicated that there may be a more general difference in 262

mesophyll and bundle sheath cells that is mediated by differences in light signalling 263

pathways between cell types 264

Given that blue light specifically induced the assembly of PSII in maize we initially 265

hypothesised that the subunits of the PSII complex and its assembly factors would be 266

upregulated under blue light However expression of a higher number of photosystem 267

sub-units increased following red light stimulation than following blue light stimulation 268

(Figure 3A see also Supplemental Figure S5-6) Hence photosystem subunit expression 269

alone could not explain the fluorescence phenotype that we observed However there 270

were differences in the induction of RNA and protein regulatory genes in response to light 271

treatments Specifically blue light preferentially induced regulators of RNA and proteins 272

that facilitate the transcription translation import and assembly of PSII proteins into the 273

chloroplast A full breakdown of these genes and their expression profiles is included in 274

Supplemental File S4-6 275

PSII is a multimeric protein with both nuclear and plastid encoded subunits Fittingly 276

nuclear transcriptional regulators that have been linked to PSII transcription were 277

preferentially induced by blue light including HYPOCOTYL ELONGATION 5 (HY5) (Ang 278

and Deng 1994) and SIGMA factors 1 2 and 5 Notably 97 different pentatricopeptide 279

repeat (PPR) containing proteins increased in abundance following blue light illumination 280

while only three increased following red light (Figure 3B) The list of blue light induced PPR 281

proteins contains several regulators of photosynthesis whose transcripts preferentially 282

accumulate in mesophyll cells including MATERNAL EFFECT EMBRYO ARREST 40 283

(MEE40) ndash which prevents delayed thylakoid development in rice (Su et al 2012) 284

PENTATRICOPEPTIDE REPEAT 5 (PRR5) ndash which prevents chloroplast ribosome 285

deficiency in maize (Beick et al 2008) and PROTEINACEOUS RNASE P 1 (PRORP1) ndash 286

which prevents a pale green phenotype in A thaliana (Zhou et al 2015) This extensive 287

induction of RNA editing proteins in addition to the blue light induction of the chloroplast-288

encoded mesophyll accumulating RNA editing protein MATURASE K (MATK) indicates 289

that mesophyll RNA editing machinery was preferentially activated by blue light 290

(Supplemental Figure S5) 291

In addition to RNA transcription and editing machinery translation chloroplast targeting 292

and import mechanisms were also preferentially activated by blue light 15 chloroplast 293

ribosome components (detailed in Supplemental File S4 under the MapMan category 294

lsquoproteinsynthesisribosomal proteinprokaryotic) were preferentially upregulated under 295

blue light Blue light also induced TRANSLOCONS OF OUTER CHLOROPLAST (TOC) 296

protein importers in addition to proteins that function as molecular chaperones such as 297

HEAT SHOCK PROTEIN 90 (HSP90) proteins and CHAPERONIN 60 (CPN60A) 298

Preferential accumulation under blue light was also apparent for PSII assembly proteins 299

(whose transcripts also accumulate preferentially in mesophyll cells) SEQUENCE 300

RECOGNITION PARTICLE 54 (SRP54) and ALBINO 3 (ALB3) which insert the PSII light 301

harvesting complex into thylakoid membranes (Schuenemann et al 1998) and PSII 302

turnover proteins (FTSH proteases FTSH2 and FTSH5) (Kato et al 2009) were all 303

preferentially activated by blue light stimulation (Supplemental File S5 Supplemental 304

Figure S1) 305

Thus while the transcripts encoding components of the PSII complex were induced by 306

both red and blue light light responsive transcripts encoding mesophyll-localised PSII 307

assembly factors were preferentially induced by blue light This suggests that the 308

mechanism of PSII accumulation in the mesophyll of mature leaves is implemented at two 309

levels ndash by blue light signalling networks acting on the post-transcriptional assembly of 310

functional PSII complexes and by blue light signalling networks promoting the 311

transcription of the requisite assembly factors in these cells This result also suggests that 312

the lack of PSII induction response under red light was because red light did not induce 313

expression of mesophyll-localised regulatory genes whose proteins are important for 314

correct expression localisation and assembly of functional PSII complexes 315

Subdivision of blue and red light signalling networks between mesophyll and 316

bundle sheath cells is a component of cell type specification in maize 317

Across multiple categories of genes that promote photosynthetic development mesophyll 318

and bundle sheath genes were differentially upregulated in response to bluered light 319

respectively (Figure 3) Given this observation we hypothesised that there would be a 320

transcriptome wide association between the responsivity of a transcript to light 321

wavelengths and the cell type preferential expression of that transcript in mesophyll and 322

bundle sheath cells In keeping with the idea that bundle sheath cells experience spectral 323

shading compared to mesophyll cells we hypothesised that transcripts that accumulated 324

in bundle sheath cells would be preferentially induced by red light and less by blue light 325

The majority of light induced genes (3153 out of the total 4316) were upregulated uniquely 326

under blue light with relatively few (119) being upregulated only under red light (Figure 327

4A) Hence we quantified how many of these uniquely blue or red light induced genes 328

were also mesophyll or bundle sheath genes 329

Lists of mesophyll and bundle sheath preferentially expressed genes in developing maize 330

leaves were combined with a curated list of C₄ cycle enzymes and transporters (Tausta et 331

al 2014) These were then compared to the lists of differentially expressed genes in 332

response to light (Supplemental File S7) Consistent with previous analysis (Burgess et al 333

2016) transcripts encoding C4 cycle enzymes and transporters in maize generally 334

increased in abundance in response to any light (Figure 4B) except for NADP-MALIC 335

ENZYME (ME) the primary decarboxylase in the maize C4 cycle (Hatch and Kagawa 336

1976) Additionally PHOSPHOENOLPYRUVATE CARBOXYKINASE (PCK) was induced 337

only by blue light which is consistent with previous observations that PCK activity is higher 338

under high light and reduced by more than 75 in shade (where the bluered light ratio is 339

further decreased) (Finnegan et al 1999 Sharwood et al 2014) 340

Generally C₄ proteins were induced by either blue or red light and did not show strong 341

preference for either blue or red wavelengths For example bundle sheath rubisco 342

subunits were not specifically induced by red light However the rubisco chaperone 343

RUBISCO ACTIVASE (RCA) whose expression is correlated with grain yield in maize 344

(Zhang et al 2019) was induced only by red light Additionally key sugar metabolism 345

genes were uniquely induced by red light including Calvin cycle enzymes FRUCTOSE 346

BISPHOSPHATASE (FBP) ALDOLASE (ALDOA) and TRANSKETOLASE (TKL) and 347

sugar transporter MALTOSE EXPORTER 1 (MEX1) Thus the expression of C₄ 348

photosynthesis sugar metabolism genes was generally consistent with the hypothesis that 349

the bundle sheath was relatively more sensitive to red light signalling 350

Overall ~35 of the 3187 transcripts that preferentially accumulate in mesophyll cells in 351

maize (Tausta et al 2014) increased in abundance in response to any light treatment 352

(Figure 4C) This is significantly more than would be expected by chance alone (Figure 353

4C) In contrast only ~11 of the 3023 transcripts that preferentially accumulate in bundle 354

sheath cells (Tausta et al 2014) were induced by any light (Figure 4C) This is 355

significantly fewer than would be expected by chance alone (Figure 4C) 356

Of the set of genes that were induced only by blue light (3153) 207 were mesophyll 357

genes 56 bundle sheath genes and the remainder were genes that were not 358

differentially expressed between these cell types In contrast the set of red-only induced 359

genes (119) was made up of 261 mesophyll genes 261 bundle sheath genes and 360

the remainder were not differentially expressed between cell types Since mesophyll and 361

bundle sheath genes each account for ~87 of all transcripts that were expressed in the 362

leaf these light response distributions indicate significant associations between cell type 363

preferential expression and light wavelength preferential induction (Figures 4D-E) Hence 364

while transcripts that preferentially accumulate in mesophyll cells were responsive to both 365

red and blue stimulation (Figure 4D amp E) transcripts that accumulate in bundle sheath 366

cells were on average more responsive to red light than expected and also less 367

responsive to blue light (Figure 4D amp E) 368

Thus the transcriptional networks that promote the accumulation of transcripts for 369

mesophyll genes and bundle sheath genes differ in terms of both general light sensitivity 370

and also responses to specific light spectra Of all transcripts that differentially 371

accumulated between bundle sheath and mesophyll cells in mature maize leaves 23 372

were detectably induced by light Of these light inducible genes the majority (61) were 373

uniquely induced by either blue or red light Thus subdivision of light signalling networks 374

between specialised C4 cell types is a component of C4 photosynthesis partitioning in 375

maize 376

Wavelength specificity of maize blue light and red light transcriptome responses is 377

not conserved in Arabidopsis 378

Given the association between light spectrum and cell specific gene expression observed 379

in maize we examined to what extent these associations were conserved or divergent in 380

orthologous genes in Arabidopsis thaliana To facilitate this analysis an analogous 381

transcriptomic dataset of gene expression following spectrum specific de-etiolation in 382

Arabidopsis was interrogated (Hartmann et al 2016) Here the complete set of 383

orthogroups described above were used for analysis If a maize gene and an Arabidopsis 384

gene from the same orthogroup behaved the same way in response to light stimulation 385

this was recorded as analogous behaviour and the light response was said to be 386

conserved for that orthogroup Otherwise the light response was deemed to be divergent 387

indicating a lack of conservation in light response behaviour in orthologous genes of these 388

two species 389

Consistent with the larger quantity of genes induced by blue light in maize these genes 390

comprised a larger number of orthogroups whose genes were responsive only to blue 391

light Overall 1914 maize orthogroups were induced only by blue light 680 orthogroups by 392

either blue or red light and 68 by red light alone In contrast in Arabidopsis 493 393

orthogroups were induced by blue light only 1516 by either type of light and 380 by red 394

light only Thus although there were more orthogroups induced by blue light than by red 395

overall the number of orthogroups in the two categories was much more similar in 396

Arabidopsis than in maize (Supplemental Figure S2) 397

As shown in Table 1 of the 680 orthogroups in which maize genes were responsive to 398

light (irrespective of wavelength) 523 contained Arabidopsis genes with consistent light 399

responses Hence ~77 of orthogroups contained genes that in both species responded 400

in the same way to light However when the wavelength of light was taken into 401

consideration the results were dramatically different Here only 7-9 of orthogroups which 402

contained a maize gene whose expression was altered by spectrum-specific light 403

treatment also contained Arabidopsis genes with consistent behaviour Thus while the 404

genes that are responsive to light are highly similar in the two species (ie 77 of 405

orthologous genes) the spectrum of light to which they respond is now different 406

Given this substantial difference in behavioural response to light wavelengths we tested 407

whether the orthogroups that exhibited divergent light responses between Arabidopsis and 408

maize were enriched for genes that perform specific functions This analysis revealed that 409

genes that were induced by blue light in maize but not in Arabidopsis were enriched for 410

regulatory genes including transcription factors and translational regulators (Table 1 also 411

detailed in Supplemental File S8) Similarly the genes that were induced only by red light 412

in maize but not in Arabidopsis were enriched for photosynthesis genes Specifically 413

these red light induced photosynthesis genes comprised PSI subunits and Calvin cycle 414

genes in addition to sugar and starch metabolism components (Table 1 also detailed in 415

Supplemental File S9) all of which are defining characteristics of bundle sheath cells in 416

maize 417

Discussion 418

C4 photosynthesis is one of the most remarkable examples of anatomical physiological 419

and biochemical convergence in eukaryotic biology (Sage 2016) The relative frequency 420

with which it has evolved suggests that such large differences must be attributable to a 421

small number of key regulatory changes (Wang et al 2017b) Here we provide insight into 422

this regulation by showing that light perception is unevenly distributed between mesophyll 423

and bundle sheath in maize We demonstrate that mesophyll cells preferentially 424

accumulate transcripts that respond to both red light and blue light while bundle sheath 425

cells preferentially accumulate transcripts that respond only to red light Consistent with 426

this partitioning we show that blue light but not red light is able to induce development of 427

PSII fluorescence a functional read-out of a protein complex that is specific to maize 428

mesophyll cells In contrast to C4 maize in C3 barley leaves both blue and red light are 429

individually sufficient to induce PSII activation We further show that the wavelength-430

specific responses observed in maize were not conserved in Arabidopsis indicating that 431

the gene regulatory networks have substantially diverged Finally we reveal that 61 of 432

the light-induced mesophyll and bundle sheath genes were induced by stimulation with 433

specifically blue light or red light but not by stimulation with both wavelengths of light 434

Taken together these data reveal that sub-division of light signalling networks is a 435

component of the regulatory mechanism that facilitates photosynthetic partitioning 436

between bundle sheath and mesophyll cells in maize 437

Although we have shown that there is extensive partitioning of the light-dependent gene 438

regulatory network between bundle sheath and mesophyll cells and that the light 439

responses of bundle sheath and mesophyll cells differ dramatically the precise molecular 440

links connecting these two phenomena were not determined Our analysis of gene 441

expression data has revealed multiple correlations between wavelength sensitivity and the 442

expression of protein-binding regulatory genes which corroborates and expands on 443

previous observations that have indicated that post-translational mechanisms provide an 444

important role in determining asymmetric protein accumulation in C4 species (Meierhoff 445

and Westhoff 1993) For example although both PSII subunits and rubisco subunits were 446

not consistently differentially sensitive to either wavelength of light assembly factors that 447

bind to these proteins were significantly differentially expressed such that PSII assembly 448

factors were preferentially upregulated by blue light and rubisco associated genes by red 449

light Experimental interrogation of light signalling networks such as the systematic 450

deletion of all maize photoreceptor genes will undoubtedly yield further insights For 451

example which (if any) of the four bundle sheath associated maize phytochrome genes is 452

responsible for the red light dependent transcriptional activation of bundle sheath specific 453

genes in maize It will take a considerable amount of time and experimentation to 454

determine the full details of light signalling network partitioning between mesophyll and 455

bundle sheath cells 456

While the work described here has focussed on a single C4 species maize it will be 457

interesting to determine the extent to which differences in light perception between bundle 458

sheath and mesophyll cells is conserved in different C4 species In this context we have 459

shown that the genes that respond to light are predominantly conserved between 460

Arabidopsis and maize and thus it is likely that these genes will also respond to light in 461

other plant species However the spectrum of light to which these genes respond has 462

changed such that the genesrsquo illumination with different wavelengths of light activates and 463

represses almost completely different sets of genes in the two species Thus it may be 464

that different sets of genes respond to spectrum specific light treatments in different C4 465

species and that bundle sheath and mesophyll cells have greater or lesser extents of 466

spectral partitioning in other C4 lineages 467

Finally we propose that the asymmetries we have shown are in part a natural 468

consequence of the differential light availability in mesophyll and bundle sheath cells in 469

maize Specifically all light that strikes a leaf surface is filtered as it penetrates through cell 470

layers such that light availability after passing through a single photosynthetic cell layer is 471

reduced by as much as 90 (Cui et al 1991 Terashima et al 2009) and depleted in 472

blue wavelengths relative to deeper penetrating red wavelengths (Slattery et al 2016 473

Vogelmann and Evans 2002) As bundle sheath cells are always positioned inwards of a 474

layer of mesophyll cells they always receive light that is dimmer and depleted in shorter 475

wavelengths than the mesophyll It is therefore tempting to speculate that this purely 476

biophysical phenomenon could represent a simple difference that became exploited and 477

exaggerated during the evolutionary transition from C3 to C4 and which helped facilitate 478

biased cell type expression of genes in C4 species (Figure 5) Thus the difference 479

between mesophyll and bundle sheath cells in C4 species may be in part just a trick of the 480

light 481

Materials and Methods 482

Identification of orthogroups and phylogenetic tree inference 483

The 58 light signalling Arabidopsis (Arabidopsis thaliana) genes (detailed in Supplemental 484

File S1) comprised all experimentally validated photoreceptors and light signalling 485

transcription factors as recently reviewed (Wang et al 2017a) circadian clock genes were 486

removed to focus the list on purely photosynthetic functions Maize (Zea mays) orthologs 487

were identified for 49 of these Arabidopsis genes by running OrthoFinder V227 (Emms 488

and Kelly 2015) with setting lsquo-S diamondrsquo on a set of 16 representative plant species 489

including both maize and Arabidopsis as well as suitable relatives and outgroups 490

(Supplemental File S10) OrthoFinder identified orthologs and these were manually 491

checked by aligning the protein sequences for the complete orthogroups using mafft-linsi 492

(Katoh and Standley 2013) and constructing maximum likelihood gene trees using 493

FastTree 2 (Price et al 2010) 494

De-etiolation of seedling leaves in light chambers 495

B73 maize seed was sterilised using 70 ethanol and 25 bleach Seeds were planted 496

on vermiculite watered and grown with the light off in a growth cabinet set to 28degC 6 9 497

and 12 day old etiolated B73 maize seedlings were put in a chamber where an LED panel 498

administered 100 micromol m-2 s-1 of blue or red light (at leaf level) over whole plants from 499

above For each of the blue light and red light treatments a minimum of 7 replicates were 500

measured each from different plants The emission spectra for the LED lights in the light 501

chamber were measured using an i-phos spectrophotometer and theremino software 502

(Supplemental Figure S3) and were consistent with the manufacturerrsquos specifications After 503

3 hours a MultispeQ v10 device (Kuhlgert et al 2016) was used to measure фPSII 2 cm 504

in from leaf tips of leaves 1 and 2 using a custom designed protocol and macro tailored to 505

the experimental settings The protocol code and analysis macro are provided in 506

De-etiolation of seedling leaves in a LI-6800 chamber 508

To obtain a time series over the 3 hour induction period etiolated leaves were clamped in 509

a LICOR LI-6800 Portable Photosynthesis System (LICOR) equipped with a multi-phase 510

flash fluorimeter head For maize 9 day old maize second leaves were sampled For 511

barley (Hordeum vulgare) the first leaf of lsquoGolden promisersquo 7 day old seedlings was 512

sampled (having been grown in the same conditions as the maize seedlings) The 513

emission spectra LICOR LEDs were measured using an i-phos spectrophotometer 514

(Supplemental Figure S3) and were consistent with manufacturer-quoted spectra 100 515

micromol m-2s-1 of either 100 red or 100 blue light was used for de-etiolation The LICOR 516

was configured with a flow rate of 500 micromol s⁻sup1 400 micromol mol⁻sup1 CO2 leaf temperature 517

28degC and 60 humidity to match the environmental conditions of the growth chamber 518

Fluorescence was measured every 15 minutes for three hours 519

To rule out whether the observed results were influenced by the fluorescence measuring 520

beam the same experimental design was repeated but only a single fluorescence 521

measurement was made after two hours The values obtained for фPSII at two hours were 522

identical to those observed for plants subjected to regular measurement over the same 523

time window (Supplemental Figure S4) Thus we concluded that the fluorescence 524

measuring pulses provided no additional developmental stimulus Negative фPSII values 525

were assumed to be measurement artefacts of fully saturated reaction centres and 526

therefore set to 0 527

It has been shown that фPSII measurements can be erroneously inflated under blue light 528

sources compared to red resulting from over-estimation of the maximal fluorescence 529

value (Evans et al 2017) It should be noted that this effect cannot explain the lack of PSII 530

induction by red light in maize nor that blue light also preferentially induced PSII 531

fluorescence when the Multispeq device was used because the Multispeq uses different 532

measuring LED spectra which administer orange light rather than red 533

RNA collection and sequencing 534

Immediately following 3 hours of de-etiolation in the LICOR chamber under either 100 535

micromol m-2s-1 of either 100 red or 100 blue light (as described above) 3 cm of maize leaf 536

tissue (starting at 2 cm from the tip) that had been exposed to blue light red light or no 537

light treatment were cut and frozen in liquid nitrogen Samples were collected in a dark 538

room at the same time of day for each replicate Frozen tissue was ground and total RNA 539

extracted and purified using the Trizol method (Rio et al 2010) in conjunction with a 540

TurboDNAse treatment Ten samples were sequenced using the BGIseq-500 RNA-Seq 541

platform four replicates of blue three of red and three of no light treatment 542

Analysis of gene expression data 543

Following transcriptome sequencing of de-etiolated maize samples raw read files were 544

trimmed using Trimmomatic version 038 (Bolger et al 2014) with settings lsquoLEADING 10 545

TRAILING 10 SLIDINGWINDOW515 MINLEN25rsquo Transcript counts and effective 546

lengths were then quantified using Salmon version 0100 (Patro et al 2017) with settings 547

lsquo-l A ndashseqBias --gcBiasrsquo Transcript counts from all gene models corresponding to the 548

same gene were summed to generate abundance estimates at the gene locus level 549

Previously published datasets were processed using the same RNA-seq analysis pipeline 550

Raw counts for each locus were analysed using DESeq2 (Love et al 2014) from which a 551

set of maize mesophyll and bundle sheath genes were defined from the DESeq2 analysis 552

using an adjusted p value cut off (q lt 001) (Supplemental File S2) 553

Functional term enrichment analysis 554

MapMan categories for maize genes were downloaded (Usadel et al 2009) and a 555

standard hypergeometric test was carried out to identify functional groups that were 556

enriched within the sets of differentially expressed genes during de-etiolation In all cases 557

the p-values obtained were subjected to Bonferroni multiple test correction When 558

functions are mentioned in the text the largest hierarchical grouping was used but full 559

detail of subgroups is available in Supplemental File S5-6 560

Monte Carlo resampling 561

The total population of maize genes was subjected to Monte Carlo resampling to generate 562

expected numbers of differentially expressed transcription factors and photosynthesis 563

regulatory genes The list of maize transcription factors was downloaded from the Plant 564

Transcription Factor Database (Jin et al 2017) P values were calculated as (1 + the 565

number of simulations where the simulated value was greater than observed value) (1 + 566

the number of simulations) 567

The total population of genes whose expression could be detected in either mesophyll or 568

bundle sheath cells in maize were subjected to Monte Carlo resampling to generate 569

expected numbers of light induced mesophyll and bundle sheath genes 99 confidence 570

intervals were used to confirm that randomly simulated data was significantly different from 571

observed data 572

Accession Numbers 573

All referenced gene names and accessions are detailed in Supplemental File S1-S2 and 574

S4-9 Additional RNA-seq data for transcriptomes used in this study were previously 575

published and available in NCBI SRA under the following accession numbers SRP009063 576

(Z mays) and SRP060410 (A thaliana) The RNA-seq data generated in this study have 577

been deposited to ArrayExpress under accession E-MTAB-7200 578

Supplemental Data 579

Supplemental File Contains supplemental data tabs S1-S11 as referenced in the main 581

text 582

Supplemental Figure S1 Differential accumulation of photosynthesis related transcripts 583

under blue and red light treatments 584

Supplemental Figure S2 Count of upregulated orthogroups by light quality 585

Supplemental Figure S3 Spectral emissions provided by the LEDs used in de-etiolation 586

experiments 587

Supplemental Figure S4 Photosystem II efficiency after two hours of de-etiolation with 588

and without repeated measuring flashes 589

Acknowledgements 590

RWH is supported by a Biotechnology and Biological Sciences Research Council 591

studentship through BBJ0144271 SK is a Royal Society University Research Fellow 592

This work was supported by the European Unionrsquos Horizon 2020 research and innovation 593

program under grant agreement number 637765 and by the BBSRC through 594

BBP0031171 595

Tables 597

Table 1 598 599

Type of

induction

Orthogroups

in which an

Arabidopsis

showed a

given light

response

Orthogroups

in which a

maize gene

showed a

given light

response

Orthogroups

maize light

response is

conserved

Arabidopsis

Proportion

conserved

orthogroups

Enrichment p

value for

conserved light

responses

Functional

groups

enriched within

divergent

orthogroups

Either

blue or

red light

1516 680 523 077 Over represented

P = 338E-271

Blue light

493 1914 137 007 Under

represented

P = 123E-241

Protein

synthesis

TCA cycle

Transcription

regulation

Red light

380 68 6 009 Under

represented

P = 571E-4

Photosynthesis

Major CHO

metabolism

Total 2389 2662 666 025 NA NA

Table 1 Conservation and divergence in light responses of orthologous Arabidopsis and 601

maize genes Light responses were observed in an Arabidopsis de-etiolation experiment 602

and a maize de-etiolation experiment Orthogroups were said to be induced by blue light 603

only red light only or either type of light based on the light responses of orthologs within 604

those orthogroups Orthogroups containing maize genes that were induced by either blue 605

or red light were likely to have Arabidopsis orthologs that were induced by either 606

wavelength as well Orthogroups with maize genes that responded to only one type of light 607

rarely had Arabidopsis orthologs that responded to the same type of light These 608

differences were statistically significant by hypergeometric testing Orthogroups with 609

divergent light-induction responses were enriched for maize MapMan functions Functions 610

are labelled according to the largest enriched hierarchical MapMan term with parentheses 611

indicating more detail about the enriched components within these functions 612

Figure Legends 614

Figure 1 Orthology and differential expression of the maize orthologs of regulators of 615

photosynthesis gene expression in Arabidopsis (A) Orthogroups wherein paralogous 616

maize genes were differentially expressed in different cell types (B) Orthogroups wherein 617

paralogous maize genes were preferentially expressed in the same cell types (C) 618

Consistent cell type preferential accumulation of phytochrome paralogs Evolutionary 619

relationships are indicated by a cladogram relating Arabidopsis photosynthesis gene 620

regulatory network components (bold font) and corresponding differentially expressed 621

maize orthologs (lightface font) Orthogroups were selected in which at least two maize 622

paralogs were differentially expressed in either of the two maize RNA-seq datasets 623

examined (DESeq2 differential expression testing with multiple test corrected p lt 001 for 624

each of two RNA-seq datasets) Yellow circles indicate significant mesophyll cell 625

preferential accumulation of messenger transcripts green circles indicate significant 626

bundle sheath cell preferential accumulation 627

Figure 2 Photosystem II (PSII) assembly is promoted by blue light stimulation in maize 628

Box plots indicating фPSII fluorescence following red (red boxes) or blue (blue boxes) light 629

stimulation (A) Measurements taken on a MultispeQ V10 after 3 hours of spectrum 630

specific de-etiolation in a large chamber (7 le n le 10 for each boxplot) De-etiolation time 631

series of (B) maize leaves and (C) barley leaves in a LICOR LI-6800 (n = 9 for each time 632

point and light treatment for both species) Boxplot tails indicate 95 confidence intervals 633

and asterisks indicate significant differences between light treatments determined by t 634

tests (p lt 005) The differences in y axis scale between part A and part B are attributable 635

to differences in the sensitivity and accuracy of the two different measurement devices 636

Figure 3 Enrichment of functional MapMan categories (y axis) in genes that were 637

differentially expressed during de-etiolation under blue or red light All displayed categories 638

contained significantly more genes that were preferentially expressed under (A) red light or 639

(B) blue light compared to genomic background (hypergeometric testing with multiple test 640

correction p lt 001) All genes and categories are listed in Supplemental File S4-6 (C) 641

The proportion of differentially expressed (DE) mesophyll and bundle sheath genes in 642

each category that were preferentially expressed in response to either blue light or red 643

light Grey bars indicate that no transcripts associated with the specified category and cell 644

type were differentially expressed in response to different wavelengths of light 645

Figure 4 Transcripts encoding genes that preferentially accumulate in bundle sheath and 646

mesophyll cells are differentially expressed depending on light wavelengths (A) The total 647

number of genes whose transcripts significantly increased in abundance following 648

spectrum specific de-etiolation (B) C4 genes grouped by cell type specificity and light 649

responses Parentheses indicate paralogs that have disparate light responses (C)-(E) 650

Observed (obs) and expected (exp) counts of transcripts encoding genes that 651

preferentially accumulated in bundle sheath or mesophyll cells following de-etiolation by 652

either colour light (C) only blue light (D) or only red light (E) Light responses were 653

observed using n = 3-4 RNA-seq replicates per light treatment and DESeq2 Error bars 654

indicate 99 confidence intervals for the mean expected counts generated by Monte Carlo 655

resampling (n = 100) and asterisks indicate significantly different observations compared 656

to null expectations at p lt 001 657

Figure 5 A model for C4 photosynthesis evolution from an ancestral C3 network (A) An 658

ancestral C3 network of blue and red light induced gene regulatory networks (depicted as 659

blue or red circles) regulate gene expression (represented by pink transcription factor on a 660

double helix) and chloroplast development within the same cell in response to blue and red 661

light beams Mature photosynthetic chloroplasts (green) contain thylakoids (stacked dark 662

green bars) that synthesise starch (white dots) (B) A derived C4 gene regulatory network 663

wherein differential accumulation and activity of blue and red light sensitive regulatory 664

components between cell types (indicated by differences in blue and red circle sizes) 665

consistent with different penetration of light beams into the two cell types help to partition 666

the expression of cell type specific genes 667

Literature Cited 669

Beick S Schmitz-Linneweber C Williams-Carrier R Jensen B Barkan A 2008 The 671 Pentatricopeptide Repeat Protein PPR5 Stabilizes a Specific tRNA Precursor in 672 Maize Chloroplasts Molecular and Cellular Biology 28 5337ndash5347 673 httpsdoiorg101128MCB00563-08 674

Bolger AM Lohse M Usadel B 2014 Trimmomatic a flexible trimmer for Illumina 675 sequence data Bioinformatics 30 2114ndash2120 676 httpsdoiorg101093bioinformaticsbtu170 677

Burgess SJ Granero-Moya I Grangeacute-Guermente MJ Boursnell C Terry MJ 678 Hibberd JM 2016 Ancestral light and chloroplast regulation form the foundations 679 for C4 gene expression Nature Plants 2 16161 680 httpsdoiorg101038nplants2016161 681

Chang Y-M Liu W-Y Shih AC-C Shen M-N Lu C-H Lu M-YJ Yang H-W 682 Wang T-Y Chen SC-C Chen SM Li W-H Ku MSB 2012 683 Characterizing Regulatory and Functional Differentiation between Maize Mesophyll 684 and Bundle Sheath Cells by Transcriptomic Analysis1[W][OA] Plant Physiol 160 685 165ndash177 httpsdoiorg101104pp112203810 686

Christie JM Blackwood L Petersen J Sullivan S 2015 Plant flavoprotein 687 photoreceptors Plant Cell Physiol 56 401ndash413 httpsdoiorg101093pcppcu196 688

Cui M Vogelmann TC Smith WK 1991 Chlorophyll and light gradients in sun and 689 shade leaves of Spinacia oleracea Plant Cell amp Environment 14 493ndash500 690 httpsdoiorg101111j1365-30401991tb01519x 691

Drozak A Romanowska E 2006 Acclimation of mesophyll and bundle sheath 692 chloroplasts of maize to different irradiances during growth Biochim Biophys Acta 693 1757 1539ndash1546 httpsdoiorg101016jbbabio200609001 694

Emms DM Kelly S 2015 OrthoFinder solving fundamental biases in whole genome 695 comparisons dramatically improves orthogroup inference accuracy Genome 696 Biology 16 157 httpsdoiorg101186s13059-015-0721-2 697

Evans JR Morgan PB von Caemmerer S 2017 Light Quality Affects Chloroplast 698 Electron Transport Rates Estimated from Chl Fluorescence Measurements Plant 699 Cell Physiol 58 1652ndash1660 httpsdoiorg101093pcppcx103 700

Evans JR Vogelmann TC 2003 Profiles of 14C fixation through spinach leaves in 701 relation to light absorption and photosynthetic capacity Plant Cell amp Environment 702 26 547ndash560 httpsdoiorg101046j1365-3040200300985x 703

Finnegan PM Suzuki S Ludwig M Burnell JN 1999 Phosphoenol pyruvate 704 Carboxykinase in the C4 Monocot Urochloa panicoides Is Encoded by Four 705 Differentially Expressed Genes Plant Physiol 120 1033ndash1042 706 httpsdoiorg101104pp12041033 707

Forger JM Bogorad L 1973 Steps in the Acquisition of Photosynthetic Competence by 708 Plastids of Maize PLANT PHYSIOLOGY 52 491ndash497 709 httpsdoiorg101104pp525491 710

Hartmann L Drewe-Boszlig P Wieszligner T Wagner G Geue S Lee H-C Obermuumlller 711 DM Kahles A Behr J Sinz FH Raumltsch G Wachter A 2016 Alternative 712 Splicing Substantially Diversifies the Transcriptome during Early 713 Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis 714 The Plant Cell 28 2715ndash2734 httpsdoiorg101105tpc1600508 715

Hatch MD Kagawa T 1976 Photosynthetic activities of isolated bundle sheath cells in 716 relation to differing mechanisms of C4 pathway photosynthesis Archives of 717 Biochemistry and Biophysics 175 39ndash53 httpsdoiorg1010160003-718 9861(76)90483-5 719

Houmlfer MU Santore UJ Westhoff P 1992 Differential accumulation of the 10- 16- 720 and 23-kDa peripheral components of the water-splitting complex of photosystem II 721 in mesophyll and bundle-sheath chloroplasts of the dicotyledonous C4 plant 722 Flaveria trinervia (Spreng) C Mohr Planta 186 304ndash312 723 httpsdoiorg101007BF00196260 724

Jin J Tian F Yang D-C Meng Y-Q Kong L Luo J Gao G 2017 PlantTFDB 725 40 toward a central hub for transcription factors and regulatory interactions in 726 plants Nucleic Acids Res 45 D1040ndashD1045 httpsdoiorg101093nargkw982 727

Kato Y Miura E Ido K Ifuku K Sakamoto W 2009 The Variegated Mutants 728 Lacking Chloroplastic FtsHs Are Defective in D1 Degradation and Accumulate 729 Reactive Oxygen Species Plant Physiology 151 1790ndash1801 730 httpsdoiorg101104pp109146589 731

Katoh K Standley DM 2013 MAFFT multiple sequence alignment software version 7 732 improvements in performance and usability Mol Biol Evol 30 772ndash780 733 httpsdoiorg101093molbevmst010 734

Kuhlgert S Austic G Zegarac R Osei-Bonsu I Hoh D Chilvers MI Roth MG 735 Bi K TerAvest D Weebadde P Kramer DM 2016 MultispeQ Beta a tool for 736 large-scale plant phenotyping connected to the open PhotosynQ network Royal 737 Society Open Science 3 160592 httpsdoiorg101098rsos160592 738

Kume A 2017 Importance of the green color absorption gradient and spectral 739 absorption of chloroplasts for the radiative energy balance of leaves J Plant Res 740 130 501ndash514 httpsdoiorg101007s10265-017-0910-z 741

Kurihara Y Makita Y Kawashima M Fujita T Iwasaki S Matsui M 2018 742 Transcripts from downstream alternative transcription start sites evade uORF-743 mediated inhibition of gene expression in Arabidopsis PNAS 115 7831ndash7836 744 httpsdoiorg101073pnas1804971115 745

Lee T-H Tang H Wang X Paterson AH 2013 PGDD a database of gene and 746 genome duplication in plants Nucleic Acids Res 41 D1152ndashD1158 747 httpsdoiorg101093nargks1104 748

Li J Li G Wang H Wang Deng X 2011 Phytochrome Signaling Mechanisms 749 Arabidopsis Book 9 httpsdoiorg101199tab0148 750

Lin C 2000 Plant blue-light receptors Trends in Plant Science 5 337ndash342 751 httpsdoiorg101016S1360-1385(00)01687-3 752

Love MI Huber W Anders S 2014 Moderated estimation of fold change and 753 dispersion for RNA-seq data with DESeq2 Genome Biology 15 550 754 httpsdoiorg101186s13059-014-0550-8 755

Markelz NH Costich DE Brutnell TP 2003 Photomorphogenic responses in maize 756 seedling development Plant Physiol 133 1578ndash1591 757 httpsdoiorg101104pp103029694 758

Meierhoff K Westhoff P 1993 Differential biogenesis of photosystem II in mesophyll 759 and bundle-sheath cells of monocotyledonous NADP-malic enzyme-type C4 plants 760 the non-stoichiometric abundance of the subunits of photosystem II in the bundle-761 sheath chloroplasts and the translational activity of the plastome-encoded genes 762 Planta 191 23ndash33 httpsdoiorg101007BF00240892 763

Muhaidat R Sage RF Dengler NG 2007 Diversity of Kranz anatomy and 764 biochemistry in C4 eudicots American Journal of Botany 94 362ndash381 765 httpsdoiorg103732ajb943362 766

Muumlller B Eichacker LA 1999 Assembly of the D1 Precursor in Monomeric 767 Photosystem II Reaction Center Precomplexes Precedes Chlorophyll andashTriggered 768 Accumulation of Reaction Center II in Barley Etioplasts The Plant Cell 11 2365ndash769 2377 httpsdoiorg101105tpc11122365 770

Nelson T Langdale JA 1989 Patterns of leaf development in C4 plants Plant Cell 1 771 3ndash13 httpsdoiorg101105tpc113 772

Ohashi-Kaneko K Matsuda R Goto E Fujiwara K Kurata K 2006 Growth of rice 773 plants under red light with or without supplemental blue light Soil Science and Plant 774 Nutrition 52 444ndash452 httpsdoiorg101111j1747-0765200600063x 775

Ort DR Zhu X Melis A 2011 Optimizing Antenna Size to Maximize Photosynthetic 776 Efficiency Plant Physiology 155 79ndash85 httpsdoiorg101104pp110165886 777

Patro R Duggal G Love MI Irizarry RA Kingsford C 2017 Salmon provides fast 778 and bias-aware quantification of transcript expression Nature Methods 14 417 779 httpsdoiorg101038nmeth4197 780

Petroutsos D Tokutsu R Maruyama S Flori S Greiner A Magneschi L Cusant 781 L Kottke T Mittag M Hegemann P Finazzi G Minagawa J 2016 A blue-782

light photoreceptor mediates the feedback regulation of photosynthesis Nature 537 783 563ndash566 httpsdoiorg101038nature19358 784

Price MN Dehal PS Arkin AP 2010 FastTree 2 ndash Approximately Maximum-785 Likelihood Trees for Large Alignments PLOS ONE 5 e9490 786 httpsdoiorg101371journalpone0009490 787

Purcell M Mabrouk YM Bogorad L 1995 Redfar-red and blue light-responsive 788 regions of maize rbcS-m3 are active in bundle sheath and mesophyll cells 789 respectively Proceedings of the National Academy of Sciences 92 11504ndash11508 790 httpsdoiorg101073pnas922511504 791

Rio DC Ares M Hannon GJ Nilsen TW 2010 Purification of RNA using TRIzol 792 (TRI reagent) Cold Spring Harb Protoc 2010 pdbprot5439 793 httpsdoiorg101101pdbprot5439 794

Rizzini L Favory J-J Cloix C Faggionato D OrsquoHara A Kaiserli E Baumeister R 795 Schaumlfer E Nagy F Jenkins GI Ulm R 2011 Perception of UV-B by the 796 Arabidopsis UVR8 protein Science 332 103ndash106 797 httpsdoiorg101126science1200660 798

Sage RF 2016 A portrait of the C4 photosynthetic family on the 50th anniversary of its 799 discovery species number evolutionary lineages and Hall of Fame J Exp Bot 67 800 4039ndash4056 httpsdoiorg101093jxberw156 801

Schepens I Duek P Fankhauser C 2004 Phytochrome-mediated light signalling in 802 Arabidopsis Curr Opin Plant Biol 7 564ndash569 803 httpsdoiorg101016jpbi200407004 804

Schuenemann D Gupta S Persello-Cartieaux F Klimyuk VI Jones JD 805 Nussaume L Hoffman NE 1998 A novel signal recognition particle targets light-806 harvesting proteins to the thylakoid membranes Proc Natl Acad Sci USA 95 807 10312ndash10316 808

Schuster G Ohad I Martineau B Taylor WC 1985 Differentiation and development 809 of bundle sheath and mesophyll thylakoids in maize Thylakoid polypeptide 810 composition phosphorylation and organization of photosystem II J Biol Chem 811 260 11866ndash11873 812

Sedelnikova OV Hughes TE Langdale JA 2018 Understanding the Genetic Basis 813 of C4 Kranz Anatomy with a View to Engineering C3 Crops Annu Rev Genet 52 814 249ndash270 httpsdoiorg101146annurev-genet-120417-031217 815

Shaikhali J Barajas-Lopeacutez J de D Oumltvoumls K Kremnev D Garcia AS Srivastava V 816 Wingsle G Bako L Strand Aring 2012 The CRYPTOCHROME1-Dependent 817 Response to Excess Light Is Mediated through the Transcriptional Activators ZINC 818 FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and 819 ZML2 in Arabidopsis The Plant Cell 24 3009ndash3025 820 httpsdoiorg101105tpc112100099 821

Sharwood RE Sonawane BV Ghannoum O 2014 Photosynthetic flexibility in maize 822 exposed to salinity and shade Journal of Experimental Botany 65 3715ndash3724 823 httpsdoiorg101093jxberu130 824

Sheen J-Y Bogorad L 1988 Differential Expression in Bundle Sheath and Mesophyll 825 Cells of Maize of Genes for Photosystem II Components Encoded by the Plastid 826 Genome Plant Physiology 86 1020ndash1026 httpsdoiorg101104pp8641020 827

Slattery RA Grennan AK Sivaguru M Sozzani R Ort DR 2016 Light sheet 828 microscopy reveals more gradual light attenuation in light-green versus dark-green 829 soybean leaves J Exp Bot 67 4697ndash4709 httpsdoiorg101093jxberw246 830

Smith H 2000 Phytochromes and light signal perception by plants--an emerging 831 synthesis Nature 407 585ndash591 httpsdoiorg10103835036500 832

Su N Hu M-L Wu D-X Wu F-Q Fei G-L Lan Y Chen X-L Shu X-L Zhang 833 X Guo X-P Cheng Z-J Lei C-L Qi C-K Jiang L Wang H Wan J-M 834

2012 Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-835 Specific Albino Phenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice 836 Production1[W][OA] Plant Physiol 159 227ndash238 837 httpsdoiorg101104pp112195081 838

Sun W Ubierna N Ma J-Y Cousins AB 2012 The influence of light quality on C4 839 photosynthesis under steady-state conditions in Zea mays and 840 Miscanthustimesgiganteus changes in rates of photosynthesis but not the efficiency of 841 the CO2 concentrating mechanism Plant Cell Environ 35 982ndash993 842 httpsdoiorg101111j1365-3040201102466x 843

Sun W Ubierna N Ma J-Y Walker BJ Kramer DM Cousins AB 2014 The 844 Coordination of C4 Photosynthesis and the CO2-Concentrating Mechanism in 845 Maize and Miscanthus times giganteus in Response to Transient Changes in Light 846 Quality Plant Physiol 164 1283ndash1292 httpsdoiorg101104pp113224683 847

Takahashi K Mineuchi K Nakamura T Koizumi M Kano H 1994 A system for 848 imaging transverse distribution of scattered light and chlorophyll fluorescence in 849 intact rice leaves Plant Cell amp Environment 17 105ndash110 850 httpsdoiorg101111j1365-30401994tb00271x 851

Tausta SL Li P Si Y Gandotra N Liu P Sun Q Brutnell TP Nelson T 2014 852 Developmental dynamics of Kranz cell transcriptional specificity in maize leaf 853 reveals early onset of C4-related processes J Exp Bot 65 3543ndash3555 854 httpsdoiorg101093jxberu152 855

Terashima I Fujita T Inoue T Chow WS Oguchi R 2009 Green light drives leaf 856 photosynthesis more efficiently than red light in strong white light revisiting the 857 enigmatic question of why leaves are green Plant Cell Physiol 50 684ndash697 858 httpsdoiorg101093pcppcp034 859

Terashima I Hikosaka K 1995 Comparative ecophysiology of leaf and canopy 860 photosynthesis Plant Cell amp Environment 18 1111ndash1128 861 httpsdoiorg101111j1365-30401995tb00623x 862

Tholen D Boom C Zhu X-G 2012 Opinion Prospects for improving photosynthesis 863 by altering leaf anatomy Plant Science 197 92ndash101 864 httpsdoiorg101016jplantsci201209005 865

Tsunoyama Y Morikawa K Shiina T Toyoshima Y 2002 Blue light specific and 866 differential expression of a plastid σ factor Sig5 in Arabidopsis thaliana FEBS 867 Letters 516 225ndash228 httpsdoiorg101016S0014-5793(02)02538-3 868

Usadel B Poree F Nagel A Lohse M Czedik-Eysenberg A Stitt M 2009 A guide 869 to using MapMan to visualize and compare Omics data in plants a case study in 870 the crop species Maize Plant Cell Environ 32 1211ndash1229 871 httpsdoiorg101111j1365-3040200901978x 872

Vogelmann TC Evans JR 2002 Profiles of light absorption and chlorophyll within 873 spinach leaves from chlorophyll fluorescence Plant Cell amp Environment 25 1313ndash874 1323 httpsdoiorg101046j1365-3040200200910x 875

von Caemmerer S Furbank RT 2016 Strategies for improving C4 photosynthesis 876 Current Opinion in Plant Biology SI 31 Physiology and metabolism 2016 31 125ndash877 134 httpsdoiorg101016jpbi201604003 878

Wang P Fouracre J Kelly S Karki S Gowik U Aubry S Shaw MK Westhoff P 879 Slamet-Loedin IH Quick WP Hibberd JM Langdale JA 2013a Evolution of 880 GOLDEN2-LIKE gene function in C3 and C4 plants Planta 237 481ndash495 881 httpsdoiorg101007s00425-012-1754-3 882

Wang P Hendron R-W Kelly S 2017a Transcriptional control of photosynthetic 883 capacity conservation and divergence from Arabidopsis to rice New Phytol 216 884 32ndash45 httpsdoiorg101111nph14682 885

Wang P Kelly S Fouracre J Langdale JA 2013b Genome-wide transcript analysis 886 of early maize leaf development reveals gene cohorts associated with the 887 differentiation of C4 Kranz anatomy Plant J 75 656ndash670 httpsdoiorgdoi 888 101111tpj12229 889

Wang P Khoshravesh R Karki S Tapia R Balahadia CP Bandyopadhyay A 890 Quick WP Furbank R Sage TL Langdale JA 2017b Re-creation of a Key 891 Step in the Evolutionary Switch from C 3 to C 4 Leaf Anatomy Current Biology 27 892 3278-3287e6 httpsdoiorg101016jcub201709040 893

Waters MT Langdale JA 2009 The making of a chloroplast EMBO J 28 2861ndash2873 894 httpsdoiorg101038emboj2009264 895

Xiao Y Tholen D Zhu X-G 2016 The influence of leaf anatomy on the internal light 896 environment and photosynthetic electron transport rate exploration with a new leaf 897 ray tracing model J Exp Bot 67 6021ndash6035 httpsdoiorg101093jxberw359 898

Xu X Paik I Zhu L Huq E 2015 Illuminating Progress in Phytochrome-Mediated 899 Light Signaling Pathways Trends in Plant Science 20 641ndash650 900 httpsdoiorg101016jtplants201506010 901

Yang L Mo W Yu X Yao N Zhou Z Fan X Zhang L Piao M Li S Yang D 902 Lin C Zuo Z 2018 Reconstituting Arabidopsis CRY2 Signaling Pathway in 903 Mammalian Cells Reveals Regulation of Transcription by Direct Binding of CRY2 to 904 DNA Cell Rep 24 585-593e4 httpsdoiorg101016jcelrep201806069 905

Yu X Liu H Klejnot J Lin C 2010 The Cryptochrome Blue Light Receptors 906 Arabidopsis Book 8 httpsdoiorg101199tab0135 907

Zhang Y Zhou Y Sun Q Deng D Liu H Chen S Yin Z 2019 Genetic 908 determinants controlling maize rubisco activase gene expression and a comparison 909 with rice counterparts BMC Plant Biol 19 351 httpsdoiorg101186s12870-019-910 1965-x 911

Zhou W Karcher D Fischer A Maximova E Walther D Bock R 2015 Multiple 912 RNA Processing Defects and Impaired Chloroplast Function in Plants Deficient in 913 the Organellar Protein-Only RNase P Enzyme PLOS ONE 10 e0120533 914 httpsdoiorg101371journalpone0120533 915

GRMZM2G026833

GLK1GLK2

GRMZM2G087804

GRMZM2G115960GRMZM2G387528

GRMZM2G062541

PIF3PIL1PIL2

PIF4PIF5

GRMZM2G180406GRMZM2G030762GRMZM2G144275GRMZM2G083504

CIL2CIB2CIB3 GRMZM2G092174

PHYBPHYD

GRMZM2G124532

PHYCGRMZM2G057935GRMZM2G129889

GRMZM2G143392

GRMZM2G080509

ZML1ZML2

GRMZM2G058479

AC2339351_FGT005

(A) (B)

60 75 90 105 120 135 150 165 180

Time under light stimulus (minutes)

Age of plant (days after planting)6 9 12

leaf 1 leaf 2leaf 1 leaf 2leaf 1

60 75 90 105 120 135 150 165 180

PSlightreactionPSI

TransportmajorintrinsicproteinsPIP

PSlightreactionPSIILHC-II

PRRrepeatContainingProtein

Proteinsynthesis

PSlightreaction

Transportsugars

Miscmyrosinases-lectin-jacalin

Transportmajorintrinsicproteins

PSlightreactionPSII

Transport

Stress

ProteindegredationubiquitinE3

MiscO-methyltransferases

TetrapyrroleSynthesis

N-metabolism

Pre-rRNAProcessingModification

Phenylpropanoidsligninbiosynthesis

Proteinfolding

RibosomalProteinprokaryotic

Proteintargetingchloroplast

RibosomeBiogenesis

RNAHelicase

AminoAcidMetabolismsynthesis

SecondaryMetabolism

RNABinding

AminoAcidMetabolism

Proteintargeting

Cellorganisation

RNAprocessing

DNAsynthesischromatinstructure

No ontology

Protein

Number of genes in categorydisplaying differential light response

Mesophyll genesBundlesheath

0 1 0 1Proportion of DE cell transcriptsthat were more highly expressedunder blue light than red

0 50 100 150 200Categories enriched for differentiallight responses

Higher expressionunder red light

Higher expressionunder blue light

CAPEPCMDHPPDKPPTOMT1TPI

AspAT(CA)(TPI)

DCT2PHTRBCS1RBCS2RBCL

FBPALDOATKLRCAMEX1

TPTPGKAlaATDCT1

MESBPPPDK-RPAlaATAspAT

3153 1044 119

Red light onlyBlue light only

Blue light or red light

(A) Count of upregulated genes by light quality

(C) All light induced genes

es(B) C4 photosynthesis genes by light induction

(D) Only induced by blue light (E) Only induced by red light

Blue only Red onlyBlueRedNot

induced

Light induced

Mesophyll Bundle sheathobs exp obs exp

C4 mesophyll cell

C4 bundle sheath cell

C3 mesophyll cell(A)

Parsed CitationsBeick S Schmitz-Linneweber C Williams-Carrier R Jensen B Barkan A 2008 The Pentatricopeptide Repeat Protein PPR5Stabilizes a Specific tRNA Precursor in Maize Chloroplasts Molecular and Cellular Biology 28 5337ndash5347httpsdoiorg101128MCB00563-08

Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title

Bolger AM Lohse M Usadel B 2014 Trimmomatic a flexible trimmer for Illumina sequence data Bioinformatics 30 2114ndash2120httpsdoiorg101093bioinformaticsbtu170

Burgess SJ Granero-Moya I Grangeacute-Guermente MJ Boursnell C Terry MJ Hibberd JM 2016 Ancestral light andchloroplast regulation form the foundations for C4 gene expression Nature Plants 2 16161 httpsdoiorg101038nplants2016161

Chang Y-M Liu W-Y Shih AC-C Shen M-N Lu C-H Lu M-YJ Yang H-W Wang T-Y Chen SC-C Chen SM Li W-HKu MSB 2012 Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells byTranscriptomic Analysis1[W][OA] Plant Physiol 160 165ndash177 httpsdoiorg101104pp112203810

Christie JM Blackwood L Petersen J Sullivan S 2015 Plant flavoprotein photoreceptors Plant Cell Physiol 56 401ndash413httpsdoiorg101093pcppcu196

Cui M Vogelmann TC Smith WK 1991 Chlorophyll and light gradients in sun and shade leaves of Spinacia oleracea Plant Cell ampEnvironment 14 493ndash500 httpsdoiorg101111j1365-30401991tb01519x

Drozak A Romanowska E 2006 Acclimation of mesophyll and bundle sheath chloroplasts of maize to different irradiances duringgrowth Biochim Biophys Acta 1757 1539ndash1546 httpsdoiorg101016jbbabio200609001

Emms DM Kelly S 2015 OrthoFinder solving fundamental biases in whole genome comparisons dramatically improves orthogroupinference accuracy Genome Biology 16 157 httpsdoiorg101186s13059-015-0721-2

Evans JR Morgan PB von Caemmerer S 2017 Light Quality Affects Chloroplast Electron Transport Rates Estimated from ChlFluorescence Measurements Plant Cell Physiol 58 1652ndash1660 httpsdoiorg101093pcppcx103

Evans JR Vogelmann TC 2003 Profiles of 14C fixation through spinach leaves in relation to light absorption and photosyntheticcapacity Plant Cell amp Environment 26 547ndash560 httpsdoiorg101046j1365-3040200300985x

Finnegan PM Suzuki S Ludwig M Burnell JN 1999 Phosphoenol pyruvate Carboxykinase in the C4 Monocot Urochloapanicoides Is Encoded by Four Differentially Expressed Genes Plant Physiol 120 1033ndash1042 httpsdoiorg101104pp12041033

Forger JM Bogorad L 1973 Steps in the Acquisition of Photosynthetic Competence by Plastids of Maize PLANT PHYSIOLOGY 52491ndash497 httpsdoiorg101104pp525491

Hartmann L Drewe-Boszlig P Wieszligner T Wagner G Geue S Lee H-C Obermuumlller DM Kahles A Behr J Sinz FH RaumltschG Wachter A 2016 Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis andCorrelates with the Energy Availability in Arabidopsis The Plant Cell 28 2715ndash2734 httpsdoiorg101105tpc1600508

Hatch MD Kagawa T 1976 Photosynthetic activities of isolated bundle sheath cells in relation to differing mechanisms of C4pathway photosynthesis Archives of Biochemistry and Biophysics 175 39ndash53 httpsdoiorg1010160003-9861(76)90483-5

Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title wwwplantphysiolorgon March 10 2020 - Published by Downloaded from

Google Scholar Author Only Title Only Author and Title

Houmlfer MU Santore UJ Westhoff P 1992 Differential accumulation of the 10- 16- and 23-kDa peripheral components of the water-splitting complex of photosystem II in mesophyll and bundle-sheath chloroplasts of the dicotyledonous C4 plant Flaveria trinervia(Spreng) C Mohr Planta 186 304ndash312 httpsdoiorg101007BF00196260

Jin J Tian F Yang D-C Meng Y-Q Kong L Luo J Gao G 2017 PlantTFDB 40 toward a central hub for transcription factorsand regulatory interactions in plants Nucleic Acids Res 45 D1040ndashD1045 httpsdoiorg101093nargkw982

Kato Y Miura E Ido K Ifuku K Sakamoto W 2009 The Variegated Mutants Lacking Chloroplastic FtsHs Are Defective in D1Degradation and Accumulate Reactive Oxygen Species Plant Physiology 151 1790ndash1801 httpsdoiorg101104pp109146589

Katoh K Standley DM 2013 MAFFT multiple sequence alignment software version 7 improvements in performance and usabilityMol Biol Evol 30 772ndash780 httpsdoiorg101093molbevmst010

Kuhlgert S Austic G Zegarac R Osei-Bonsu I Hoh D Chilvers MI Roth MG Bi K TerAvest D Weebadde P KramerDM 2016 MultispeQ Beta a tool for large-scale plant phenotyping connected to the open PhotosynQ network Royal Society OpenScience 3 160592 httpsdoiorg101098rsos160592

Kume A 2017 Importance of the green color absorption gradient and spectral absorption of chloroplasts for the radiative energybalance of leaves J Plant Res 130 501ndash514 httpsdoiorg101007s10265-017-0910-z

Kurihara Y Makita Y Kawashima M Fujita T Iwasaki S Matsui M 2018 Transcripts from downstream alternative transcriptionstart sites evade uORF-mediated inhibition of gene expression in Arabidopsis PNAS 115 7831ndash7836httpsdoiorg101073pnas1804971115

Lee T-H Tang H Wang X Paterson AH 2013 PGDD a database of gene and genome duplication in plants Nucleic Acids Res 41D1152ndashD1158 httpsdoiorg101093nargks1104

Li J Li G Wang H Wang Deng X 2011 Phytochrome Signaling Mechanisms Arabidopsis Book 9 httpsdoiorg101199tab0148Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title

Lin C 2000 Plant blue-light receptors Trends in Plant Science 5 337ndash342 httpsdoiorg101016S1360-1385(00)01687-3Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title

Love MI Huber W Anders S 2014 Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 GenomeBiology 15 550 httpsdoiorg101186s13059-014-0550-8

Markelz NH Costich DE Brutnell TP 2003 Photomorphogenic responses in maize seedling development Plant Physiol 1331578ndash1591 httpsdoiorg101104pp103029694

Meierhoff K Westhoff P 1993 Differential biogenesis of photosystem II in mesophyll and bundle-sheath cells of monocotyledonousNADP-malic enzyme-type C4 plants the non-stoichiometric abundance of the subunits of photosystem II in the bundle-sheathchloroplasts and the translational activity of the plastome-encoded genes Planta 191 23ndash33 httpsdoiorg101007BF00240892

Muhaidat R Sage RF Dengler NG 2007 Diversity of Kranz anatomy and biochemistry in C4 eudicots American Journal of Botany94 362ndash381 httpsdoiorg103732ajb943362

Muumlller B Eichacker LA 1999 Assembly of the D1 Precursor in Monomeric Photosystem II Reaction Center Precomplexes Precedes wwwplantphysiolorgon March 10 2020 - Published by Downloaded from

Chlorophyll andashTriggered Accumulation of Reaction Center II in Barley Etioplasts The Plant Cell 11 2365ndash2377httpsdoiorg101105tpc11122365

Nelson T Langdale JA 1989 Patterns of leaf development in C4 plants Plant Cell 1 3ndash13 httpsdoiorg101105tpc113Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title

Ohashi-Kaneko K Matsuda R Goto E Fujiwara K Kurata K 2006 Growth of rice plants under red light with or withoutsupplemental blue light Soil Science and Plant Nutrition 52 444ndash452 httpsdoiorg101111j1747-0765200600063x

Ort DR Zhu X Melis A 2011 Optimizing Antenna Size to Maximize Photosynthetic Efficiency Plant Physiology 155 79ndash85httpsdoiorg101104pp110165886

Patro R Duggal G Love MI Irizarry RA Kingsford C 2017 Salmon provides fast and bias-aware quantification of transcriptexpression Nature Methods 14 417 httpsdoiorg101038nmeth4197

Petroutsos D Tokutsu R Maruyama S Flori S Greiner A Magneschi L Cusant L Kottke T Mittag M Hegemann P FinazziG Minagawa J 2016 A blue-light photoreceptor mediates the feedback regulation of photosynthesis Nature 537 563ndash566httpsdoiorg101038nature19358

Price MN Dehal PS Arkin AP 2010 FastTree 2 ndash Approximately Maximum-Likelihood Trees for Large Alignments PLOS ONE 5e9490 httpsdoiorg101371journalpone0009490

Purcell M Mabrouk YM Bogorad L 1995 Redfar-red and blue light-responsive regions of maize rbcS-m3 are active in bundlesheath and mesophyll cells respectively Proceedings of the National Academy of Sciences 92 11504ndash11508httpsdoiorg101073pnas922511504

Rio DC Ares M Hannon GJ Nilsen TW 2010 Purification of RNA using TRIzol (TRI reagent) Cold Spring Harb Protoc 2010pdbprot5439 httpsdoiorg101101pdbprot5439

Rizzini L Favory J-J Cloix C Faggionato D OHara A Kaiserli E Baumeister R Schaumlfer E Nagy F Jenkins GI Ulm R2011 Perception of UV-B by the Arabidopsis UVR8 protein Science 332 103ndash106 httpsdoiorg101126science1200660

Sage RF 2016 A portrait of the C4 photosynthetic family on the 50th anniversary of its discovery species number evolutionarylineages and Hall of Fame J Exp Bot 67 4039ndash4056 httpsdoiorg101093jxberw156

Schepens I Duek P Fankhauser C 2004 Phytochrome-mediated light signalling in Arabidopsis Curr Opin Plant Biol 7 564ndash569httpsdoiorg101016jpbi200407004

Schuenemann D Gupta S Persello-Cartieaux F Klimyuk VI Jones JD Nussaume L Hoffman NE 1998 A novel signalrecognition particle targets light-harvesting proteins to the thylakoid membranes Proc Natl Acad Sci USA 95 10312ndash10316

Schuster G Ohad I Martineau B Taylor WC 1985 Differentiation and development of bundle sheath and mesophyll thylakoids inmaize Thylakoid polypeptide composition phosphorylation and organization of photosystem II J Biol Chem 260 11866ndash11873

Sedelnikova OV Hughes TE Langdale JA 2018 Understanding the Genetic Basis of C4 Kranz Anatomy with a View toEngineering C3 Crops Annu Rev Genet 52 249ndash270 httpsdoiorg101146annurev-genet-120417-031217

Shaikhali J Barajas-Lopeacutez J de D Oumltvoumls K Kremnev D Garcia AS Srivastava V Wingsle G Bako L Strand Aring 2012 TheCRYPTOCHROME1-Dependent Response to Excess Light Is Mediated through the Transcriptional Activators ZINC FINGER PROTEINEXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis The Plant Cell 24 3009ndash3025httpsdoiorg101105tpc112100099

Sharwood RE Sonawane BV Ghannoum O 2014 Photosynthetic flexibility in maize exposed to salinity and shade Journal ofExperimental Botany 65 3715ndash3724 httpsdoiorg101093jxberu130

Sheen J-Y Bogorad L 1988 Differential Expression in Bundle Sheath and Mesophyll Cells of Maize of Genes for Photosystem IIComponents Encoded by the Plastid Genome Plant Physiology 86 1020ndash1026 httpsdoiorg101104pp8641020

Slattery RA Grennan AK Sivaguru M Sozzani R Ort DR 2016 Light sheet microscopy reveals more gradual light attenuationin light-green versus dark-green soybean leaves J Exp Bot 67 4697ndash4709 httpsdoiorg101093jxberw246

Smith H 2000 Phytochromes and light signal perception by plants--an emerging synthesis Nature 407 585ndash591httpsdoiorg10103835036500

Su N Hu M-L Wu D-X Wu F-Q Fei G-L Lan Y Chen X-L Shu X-L Zhang X Guo X-P Cheng Z-J Lei C-L Qi C-KJiang L Wang H Wan J-M 2012 Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-Specific AlbinoPhenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice Production1[W][OA] Plant Physiol 159 227ndash238httpsdoiorg101104pp112195081

Sun W Ubierna N Ma J-Y Cousins AB 2012 The influence of light quality on C4 photosynthesis under steady-state conditions inZea mays and Miscanthustimesgiganteus changes in rates of photosynthesis but not the efficiency of the CO2 concentrating mechanismPlant Cell Environ 35 982ndash993 httpsdoiorg101111j1365-3040201102466x

Sun W Ubierna N Ma J-Y Walker BJ Kramer DM Cousins AB 2014 The Coordination of C4 Photosynthesis and the CO2-Concentrating Mechanism in Maize and Miscanthus times giganteus in Response to Transient Changes in Light Quality Plant Physiol 1641283ndash1292 httpsdoiorg101104pp113224683

Takahashi K Mineuchi K Nakamura T Koizumi M Kano H 1994 A system for imaging transverse distribution of scattered lightand chlorophyll fluorescence in intact rice leaves Plant Cell amp Environment 17 105ndash110 httpsdoiorg101111j1365-30401994tb00271x

Tausta SL Li P Si Y Gandotra N Liu P Sun Q Brutnell TP Nelson T 2014 Developmental dynamics of Kranz celltranscriptional specificity in maize leaf reveals early onset of C4-related processes J Exp Bot 65 3543ndash3555httpsdoiorg101093jxberu152

Terashima I Fujita T Inoue T Chow WS Oguchi R 2009 Green light drives leaf photosynthesis more efficiently than red light instrong white light revisiting the enigmatic question of why leaves are green Plant Cell Physiol 50 684ndash697httpsdoiorg101093pcppcp034

Terashima I Hikosaka K 1995 Comparative ecophysiology of leaf and canopy photosynthesis Plant Cell amp Environment 18 1111ndash1128 httpsdoiorg101111j1365-30401995tb00623x

Tholen D Boom C Zhu X-G 2012 Opinion Prospects for improving photosynthesis by altering leaf anatomy Plant Science 19792ndash101 httpsdoiorg101016jplantsci201209005

Tsunoyama Y Morikawa K Shiina T Toyoshima Y 2002 Blue light specific and differential expression of a plastid σ factor Sig5 inArabidopsis thaliana FEBS Letters 516 225ndash228 httpsdoiorg101016S0014-5793(02)02538-3

Usadel B Poree F Nagel A Lohse M Czedik-Eysenberg A Stitt M 2009 A guide to using MapMan to visualize and compareOmics data in plants a case study in the crop species Maize Plant Cell Environ 32 1211ndash1229 httpsdoiorg101111j1365-3040200901978x

Vogelmann TC Evans JR 2002 Profiles of light absorption and chlorophyll within spinach leaves from chlorophyll fluorescencePlant Cell amp Environment 25 1313ndash1323 httpsdoiorg101046j1365-3040200200910x

von Caemmerer S Furbank RT 2016 Strategies for improving C4 photosynthesis Current Opinion in Plant Biology SI 31Physiology and metabolism 2016 31 125ndash134 httpsdoiorg101016jpbi201604003

Wang P Fouracre J Kelly S Karki S Gowik U Aubry S Shaw MK Westhoff P Slamet-Loedin IH Quick WP Hibberd JMLangdale JA 2013a Evolution of GOLDEN2-LIKE gene function in C3 and C4 plants Planta 237 481ndash495httpsdoiorg101007s00425-012-1754-3

Wang P Hendron R-W Kelly S 2017a Transcriptional control of photosynthetic capacity conservation and divergence fromArabidopsis to rice New Phytol 216 32ndash45 httpsdoiorg101111nph14682

Wang P Kelly S Fouracre J Langdale JA 2013b Genome-wide transcript analysis of early maize leaf development reveals genecohorts associated with the differentiation of C4 Kranz anatomy Plant J 75 656ndash670 httpsdoiorgdoi 101111tpj12229

Wang P Khoshravesh R Karki S Tapia R Balahadia CP Bandyopadhyay A Quick WP Furbank R Sage TL Langdale JA2017b Re-creation of a Key Step in the Evolutionary Switch from C 3 to C 4 Leaf Anatomy Current Biology 27 3278-3287e6httpsdoiorg101016jcub201709040

Waters MT Langdale JA 2009 The making of a chloroplast EMBO J 28 2861ndash2873 httpsdoiorg101038emboj2009264Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title

Xiao Y Tholen D Zhu X-G 2016 The influence of leaf anatomy on the internal light environment and photosynthetic electrontransport rate exploration with a new leaf ray tracing model J Exp Bot 67 6021ndash6035 httpsdoiorg101093jxberw359

Xu X Paik I Zhu L Huq E 2015 Illuminating Progress in Phytochrome-Mediated Light Signaling Pathways Trends in PlantScience 20 641ndash650 httpsdoiorg101016jtplants201506010

Yang L Mo W Yu X Yao N Zhou Z Fan X Zhang L Piao M Li S Yang D Lin C Zuo Z 2018 Reconstituting ArabidopsisCRY2 Signaling Pathway in Mammalian Cells Reveals Regulation of Transcription by Direct Binding of CRY2 to DNA Cell Rep 24 585-593e4 httpsdoiorg101016jcelrep201806069

Yu X Liu H Klejnot J Lin C 2010 The Cryptochrome Blue Light Receptors Arabidopsis Book 8 httpsdoiorg101199tab0135Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title

Zhang Y Zhou Y Sun Q Deng D Liu H Chen S Yin Z 2019 Genetic determinants controlling maize rubisco activase geneexpression and a comparison with rice counterparts BMC Plant Biol 19 351 httpsdoiorg101186s12870-019-1965-x

Zhou W Karcher D Fischer A Maximova E Walther D Bock R 2015 Multiple RNA Processing Defects and Impaired ChloroplastFunction in Plants Deficient in the Organellar Protein-Only RNase P Enzyme PLOS ONE 10 e0120533 wwwplantphysiolorgon March 10 2020 - Published by Downloaded from

httpsdoiorg101371journalpone0120533Pubmed Author and TitleGoogle Scholar Author Only Title Only Author and Title

Parsed Citations

Article File

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5