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Title Phototrophic potential and form II ribulose-1,5-bisphosphate carboxylase/oxygenase expression in five organs of the fluted giant clam, Tridacna squamosa Author(s) Jeslyn S. T. Poo, Celine Y. L. Choo, Kum C. Hiong, Mel V. Boo, Wai P. Wong, Shit F. Chew, and Yuen K. Ip Source Coral Reefs, 39, 361–374 Published by Springer

Copyright © 2020 Springer

This is a post-peer-review, pre-copy/edit version of an article published in Coral Reefs. The final authenticated version is available online at: https://doi.org/10.1007/s00338-020-01898-7

Notice: Changes introduced as a result of publishing processes such as copy-editing and formatting may not be reflected in this document.

1 Phototrophic potential and form II ribulose-1,5-bisphosphate

2 carboxylase/oxygenase expression in five organs of the fluted giant clam,

3 Tridacna squamosa

4

5 Jeslyn S. T. Poo1, Celine Y. L. Choo1, Kum C. Hiong1, Mel V. Boo1, Wai P. Wong1, Shit

6 F. Chew2 and Yuen K. Ip1*

7 1Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore

8 117543, Republic of Singapore

9 2Natural Sciences and Science Education, National Institute of Education, Nanyang

10 Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore

11 *author for correspondence

12 13 Running head: RuBisCO in T. squamosa

14 ------

15 Correspondence address: 16 Dr. Y. K. Ip 17 Professor 18 Department of Biological Sciences 19 National University of Singapore 20 Kent Ridge 21 Singapore 117543 22 Republic of Singapore 23 24 Phone: (65)-6516-2702 25 Fax: (65)-6779-2486 26 Email: [email protected] 27

28 Keywords: Coral reefs, light-enhanced calcification, photosynthesis, symbiosis, zooxanthellae

29

0 30 Abstract

31 Despite living in oligotrophic tropical waters, giant clams can grow to large sizes because they

32 live in symbiosis with extracellular phototrophic dinoflagellates (zooxanthellae) and receive

33 photosynthates from them. The physical presence of zooxanthellae in five organs (colorful outer

34 , whitish inner mantle, ctenidium, and foot muscle) of Tridacna

35 squamosa had been confirmed by microscopy, and high densities of zooxanthellae were

36 detected in specific regions of the inner mantle and foot muscle. Symbiotic dinoflagellates use

37 form II ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) to fix inorganic carbon

38 during C3 photosynthesis. Using qPCR primers that were designed comprehensively against all

39 known zooxanthellal form II RuBisCO gene sequences (rbcII) in existing databases, we

40 demonstrated that the outer mantle of T. squamosa (TS) had the greatest phototrophic potential

41 as reflected by its high zooxanthellal rbcII (TSZrbcII) transcript level, which varied among

42 different regions of the outer mantle. The other four organs also expressed moderate levels of

43 TSZrbcII, despite the lack of iridophores and direct light exposure. Importantly, light exposure

44 led to significant increases in the protein abundance of TSZRBCII in the outer mantle but not

45 the other four organs. Taken together, these results indicate that organs inside the mantle cavity

46 had low phototrophic potentials, but zooxanthellae residing inside these organs might serve

47 some unidentified functions to benefit the host.

1 48 Introduction

49 Dinoflagellates (Phylum: Dinoflagellata, Division: Pyrrhophyta) are a group of unicellular

50 alveolates with unique characteristics (Carty 2003). They can be phototrophic, heterotrophic or

51 mixotrophic, depending on their reliance on photosynthesis or food ingestion, or both, for

52 energy and nutrition needs (Carty and Parrow 2015). Nonetheless, all of them need inorganic

53 carbon (Ci), phosphorus and nitrogen for growth and reproduction. Some dinoflagellates

54 (Symbiodiniaceae) have free-living and symbiotic stages, and can live as intracellular or

55 extracellular symbionts inside host animals (Trench 1987). The symbiotic stage of these

56 dinoflagellates lack flagella, and are known as zooxanthellae. Phototrophic animal-

57 zooxanthellae associations, including giant clams, scleractinian corals and symbiotic anemones,

58 can flourish in nutrient-poor tropical waters where light is adequately available (de Goeij et al.

59 2013).

60 Giant clams belong to Phylum: Mollusca, Family: Cardiidae, Subfamily: Tridacninae,

61 and Genus: Tridacna or Hippopus. The host clam is known to associate with three genera of

62 dinoflagellates, Symbiodinium, Cladocopium, and Durusdinium (LaJeunesse et al. 2018), which

63 were named previously as Symbiodinium clades A, C and D, respectively (LaJeunesse et al.

64 2004; Takabayashi et al. 2004; Hernawan 2008; Lee et al. 2015). The host harbors extracellular

65 zooxanthellae in a branched tubular system surrounded by hemolymph (Norton et al. 1992),

66 and the majority of zooxanthellae reside in the tiny tertiary zooxanthellal tubules located in the

67 fleshy, colorful and extensible outer mantle peculiar to giant clams (Norton et al. 1992; Hiong

68 et al. 2017a; Ip et al. 2017a). During insolation, these symbionts conduct photosynthesis and

69 donate >95% of the photosynthates to the host, satisfying a major portion of the host’s energy

70 requirements (Fisher et al. 1985; Klumpp et al. 1992). This helps to sustain light-enhanced shell

71 formation and a high growth rate in the host clam (Sano et al. 2012; Ip et al. 2017a). In turn,

72 the host must supply essential nutrients to the symbionts that have no access to the ambient

73 seawater.

2 74 In giant clams, the outer mantle possesses host pigments and iridophores, which are

75 aggregations of special iridocytes containing tiny reflective platelets (Griffiths et al. 1992).

76 These platelets scatter light of photosynthetically conducive wavelengths to the zooxanthellae

77 embedded in the tissue while back-reflecting light of other wavelengths (Holt et al. 2014),

78 engendering multiple and variable colors to the outer mantle. Due to its prominent coloration

79 and ability to extend fully during insolation, research on giant clams in the past has focused on

80 the fleshy outer mantle and its zooxanthellae, with the general notion that the primary function

81 of these phototrophic zooxanthellae is to conduct photosynthesis and share the photosynthates

82 with the host clam. By contrast, the inner mantle adjacent to the extrapallial fluid, as demarcated

83 by the of the shell-, is thin and whitish, and is involved principally in shell

84 formation (calcification). It has no direct exposure to light and lacks iridophores, yet the region

85 of the inner mantle adjacent to the hinge of the shell-valves is always brownish in color,

86 indicating the probable presence of zooxanthellae (supplementary material, Fig. S1). Other

87 organs, like the ctenidia, hepatopancreas and foot muscle, also lack direct illumination and have

88 no iridophores, as they are located inside the mantle cavity and shaded from light by the

89 siphonal mantle. However, the foot muscle may possess a substantial quantity of zooxanthellae

90 at the tip that is also brownish in color (supplementary material, Fig. S1). Although the ctenidia

91 can be visible at an angle when the incurrent is open, they are located below the siphonal

92 mantle and not directly under the opening. Hence, the intensity of light reaching the ctenidia

93 could be much lower than that received by the outer mantle. Taken together, zooxanthellae

94 residing in these four tissues/organs shaded from light might not be able to perform

95 photosynthesis effectively. Zooxanthellae conduct C3 photosynthesis (Streamer et al. 1993),

96 and the fixation of Ci in the Calvin cycle is catalyzed by form II ribulose-1,5-bisphosphate

97 carboxylase/oxygenase (RuBisCO) (Rowan et al. 1996; Mayfield et al. 2014). The form II

98 RuBisCO gene (rbcII) has been cloned and characterized from zooxanthellae of Tridacna gigas

99 (Rowan et al. 1996), and reported to be completely different from form I RuBisCO gene (rbcL)

3 100 of eukaryotes, as it bears ~65% similarity with RuBisCO gene (cbbM) of the proteobacterium,

101 Rhodospirillum rubrum (Rowan et al. 1996). Therefore, it is important to ask the foundational

102 question whether these four iridophore-free tissues/organs of giant clams would display any

103 phototrophic potential as reflected by the transcript and protein expression levels of

104 rbcII/RBCII of zooxanthellal origin.

105 Unlike the oligomeric structure of form I RuBisCO with both large and small subunits,

106 form II RuBisCO is devoid of the small subunit, and has the quaternary structure of (L2)n (Tabita

107 et al. 2008). The estimated molecular masses of the monomer and the native protein isolated

108 from the zooxanthellae of Tridacna gigas are 56 kDa and 300–350 kDa, respectively (Whitney

109 and Yellowlees 1995), suggesting a value of 3 for n. Besides structural differences, form II

110 RuBisCO also differs from form I RuBisCO in terms of kinetics and efficiency. Form II

111 RuBisCO cannot differentiate CO2 from O2 as effectively as form I RuBisCO (Morse et al.

112 1995; Tabita et al. 2008). The evolution of form I RuBisCO to associate with its small subunits

113 and assemble into an oligomer with the quaternary structure of L8S8 greatly improves its

114 catalytic efficiency and specificity (Erb and Zarzycki 2018). Consequently, form I RuBisCO

115 can support higher rates of CO2 fixation than form II RuBisCO. Nonetheless, both form I and

116 form II RuBisCO catalyze the same carboxylation and oxygenation reactions. As form I

117 RuBisCO is the main rate-limiting enzyme of CO2 fixation in the Calvin cycle, form II

118 RuBisCO can probably serve the same role (Rowan et al. 1996; Mayfield et al. 2014).

119 Therefore, it is logical to hypothesize that the transcript level of rcbII could probably act as

120 an indicator of the phototrophic potential of zooxanthellae in various organs of giant clams.

121 The first objective of this study was to confirm the presence of zooxanthellae in the five

122 organs (colorful outer mantle, whitish inner mantle, ctenidium, hepatopancreas and foot muscle)

123 of the fluted giant clam, Tridacna squamosa, which were obtained from Vietnam, by ethanol

124 treatment as well as differential interference contrast (DIC) and fluorescence (red channel)

125 microscopy. The second objective was to estimate the phototrophic potential, by determining

4 126 the transcript levels of T. squamosa zooxanthellal rcbII (TSZrbcII), in these five organs using

127 quantitative real-time PCR (qPCR). Efforts were made to design a set of qPCR primers that

128 would react comprehensively with all known sequences of rbcII available in existing databases

129 for Symbiodinium, Cladocopium, and Durusdinium (Bayer et al. 2012; Rosic et al. 2015;

130 Aranda et al. 2016; Levin et al. 2016; Liew et al. 2016; Shoguchi et al. 2018). The third objective

131 was to quantify the transcript levels of TSZrbcII in eight arbitrarily defined regions of the outer

132 mantle of T. squamosa, in order to verify whether the distribution of zooxanthellae in the outer

133 mantle would be uniform. Based on all the deduced amino acid sequences of RBCII from

134 various databases, a comprehensive anti-RBCII antibody was custom-made commercially to

135 achieve the fourth objective of confirming the localization of TSZRBCII in the plastids

136 (chloroplasts) of zooxanthellae in the outer mantle of T. squamosa. Finally, the fifth objective

137 was to test the hypothesis that the gene and protein expression levels of TSZrbcII/TSZRBCII

138 in the outer mantle, but not those in the other organs shaded from light, would be upregulated

139 during light exposure.

140 Due to anthropogenic activities, pollution and overharvesting for food and aquarium

141 trade, giant clam populations have been remarkably reduced in the wild, and they have been

142 listed in CITES Appendix II since 1985 (Wells and Barzdo 1991). In particular, the internal

143 population of zooxanthellae in giant clams can decrease drastically through a bleaching process

144 under certain environmental conditions, especially in relation to climate change, resulting in

145 the disruption of giant clam-zooxanthellae symbiotic associations (Leggat et al. 2003).

146 Traditionally, zooxanthellae have been assumed to be located predominantly in the colorful

147 outer mantle, and discoloration of the outer mantle is regarded as a major facet of the bleaching

148 process. Results obtained from this study were expected to shed light on the presence of

149 zooxanthellae in organs that are shaded from light in T. squamosa and draw attentions to their

150 possible roles, besides phototrophy, in the giant clam-zooxanthellae association.

151

5 152 Materials and Methods

153 Maintenance of animals

154 Institutional approval was not required for research on giant clams (National University of

155 Singapore Institutional Animal Care and Use Committee). Adult T. squamosa individuals (550

156 ± 50 g, mean ± SD; N=38) were purchased from Xanh Tuoi Tropical Fish, Ltd (Vietnam) and

157 housed in an indoor aquarium in three glass tanks (L90 × W62 × H60 cm) with recirculating

158 seawater. The conditions of the seawater maintained as follows: temperature at 26 ± 1°C;

159 salinity of 30–32; pH 8.1–8.3; hardness 143–179 ppm; calcium at 280–400 ppm; phosphate at

160 <0.25 ppm; nitrate at 0 ppm; total ammonia at <0.25 ppm. Giant clams were kept under a 12 h

161 light:12 h dark regime, and the light intensity measured under water at the level of the giant

162 clams was 120 μmol photons m-2 s-1 throughout the 12-h light period.

163 The light intensity used for experimental conditions should mimic the actual light

164 intensity received by the clams in their natural habitats. Although peak irradiances at the water

165 surface at noon on a sunny day can reach 2000 µmol photons m-2 s-1 in the tropical Pacific

166 (McFarland and Munz 1975), such high light intensities last several hours at the most (Marra

167 1978). Furthermore, only 5-8% of the incident light at the surface would reach the sea floor at

168 25 m, because of light attenuation in water (Fine et al. 2013). Tridacna squamosa happens to

169 be a deep water dwelling species, as the depth of occurrence ranges from 11 m to 20 m (Juinio

170 et al. 1989; Weber 2009; Andréfouët et al. 2014) and mature individuals can be found up to 42

171 m deep (Jantzen et al. 2008). As follows, Jantzen et al. (2008) exposed T. squamosa to 128 ±

172 59 μmol photons m-2 s-1, corresponding to the actual light intensity at ~20 m water depth, in

173 their study. Therefore, it is logical to postulate that zooxanthellae in the extensible outer mantle

174 of T. squamosa could display their full phototrophic potential as they would receive a light

175 intensity of 120 µmol photons m-2 s-1 in this study. Using light intensities that are

176 physiologically too high poses the danger of inducing photo-inhibition and even bleaching. In

177 fact, the photochemical efficiencies of corals (Montipora digitate and Stylophora pistillata) are

6 178 the lowest at noon, but increase as light intensity dropped (Jones and Hoegh‐Guldberg 2001).

179 Furthermore, the photosynthetic activity of several free-living dinoflagellates species could be

180 reduced to 20-30% of its maximum when exposed to high light intensities at mid-day (Ryther

181 1956).

182 Exposure of animals to experimental conditions for organ/tissue collection

183 After a month of acclimation to laboratory conditions following procurement, a clam was

184 sacrificed for ethanol treatment as well as DIC and fluorescence microscopy (N=1) to confirm

185 the presence of zooxanthellae in the five organs of T. squamosa, while another three clams were

186 used to determine the localization of TSZRBCII using immunofluorescence microscopy (N=3).

187 Various organ samples were collected from another ten clams for analyses of the zooxanthellae

188 populations by qPCR (N=10). Of these ten clams, three clams were also analyzed for the

189 distribution of zooxanthellae in different regions of the outer mantle, while five clams were

190 used to examine the distribution of zooxanthellae between the brown region and the white

191 region of the inner mantle and the foot muscle. To examine the effects of light on the transcript

192 level and protein abundance of TSZrbcII/TSZRBCII, the remaining 24 clams were maintained

193 in darkness for 12 h to be used as controls or exposed to 3, 6 or 12 h of light (N=6 for each time

194 point) before organ collection. The 12-h light intensity measured at the level of these giant

195 clams was 120 μmol photons m-2 s-1. Clams were anaesthetized with 0.2% phenoxyethanol, and

196 were forced open to cut the adductor muscles. The colorful outer mantle, inner mantle,

197 ctenidium, hepatopancreas and foot muscle were excised, freeze-clamped with pre-cooled

198 aluminium tongs and stored at –80°C until further processing for molecular analyses.

199 Photography, fluorescence microscopy and immunofluorescence microscopy

200 Organs excised from T. squamosa were fixed with 3.7% paraformaldehyde in seawater for 18

201 h, before dehydration in 70% ethanol for another 18 h at 4°C. Images of the five organs before

202 and after dehydration in 70% ethanol were obtained. Dehydration was continued with

203 increasing ethanol concentrations and Histoclear (Sigma-Aldrich Co., St. Louis, MO, USA).

7 204 The organs were embedded in paraplast (Sigma-Aldrich Co.) and sectioned to 5 μm, followed

205 by deparaffinization and rehydration in order to capture DIC and fluorescence microscopy (red

206 channel) images. For immunofluorescence microscopy, antigen retrieval was performed on the

207 deparaffinized sections with 1% sodium dodecyl sulfate in TPBS (0.05% Tween 20 in

-1 -1 -1 208 phosphate-buffered saline: 10 mmol l Na2HPO4, 1.8 mmol l KH2PO4, 137 mmol l NaCl,

209 2.7 mmol l-1 KCl, pH 7.4) for 10 min, and blocked with 1% BSA in TPBS for 30 min at room

210 temperature. The sections were incubated with the custom-made anti-RBCII antibody (2.5 µg

211 ml-1 in TPBS) for 1.5 h followed by Alexa-fluor-488 secondary antibody (2.5 µg ml-1 in TPBS)

212 for 1 h at 37°C. Nuclei were then stained with 6-diamidino-2-phenylindole dihydrochloride

213 (DAPI, Sigma-Aldrich Co.) for 10 min before capturing of images. All microscopy images were

214 captured using the Olympus microscope imaging system with universally adjusted brightness

215 and contrast, and processed by Adobe Photoshop CC (Adobe Systems, CA, USA).

216 A rabbit polyclonal anti-RBCII antibody was custom-made by GenScript (Piscataway,

217 NJ, USA) with the epitope ALDQSSRYADLSLD, which was designed at a conserved region

218 of 13 CbbM/RBCII sequences of various proteobacteria and dinoflagellates that were retrieved

219 from GenBank (supplementary material, Table S1). The epitope sequence had an 85.7-100%

220 identity with all these CbbM/RBCII sequences. Hence, in theory, this anti-RBCII antibody

221 could react comprehensively with the TSZRBCII sequences from all species of Symbiodinium,

222 Cladocopium and Durusdinium in T. squamosa.

223 Extraction of total RNA and cDNA synthesis

224 Total RNA from the various excised organs was extracted using TRI Reagent® (Sigma-Aldrich)

225 and purified with the PureLinkTM RNA Mini Kit (Invitrogen, Thermo Fisher Scientific Inc.,

226 Waltham, MA, USA). The concentration of purified RNA was determined with a Shimadzu

227 BioSpec-nano spectrophotometer (Shimadzu Corporation, Tokyo, Japan), after which RNA

228 integrity was verified with electrophoresis before being reverse-transcribed into cDNA with

229 RevertAidTM first strand cDNA synthesis kit (Thermo Fisher Scientific Inc.).

8 230 Determination of mRNA expression by quantitative real-time PCR (qPCR)

231 The mRNA transcript levels of TSZrbcII in various organs of T. squamosa were quantified

232 through qPCR with a StepOnePlusTM Real-Time PCR System (Applied Biosystems, Carlsbad,

233 CA, USA), following the methods described in Ip et al. (2017b). A set of gene-specific forward

234 and reverse qPCR primers (forward: 5’-CAGTTCTTGCACTACCACCG-3’; reverse: 5’-

235 CATCTTGCCGAAGCTCATGG-3’) was designed at a conserved region of all available rbcII

236 sequences from various dinoflagellate databases. These included 19 sequences from

237 Symbiodinium databases (Bayer et al. 2012; Aranda et al. 2016), three sequences from

238 Cladocopium databases (Levin et al. 2016; Liew et al. 2016; Shoguchi et al. 2018) and six

239 sequences from Durusdinium database (Rosic et al. 2015). This set of TSZrbcII qPCR primers

240 would theoretically react comprehensively with all known rbcII sequences from Symbiodinium,

241 Cladocopium and Durusdinium (see supplementary material, Table S2 for primer design), and

242 had an overall amplification efficiency of 95.2%. The absolute transcript levels of TSZrbcII

243 were calculated using a plasmid standard curve, and expressed as copies of transcript per ng

244 total RNA.

245 Western blotting

246 Proteins were extracted from various excised organs of T. squamosa according to the protocol

247 of Hiong et al. (2017b). Twenty micrograms (for the outer mantle) or 100 μg (for the other four

248 organs) of protein were heated at 95°C for 5 min before running through 10% SDS-PAGE and

249 transferred onto nitrocellulose membranes. Western blotting was then conducted with Pierce

250 Fast Western Blot kit, SuperSignal® West Pico Substrate (Thermo Fisher Scientific Inc.),

251 adhering to the manufacturer’s instructions. For the outer mantle samples, the membrane was

252 incubated with the custom-made anti-RBCII antibody at a 1:2000 dilution in Fast Western

253 Antibody Diluent, while the same antibody was used at 1:1000 dilution for the other four organ

254 samples. Bands were visualized via chemiluminescence using ChemiDocTM Imaging Systems

255 (Bio-Rad Laboratories, Hercules, CA, USA). The optical density of the bands was calculated

9 256 using ImageJ (version 1.50, NIH) after calibration with a 21-step reflection scanner scale (1″9

257 8″; Stouffer #R3705-1C). The protein abundance of TSZRBCII was expressed as arbitrary

258 densitometric units (a.u.) per 20 μg protein from the outer mantle or per 100 μg protein from

259 each of the other four organs. In this study, the protein abundance of the targeted protein in each

260 of the five organs was not normalized with a reference protein because the assumption of a

261 constant expression of the reference protein across different organs could not be justified. It has

262 been established that commonly used reference proteins such as tubulin and actin do not serve

263 as good reference proteins for studying relative expression in various tissues/organs because of

264 variable expression among different tissues, cell lines or experimental conditions (Thorrez et

265 al. 2008).

266 Statistics

267 Results were presented as means + S.E.M. Data obtained were analyzed with the SPSS Statistics

268 version 20 software (IBM Corporation, Armonk, NY, USA). Levene’s test was used to test the

269 homogeneity of variance. Following the fulfilment of the assumption of equal variance, either

270 independent t-test or one-way analysis of variance (ANOVA) was conducted to analyze the

271 differences between or among the means. After performing one-way ANOVA, the Tukey’s test

272 was conducted to evaluate the differences among the means of multiple experimental groups.

273 When the assumption of equal variance was not fulfilled, the differences among the means of

274 these experimental groups were analyzed using the Dunnett’s T3 test. Differences between

275 means with a P value that is less than 0.05 were regarded as statistically significant.

10 276 Results

277 Zooxanthellae are present in all five organs of T. squamosa

278 The originally brown outer mantle turned green after alcohol treatment, which was indicative

279 of a high chlorophyll content (Fig. 1a). In comparison, the inner mantle appeared to contain less

280 zooxanthellae, which were concentrated in a tiny region at the edge near the hinge, rendering it

281 a brownish color (supplementary material, Fig. S1), or green after alcohol treatment as

282 compared to the whitish middle part of the mantle (Fig. 1b). Similarly, the amount of

283 zooxanthellae present in the ctenidium seemed to be small, as indicated by the light

284 brown/green coloration observed in the middle ctenidial suspensory (Fig. 1c). The

285 hepatopancreas also contained zooxanthellae, but they were not concentrated in a specific

286 region (Fig. 1d). In contrast, the tip of the foot muscle appeared to have high concentrations of

287 zooxanthellae as compared to the whitish region of the same organ (Fig. 1e; supplementary

288 material, Fig. S1).

289 In histological sections, red auto-fluorescence of chlorophyll under blue light made it

290 possible to identify and localize zooxanthellae. The overlay of DIC images with the red channel

291 revealed the localization of auto-fluorescing zooxanthellae inside the tubular networks of the

292 five organs (Fig. 2). In the outer mantle, the tertiary zooxanthellal tubules contained high

293 densities of zooxanthellae, arranged in a columnar-like pattern (Fig. 2a). In the inner mantle,

294 the tertiary tubules and the associated zooxanthellae were located closer to the seawater-facing

295 epithelium than the shell-facing epithelium. The amount of zooxanthellae present in the whitish

296 middle part of the inner mantle (Fig. 2b) was lower than that in the brownish region close to the

297 valve hinge (Fig. 2c). Zooxanthellae were distributed scarcely in the ctenidium, as only a few

298 zooxanthellae were found in the middle ctenidial suspensory ligament (Fig. 2d). In the

299 hepatopancreas, morphologically intact zooxanthellae and degraded zooxanthellae could be

300 found within the macrophage centers (Fig. 2e). No zooxanthella was found in the whitish part

301 of the foot muscle (Fig. 2f), but the tip of the foot muscle harbored high densities of

11 302 zooxanthellae (Fig. 2g). Immunofluorescence microscopy using the anti-RBCII antibody

303 confirmed the green staining of TSZRBCII in the pyrenoids of zooxanthellae (Fig. 2h), which

304 was the correct localization of RBCII in algae and dinoflagellates (with reproducible results

305 obtained from three individuals).

306 TSZrbcII is detected not only in the outer mantle, but also other organs that are shaded

307 from light

308 TSZrbcII transcripts were detected in all five organs of T. squamosa examined, of which, the

309 inner mantle, ctenidium, hepatopancreas and foot muscle have no direct exposure to light (Fig.

310 3). The TSZrbcII transcript level in the outer mantle was significantly higher than those in other

311 organs (P<0.05; Fig. 3a), which was in agreement with the results from fluorescence

312 microscopy. Furthermore, TSZrbcII transcript levels in the inner mantle and foot muscle were

313 comparable, and they were significantly greater than those in the ctenidium and the

314 hepatopancreas. The brown regions of the inner mantle and the foot muscle contained

315 significantly more TSZrbcII transcripts than the corresponding white regions (P<0.05; Fig. 3b).

316 TSZrbcII transcripts are distributed non-uniformly in the colorful outer mantle

317 The transcript levels of TSZrbcII were apparently non-uniform across the length of the colorful

318 outer mantle of all three clams examined (Table 1), with differences ranging between 2- and

319 4.5-fold, indicating that certain regions of the outer mantle might contain more zooxanthellae

320 than others. Consequently, the mean TSZrbcII transcript levels across the eight arbitrarily

321 defined regions of the outer mantle displayed high percentage deviations (26-44%).

322 Effects of 3, 6 or 12 h of light exposure on the transcript level and protein abundance of

323 TSZrbcII/TSZRBCII in the outer mantle

324 The transcript level of TSZrbcII remained unchanged in the outer mantle of T. squamosa after

325 exposure to light for 3, 6 or 12 h as compared with the control kept in darkness for 12 h (Fig.

326 4). Western blotting revealed a band of interest at ~50 kDa, which corresponded to the estimated

327 molecular size of the RBCII monomer (Fig. 5a). The protein abundance of TSZRBCII (in

12 328 arbitrary units) increased significantly by ~4 fold in the outer mantle of T. squamosa after

329 exposure to 12 h of light as compared to that of the control kept in 12 h of darkness (P<0.05;

330 Fig. 5b).

331 Effects of light exposure on the protein abundance of TSZRBCII in the inner mantle,

332 ctenidium, hepatopancreas and foot muscle

333 The protein abundances of TSZRBCII (in arbitrary units) in the inner mantle, ctenidium,

334 hepatopancreas and foot muscle were apparently lower than that in the outer mantle. In contrast

335 with the outer mantle, exposure to light for 3, 6 or 12 h had no significant effect on the protein

336 abundances of TSZRBCII in these four organs as compared with the corresponding control kept

337 in darkness for 12 h (Fig. 6).

13 338 Discussion

339 In giant clams, the zooxanthellal tubular system originates from the stomach as a single primary

340 zooxanthellal tube, which passes through the digestive diverticula and the muscular wall that

341 encloses the digestive mass and reproductive organ, and then divides into two secondary tubes

342 that pass through the kidney and the adductor muscle, followed by the mantle tissues (Norton

343 et al. 1992). The secondary zooxanthellal tubes branch into the upper portion of the fleshy and

344 colorful outer mantle where they terminate in convolutions of tertiary zooxanthellal tubules

345 containing zooxanthellae (Norton et al. 1992). Other secondary zooxanthellal tubes form

346 tertiary zooxanthellal tubules in organs such as the ctenidium (gill), the connective tissue

347 surrounding the adductor muscle, connective tissues of the bulbus arteriosus of the heart and

348 some areas of the inner mantle adjacent to the shell (Norton et al. 1992). Overall, tertiary tubules

349 are located mainly in the surface tissues of the outer mantle, which harbor the highest density

350 of zooxanthellae, and are surrounded by iridocytes (Ip et al. 2018). However, apart from the

351 outer mantle, the structure of the tubular system denotes the presence of zooxanthellae in organs

352 located inside the mantle cavity, which is supported by results obtained from this study.

353 Besides the outer mantle, zooxanthellae are present in organs that have no direct exposure

354 to light

355 Among the five organs of T. squamosa examined, the outer mantle, which contains iridophores

356 and is fully extensible during insolation, had the greatest density of zooxanthellae and the

357 highest transcript level of TSZrbcII. Nevertheless, even with direct light exposure, the amount

358 of light reaching the deeper layers of the outer mantle (which is several millimetres thick) is

359 low, and zooxanthellae therein would receive low irradiance due to shading by the layers of

360 cells on top (Holt et al. 2014). Therefore, the host iridophores peculiar to the outer mantle are

361 crucial for zooxanthellal photosynthesis, as they forward-scatter light to the underlying

362 zooxanthellae. This would enhance the quantum of light reaching the zooxanthellae by five-

363 fold as compared to the absence of iridophores. However, even with the help of iridophores,

14 364 only ~5-10% of the incident light can penetrate into the deeper cell layers of the outer mantle

365 (Holt et al. 2014), and the quantum of light reaching the zooxanthellae without iridophores

366 would presumably be negligible.

367 As the inner mantle, ctenidium, hepatopancreas and foot muscle of T. squamosa are

368 located inside the mantle cavity, they would logically receive low levels of illumination.

369 However, our results demonstrated that they contained considerable amounts of zooxanthellae,

370 with auto-fluorescing zooxanthellae being detected by fluorescence microscopy. Furthermore,

371 specific regions of the inner mantle (near the valve hinge) and the foot muscle (at the tip)

372 contained substantial quantities of zooxanthellae as revealed by the green coloration after

373 ethanol treatment and the relatively high TSZrbcII expression levels. It has been accepted

374 traditionally that the primary function of zooxanthellae is to conduct photosynthesis and share

375 the photosynthates with the host (Klumpp et al. 1992). As follows, the presence of considerable

376 quantities of zooxanthellae in these four organs shaded by the siphonal mantle is intriguing.

377 Although all four organs expressed moderate levels of TSZrbcII, the phototrophic potentials of

378 these organs are unlikely to be high as they lack both iridophores and direct exposure to light.

379 In fact, correlations between insufficient light and reduced carbon fixation by form I RuBisCO,

380 as well as reduced efficiency of photosystem II, have been reported in plants (Sui et al. 2012).

381 Nonetheless, the discovery of substantial quantities of zooxanthellae in special locations of the

382 inner mantle and the foot muscle of T. squamosa suggests that they might serve some special

383 functions, besides photosynthesis, yet to be elucidated in these two organs.

384 TSZrbcII is distributed unevenly across different regions of the outer mantle

385 The distribution of TSZrbcII transcripts across eight arbitrarily defined regions of the colorful

386 outer mantle of T. squamosa was non-uniform, as reflected by the high variability (26-44%) in

387 the mean transcript levels among these eight regions. These results indicate the presence of

388 disparate quantities of zooxanthellae in different regions of the outer mantle. Notably, it has

389 been reported that the two halves of the outer mantle of Tridacna maxima showed different

15 390 susceptibility to bleaching (Rouzé and Hédouin 2018). This supports the proposition that

391 different parts of a giant clam might contain dissimilar zooxanthellae communities, possibly

392 correlated with differences in bleaching tolerances. The high variability in transcript levels of

393 TSZrbcII in the outer mantle of T. squamosa could result from the difference in densities of

394 tertiary zooxanthellal tubules in these eight regions. As the distribution of zooxanthellae in the

395 outer mantle was non-uniform, it should be noted that tissue clipping of the outer mantle may

396 not be a valid method of representative sampling of zooxanthellae from this organ.

397 Light exposure upregulates the protein abundance of TSZRBCII in the outer mantle,

398 indicating an increased rate of CO2 fixation

399 The transcript levels of TSZrbcII in the outer mantle of T. squamosa remained statistically

400 unchanged after 12 h of light exposure. As the baseline transcript level of TSZrbcII in the outer

401 mantle of control clams exposed to 12 h of darkness was very high (x106 copies), any further

402 increase in the transcript level in response to light would not make a substantial difference.

403 Hence, regulation of TSZrbcII expression at the translational level could be more effective, as

404 has been suggested by Mayfield et al. (2014) for symbiotic dinoflagellates. Indeed, the protein

405 abundance of TSZRBCII increased significantly in the outer mantle of T. squamosa after 12 h

406 of light exposure compared to the control kept in darkness for 12 h, denoting that TSZRBCII

407 expression is light-dependent. It can be seen that the increase in expression of TSZRBCII

408 occurred progressively in the outer mantle between hour 6 and hour 12. As TSZRBCII is

409 presumed to be the main rate-limiting enzyme in the Calvin cycle (Rowan et al. 1996), an

410 upregulation of its expression in the outer mantle of T. squamosa would lead to an increase in

411 CO2 fixation and the production of photosynthates during insolation.

412 Although the expression of rbcL in some cyanobacteria and phytoplankton peaks at

413 sunrise (Pichard et al. 1996; Zinser et al. 2009), the expression of rbcII in cultured zooxanthellae

414 isolated from the sea anemone, Aiptasia pulchella, increases with light and peaks after 12 h of

415 light exposure (Mayfield et al. 2014). As suggested by Mayfield et al. (2014), regulation of

16 416 photosynthetic genes and proteins may differ between free-living and symbiotic phototrophs.

417 Free-living dinoflagellates have direct access to inorganic nutrients in the ambient seawater,

418 but zooxanthellae have to depend on their host for a regular supply of inorganic nutrients.

419 Although light may be readily available from morning to noon, photosynthesis in zooxanthellae

420 may be limited by the availability of Ci. In T. squamosa, the host clam conducts light-enhanced

421 absorption of Ci through a light-dependent mechanism consisting of Dual-Domain Carbonic

422 Anhydrase (DDCA; Koh et al. 2018), Vacuolar-type H+-ATPase (VHA; Ip et al. 2018), and

423 Na+/H+ Exchanger 3-like (NHE3-like; Hiong et al. 2017b) in its ctenidia. Evidently, the

424 transcript and protein levels of these enzymes and transporters are only significantly

425 upregulated in the ctenidium of T. squamosa between hour 6 and hour 12 of light exposure to

426 augment Ci absorption and assimilation (Hiong et al. 2017b; Ip et al. 2018; Koh et al. 2018).

427 Hence, even with an upregulation of the host carbon-concentrating mechanism (CCM) to

428 translocate Ci from the hemolymph to the tubular fluid at hour 3 of light exposure (Ip et al.

429 2017b, 2018), it is unlikely that the Ci available in the hemolymph at that time point would

430 support the peak capacity of carbon-fixation. In fact, the pattern of light-dependent expression

431 of TSZRBCII in the outer mantle of T. squamosa aligns well with that of the Ci uptake

432 mechanisms in the ctenidium.

− 433 The absorbed Ci is transferred as HCO3 in the hemolymph to other parts of clam’s

434 body, and it must permeate both the basolateral and apical membranes of the epithelial cells of

435 the tertiary zooxanthellal tubules before it can be absorbed by the symbionts. This is achieved

436 through a host-mediated and light-dependent CCM that increases the translocation of Ci from

437 the hemolymph to the tubular fluid. VHA (Ip et al. 2018) and Carbonic Anhydrase 2-like (CA2-

438 like; Ip et al. 2017b) constitute the host CCM that involves iridocytes and tubular epithelial

439 cells in the outer mantle of T. squamosa. Specifically, the transcript and protein expression

440 levels of VHA subunit A (ATP6V1A/ATP6V1A) increase significantly in the outer mantle of T.

441 squamosa during light exposure. In the outer mantle, the iridocytes, which deflect light of useful

17 442 wavelengths to the zooxanthellae, are strongly ATP6V1A-immunopositive. In light, they can

+ − 443 increase the secretion of H to the hemolymph sinuses to promote the dehydration of HCO3 to

444 CO2, which is then transported across the basolateral membrane of the epithelial cells of the

445 zooxanthellal tubules. Notably, iridocytes are known to be present only in the outer mantle and

− 446 not in any other organ in giant clams. Inside the epithelial cells, CO2 is converted to HCO3

− 447 catalyzed by CA2-like, and HCO3 is then transported across the apical membrane into the

448 tubular fluid of the zooxanthellal tubules. Simultaneously, VHA located in the apical membrane

449 (Armstrong et al. 2018; Ip et al. 2018) secretes H+ into the tubular fluid to promote the

− 450 dehydration of HCO3 to CO2, augmenting the supply of Ci to the zooxanthellae residing in the

451 lumen of the tubule. Overall, the entire host CCM present in the outer mantle can effectively

452 supply photosynthesizing zooxanthellae inside the tertiary tubules with the amount of CO2

453 needed to produce adequate quantities of photosynthates for the host-symbiont association

454 during insolation.

455 The protein abundances of TSZRBCII in the other four organs shaded from light remain

456 unchanged during light exposure

457 TSZRBCII was also detected in the inner mantle, ctenidium, hepatopancreas and foot muscle

458 of T. squamosa, although at levels considerably lower than that in the outer mantle. However,

459 unlike the outer mantle, the protein abundance of TSZRBCII in these four organs remained

460 statistically unchanged during 12 h of light exposure as compared with the control kept in 12 h

461 of darkness. Besides being shaded from light, these four organs do not have iridophores, and

462 therefore lack the mechanism (VHA of iridocytes; Ip et al. 2018) that augments the supply of

463 Ci from the hemolymph into the epithelial cells of zooxanthellal tubules. Even with the presence

464 of VHA in the epithelial cells (Armstrong et al. 2018; Ip et al. 2018), the host CCM is

465 incomplete and the transport of Ci from the hemolymph through the basolateral membrane into

466 the epithelial cells of the zooxanthellal tubules would be inefficient in the absence of iridocytes.

467 This would imply that zooxanthellae residing in these organs would be deprived of an efficient

18 468 supply of Ci absorbed by the host clam to support light-enhanced CO2 fixation. Taken altogether,

469 it can be concluded that these four organs have low phototrophic potentials. It could be that the

470 transport of nutrients through the open circulatory system of giant clams is slow and inefficient,

471 and therefore these organs need to possess some zooxanthellae in order to produce small

472 quantities of photosynthates under low light intensities. Nevertheless, the possibility of these

473 zooxanthellae having some special physiological functions unrelated to photosynthesis in these

474 organs of the giant clam holobiont cannot be ignored.

475 Notably, plastids can perform important functions other than photosynthesis (Füssy et

476 al. 2019). In many non-photosynthetic lineages including stramenopiles and apicomplexans,

477 plastids are retained despite the loss of photosynthetic capabilities. In apicomplexans, plastids

478 (known as apicoplasts) perform important biosynthetic functions including the synthesis of Fe-

479 S clusters, fatty acids, isoprenoids and heme (van Dooren and Hapuarachchi 2017), which are

480 essential for the growth of the parasite in its host (van Dooren and Striepen 2013). Similarly, in

481 non-photosynthetic organs of plants such as the tubers, roots and seeds, plastids may

482 differentiate into colorless leucoplasts that lack photosynthetic pigments (Heldt and Piechulla

483 2011). Instead of photosynthesis, they may be specialized for the storage of starch, lipids or

484 proteins (Zhu et al. 2018; Sadali et al. 2019). Additionally, leucoplasts may possess biosynthetic

485 functions, including syntheses of fatty acids, amino acids and tetrapyrrole compounds such as

486 heme (Zhu et al. 2018). In roots where nitrate assimilation occurs, the reduction of nitrite to

487 ammonia occurs in the leucoplasts (Heldt and Piechulla 2011). Even in phototrophs, the

488 syntheses of fatty acids, terpenoids and tetrapyrroles occur solely in the plastids of chromerids

489 (Füssy et al. 2019). Therefore, it is highly probable that plastids of zooxanthellae with low light

490 exposure might engage in some important physiological functions, such as the biosyntheses of

491 fatty acids and amino acids, to benefit the host. Furthermore, it is logical to deduce that some

492 of these functions could be organ specific, for instance, to support protein synthesis in the foot

493 muscle or light-enhanced calcification in the inner mantle.

19 494 Zooxanthellae of the inner mantle, ctenidium, hepatopancreas and foot muscle naturally

495 live in conditions of very low light intensities. Therefore, they should not be affected too

496 severely during the bleaching of the outer mantle caused by a lack of insolation due to floating

497 sediments resulting from anthropogenic activities. Theoretically, the survival of zooxanthellae

498 outside the outer mantle may act as ‘seeds’ for the build-up of the zooxanthellae population

499 during recovery in subsequently more favourable environmental conditions. Upon migrating to

500 the outer mantle during recovery, plastids of these zooxanthellae may then engage in

501 photosynthesis with illumination. In particular, this phenomenon has been well documented in

502 etioplasts of plants. In the absence of light during leaf development, proplastids differentiate

503 into etioplasts which are chloroplast progenitors (Kowalewska et al. 2016) without chlorophyll

504 pigments (Plöscher et al. 2011). Then, with illumination, etioplasts can differentiate into

505 functioning chloroplasts (Solymosi and Schoefs 2010).

506 Perspective

507 Based on microscopy and TSZrbcII/TSZRBCII expression, we have demonstrated for the first

508 time the presence of zooxanthellae in five different organs of T. squamosa, with the colorful

509 outer mantle having the highest phototrophic potential among them. The discoveries of the

510 presence of zooxanthellae in special locations of the inner mantle and foot muscle, the existence

511 of substantial quantities of intact zooxanthellae in the hepatopancreas, and the apparent non-

512 uniform distribution of zooxanthellae in the colorful outer mantle are novel. As Symbiodinium

513 is known to require high light intensities to flourish (Ikeda et al. 2017) while Cladocopium may

514 be better adapted to low light conditions (Grasso 2015), the abundance of Symbiodinium could

515 be lower than that of Cladocopium in the shaded organs. It is possible that T. squamosa would

516 harbor Symbiodinium, Cladocopium and Durusdinium in unequal proportions in various organs,

517 as defined by their exposure to different light intensities, but future work is needed to confirm

518 this proposition. Importantly, it is logical to deduce that zooxanthellae residing in organs shaded

519 from light serve some kind of physiological functions, besides photosynthesis, to benefit the

20 520 host. Therefore, efforts should be made in the future to elucidate the functional roles of

521 zooxanthellae in the shaded organs of T. squamosa, and to examine their responses to

522 environmental conditions that would induce bleaching.

21 523 Acknowledgements

524 This study was supported by the Singapore Ministry of Education through grants (R-154-000-

525 A37-114 and R‐154‐000‐B69-114) to Ip YK.

526 Ethical approval

527 Institutional approval was not required for research on giant clams (National University of

528 Singapore Institutional Animal Care and Use Committee). Nonetheless, all applicable

529 international, national, and/or institutional guidelines for the care and use of animals were

530 followed.

531 Conflict of interest

532 The authors declare that the research was conducted in the absence of any commercial or

533 financial relationships that could be construed as a potential conflict of interest.

22 534 References

535 Andréfouët S, Simon Van Wynsberge, Fauvelot C, Bruckner AW, Remoissenet G (2014) 536 Significance of new records of Tridacna squamosa Lamarck, 1819, in the Tuamotu 537 and Gambier Archipelagos (French Polynesia). Molluscan Res 34:277-284 538 Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, Piel J, Ashoor H, 539 Bougouffa S, Bajic VB, Ryu T, Ravasi T, Bayer T, Micklem G, Kim H, Bhak J, 540 LaJeunesse TC, Voolstra CR (2016) Genomes of coral dinoflagellate symbionts 541 highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci Rep 6:39734 542 [doi: 10.1038/srep39734] 543 Armstrong EJ, Roa JN, Stillman JH, Tresguerres M (2018) Symbiont photosynthesis in giant 544 clams is promoted by V-type H+-ATPase from host cells. J Exp Biol 221:177220 [doi: 545 10.1242/jeb.177220] 546 Bayer T, Aranda M, Sunagawa S, Yum LK, DeSalvo MK, Lindquist E, Coffroth MA, 547 Voolstra CR, Medina M (2012) Symbiodinium transcriptomes: genome insights into 548 the dinoflagellate symbionts of reef-building corals. PLoS ONE 7:e35269 549 [https://doi.org/10.1371/journal.pone.0035269] 550 Carty S (2003) Dinoflagellates. In: Wehr JD, Sheath RG (eds) Freshwater algae of North 551 America: ecology and classification. Academic Press, San Diego, USA, pp 685-714 552 Carty S, Parrow MW (2015) Dinoflagellates. In: Wehr JD, Sheath RG, Kociolek JP (eds) 553 Freshwater algae of North America: ecology and classification, second edition. 554 Academic Press, San Diego, USA, pp 773-807 555 de Goeij JM, van Oevelen D, Vermeij MJA, Osinga R, Middelburg JJ, de Goeij AFPM, 556 Admiraal W (2013) Surviving in a marine desert: the sponge loop retains resources 557 within coral reefs. Science 342:108-110 558 Erb TJ, Zarzycki J (2018) A short history of RubisCO: the rise and fall (?) of Nature's 559 predominant CO2 fixing enzyme. Curr Opin Biotech 49:100-107 560 Fine M, Sabbah S, Shashar N, Hoegh-Guldberg O (2013) Light from down under. J Exp Biol 561 216:4341-4346 562 Fisher CR, Fitt WK, Trench RK (1985) Photosynthesis and respiration in Tridacna gigas as a 563 function of irradiance and size. Biol Bull 169:230-245 564 Füssy Z, Faitová T, Oborník M (2019) Subcellular Compartments Interplay for Carbon and 565 Nitrogen Allocation in Chromera velia and Vitrella brassicaformis. Genome Biol 566 Evol 11:1765-1779 567 Grasso CR (2015) Investigating the effects of high light versus low light in two different 568 types of Symbiodinium within the reef-building coral, Acropora millepora. Ph.D. 569 thesis, University of Delaware 570 Griffiths DJ, Winsor H, Luongvan T (1992) Iridophores in the mantle of giant clams. Aust J 571 Zool 40:319-326 572 Heldt H, Piechulla B (2011) A leaf cell consists of several metabolic compartments. In: Plant 573 biochemistry (fourth edition). Academic Press, San Diego, USA, pp 1-42

23 574 Hernawan UE (2008) Review: symbiosis between the giant clams (: Cardiidae) and 575 zooxanthellae (Dinophyceae). Biodiversitas 9:53-58 576 Hiong KC, Choo CYL, Boo MV, Ching B, Wong WP, Chew SF, Ip YK (2017a) A light- 577 dependent ammonia-assimilating mechanism in the ctenidia of a giant clam. Coral 578 Reefs 36:311-323 579 Hiong KC, Cao-Pham AH, Choo CYL, Boo MV, Wong WP, Chew SF, Ip YK (2017b) Light- 580 dependent expression of a Na+/H+ exchanger 3-like transporter in the ctenidium of the 581 giant clam, Tridacna squamosa, can be related to increased H+ excretion during light- 582 enhanced calcification. Physiol Rep 5:e13209 [doi: 10.14814/phy2.13209] 583 Holt AL, Vahidinia S, Gagnon YL, Morse DE, Sweeney AM (2014) Photosymbiotic giant 584 clams are transformers of solar flux. J Roy Soc Interface 11:20140678 585 [doi: 10.1098/rsif.2014.0678] 586 Ikeda S, Yamashita H, Kondo S, Inoue K, Morishima S, Koike K (2017) Zooxanthellal 587 genetic varieties in giant clams are partially determined by species-intrinsic and 588 growth-related characteristics. PLoS ONE 12:e0172285 589 [https://doi.org/10.1371/journal.pone.0172285] 590 Ip YK, Hiong KC, Goh EJK, Boo MV, Choo CYL, Ching B, Wong WP, Chew SF (2017a) 591 The whitish inner mantle of the giant clam, Tridacna squamosa, expresses an apical 592 Plasma Membrane Ca2+-ATPase (PMCA) which displays light-dependent gene and 593 protein expressions. Front Physiol 8:781 [https://doi.org/10.3389/fphys.2017.00781] 594 Ip YK, Koh CZY, Hiong KC, Choo CYL, Boo MV, Wong WP, Neo ML, Chew SF (2017b) 595 Carbonic anhydrase 2-like in the giant clam, Tridacna squamosa: characterization, 596 localization, response to light, and possible role in the transport of inorganic carbon 597 from the host to its symbionts. Physiol Rep 5:e13494 [doi: 10.14814/phy2.13494] 598 Ip YK, Hiong KC, Lim LJY, Choo CYL, Boo MV, Wong WP, Neo ML, Chew SF (2018) 599 Molecular characterization, light-dependent expression, and cellular localization of a 600 host vacuolar-type H+-ATPase (VHA) subunit A in the giant clam, Tridacna 601 squamosa, indicate the involvement of the host VHA in the uptake of inorganic carbon 602 and its supply to the symbiotic zooxanthellae. Gene 659:137-148 603 Jantzen C, Wild C, Mohammed E, Roa-Quiaoit HA, Haacke C, Richter C (2008) 604 Photosynthetic performance of giant clams, Tridacna maxima and T. squamosa, Red 605 Sea. Mar Biol 155:211-221 606 Jones RJ, Hoegh-Guldberg O (2001) Diurnal changes in the photochemical efficiency of the 607 symbiotic dinoflagellates (Dinophyceae) of corals: photoprotection, photoinactivation 608 and the relationship to coral bleaching. Plant Cell Environ 24:89-99 609 Juinio MAR, Menez LAB, Villanoy CL, Gomez ED (1989) Status of giant clam resources of 610 the Philippines. J Molluscan Stud 55:431-440 611 Klumpp DW, Bayne BL, Hawkins AJS (1992) Nutrition of the giant clam Tridacna gigas (L.) 612 I. Contribution of filter feeding and photosynthates to respiration and growth. J Exp 613 Mar Biol Ecol 155:105-122 614 Koh CZY, Hiong KC, Choo CYL, Boo MV, Wong WP, Chew SF, Neo ML, Ip YK (2018) 615 Molecular characterization of a Dual Domain Carbonic Anhydrase from the ctenidium 616 of the giant clam, Tridacna squamosa, and its expression levels after light exposure, 24 617 cellular localization, and possible role in the uptake of exogenous inorganic carbon. 618 Front Physiol 9:281 [https://doi.org/10.3389/fphys.2018.00281] 619 Kowalewska L, Mazur R, Suski S, Garstka M, Mostowska A (2016) Three-dimensional 620 visualization of the tubular-lamellar transformation of the internal plastid membrane 621 network during runner bean chloroplast biogenesis. Plant Cell 28:875-891 622 LaJeunesse TC, Parkinson JE, Gabrielson PW, Jeong HJ, Reimer JD, Voolstra CR, Santos SR 623 (2018) Systematic revision of Symbiodiniaceae highlights the antiquity and diversity 624 of coral endosymbionts. Curr Biol 28:2570-2580 625 LaJeunesse TC, Bhagooli R, Hidaka M, DeVantier L, Done T, Schmidt GW, Fitt WK, 626 Hoegh-Guldberg O (2004) Closely related Symbiodinium spp. differ in relative 627 dominance in coral reef host communities across environmental, latitudinal and 628 biogeographic gradients. Mar Ecol Prog Ser 284:147-161 629 Lee SY, Jeong HJ, Kang NS, Jang TY, Jang SH, Lajeunesse TC (2015) Symbiodinium 630 tridacnidorum sp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a 631 revised morphological description of Symbiodinium microadriaticum Freudenthal, 632 emended Trench & Blank. Eur J Phycol 50:155-172 633 Leggat W, Buck BH, Grice A, Yellowlees D (2003) The impact of bleaching on the metabolic 634 contribution of dinoflagellate symbionts to their giant clam host. Plant Cell Environ 635 26:1951-1961 636 Levin RA, Beltran VH, Hill R, Kjelleberg S, Mcdougald D, Steinberg PD, van Oppen MJH 637 (2016) Sex, scavengers, and chaperones: transcriptome secrets of divergent 638 Symbiodinium thermal tolerances. Mol Biol Evol 33:2201-2215 639 Liew YJ, Aranda M, Voolstra CR (2016) Reefgenomics.Org - a repository for marine 640 genomics data. Database 2016:baw152 [doi: 10.1093/database/baw152] 641 Marra J (1978) Effect of short-term variations in light intensity on photosynthesis of a marine 642 phytoplankter: a laboratory simulation study. Mar Biol 46:191-202 643 Mayfield AB, Hsiao YY, Chen HK, Chen CS (2014) Rubisco expression in the dinoflagellate 644 Symbiodinium sp. is influenced by both photoperiod and endosymbiotic lifestyle. Mar 645 Biotechnol 16:371-384 646 McFarland WN, Munz FW (1975) Part II: the photic environment of clear tropical seas during 647 the day. Vision Res 15:1063-1070 648 Morse D, Salois P, Markovic P, Hastings JW (1995) A nuclear-encoded form II RuBisCO in 649 dinoflagellates. Science 268:1622-1624 650 Norton JH, Shepherd MA, Long HM, Fitt WK (1992) The zooxanthellal tubular system in the 651 giant clam. Biol Bull 183:503-506 652 Pichard SL, Campbell L, Kang JB, Tabita FR, Paul JH (1996) Regulation of ribulose 653 bisphosphate carboxylase expression in natural phytoplankton communities. I. Diel 654 rhythms. Mar Ecol Prog Ser 139:257-265 655 Plöscher M, Reisinger V, Eichacker LA (2011) Proteomic comparison of etioplast and 656 chloroplast protein complexes. J Proteomics 74:1256-1265

25 657 Rosic N, Yew ESL, Chan CKK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg 658 O (2015) Unfolding the secrets of coral–algal symbiosis. ISME J 9:844-856 659 Rouzé H, Hédouin L (2018) Bilateral asymmetry in bleaching susceptibility within a giant 660 clam, Tridacna maxima. Coral Reefs 37:825 661 Rowan R, Whitney SM, Fowler A, Yellowlees D (1996) Rubisco in marine symbiotic 662 dinoflagellates: form II enzymes in eukaryotic oxygenic phototrophs encoded by a 663 nuclear multigene family. Plant Cell 8:539-553 664 Ryther JH (1956) Photosynthesis in the ocean as a function of light intensity. Limnol 665 Oceanogr 1:61-70 666 Sadali NM, Sowden RG, Ling Q, Jarvis RP (2019) Differentiation of chromoplasts and other 667 plastids in plants. Plant Cell Rep 38:803-818 668 Sano Y, Kobayashi S, Shirai K, Takahata N, Matsumoto K, Watanabe T, Sowa K, Iwai K 669 (2012) Past daily light cycle recorded in the strontium/calcium ratios of giant clam 670 shells. Nat Commun 3:761 [doi: 10.1038/ncomms1763] 671 Shoguchi E, Beedessee G, Tada I, Hisata K, Kawashima T, Takeuchi T, Arakaki N, Fujie M, 672 Koyanagi R, Roy MC, Kawachi M, Hidaka M, Satoh N, Shinzato C (2018) Two 673 divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen 674 biosynthesis and recently lost genes. BMC Genomics 19:458 [doi: 10.1186/s12864- 675 018-4857-9] 676 Solymosi K, Schoefs B (2010) Etioplast and etio-chloroplast formation under natural 677 conditions: the dark side of chlorophyll biosynthesis in angiosperms. Photosynth 678 Res, 105:143-166 679 Streamer M, McNeil YR, Yellowlees D (1993) Photosynthetic carbon dioxide fixation in 680 zooxanthellae. Mar Biol 115:195-198 681 Sui X, Mao S, Wang L, Zhang B, Zhang Z (2012) Effect of low light on the characteristics of 682 photosynthesis and chlorophyll a fluorescence during leaf development of sweet 683 pepper. J Integr Agr 11:1633-1643 684 Tabita FR, Satagopan S, Hanson TE, Kreel NE, Scott SS (2008) Distinct form I, II, III, and IV 685 Rubisco proteins from the three kingdoms of life provide clues about Rubisco 686 evolution and structure/function relationships. J Exp Bot 59:1515-1524 687 Takabayashi M, Santos SR, Cook CB (2004) Mitochondrial DNA phylogeny of the symbiotic 688 dinoflagellates (Symbiodinium, Dinophyta). J Phycol 40:160-164 689 Thorrez L, Van Deun K, Tranchevent L-C, Van Lommel L, Engelen K, Marchal K, Moreau 690 Y, Van Mechelen I, Schuit F (2008) Using ribosomal protein genes as reference: a tale 691 of caution. PLoS ONE 3:e1854 [doi: 10.1371/journal.pone.0001854] 692 Trench RK (1987) Dinoflagellates in non-parasitic symbiosis. In: Taylor FJR (ed) The 693 biology of dinoflagellates. Blackwell Scientific, Oxford, UK, pp 530-570 694 van Dooren GG, Striepen B (2013) The algal past and parasite present of the apicoplast. Annu 695 Rev Microbiol 67:271-289 696 van Dooren GG, Hapuarachchi SV (2017) The dark side of the chloroplast: biogenesis, 697 metabolism and membrane biology of the apicoplast. Adv Bot Res 84:145-185 26 698 Weber M (2009) The biogeography and evolution of Symbiodinium in giant clams 699 (Tridacnidae). Ph.D. thesis, University of California 700 Wells SM, Barzdo JG (1991) International trade in marine species: Is CITES a useful control 701 mechanism? Coast Manage 19:135-154 702 Whitney SM, Yellowlees D (1995) Preliminary investigations into the structure and activity 703 of ribulose bisphosphate carboxylase from two photosynthetic dinoflagellates. J 704 Phycol 31:138-146 705 Zhu M, Lin J, Ye J, Wang R, Yang C, Gong J, Liu Y, Deng C, Liu P, Chen C, Cheng Y, Deng 706 X, Zeng Y (2018) A comprehensive proteomic analysis of elaioplasts from citrus 707 fruits reveals insights into elaioplast biogenesis and function. Hortic Res 5:6 708 [doi: 10.1038/s41438-017-0014-x] 709 Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, 710 Rector T, Steen R, McNulty N, Thompson LR, Chisholm SW (2009) Choreography of 711 the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, 712 Prochlorococcus. PLoS ONE 4:e5135 [doi: 10.1371/journal.pone.0005135] 713

27 714 Table 1. Transcript levels (x106 copies of transcript per ng total RNA) of Tridacna squamosa

715 zooxanthellal form II ribulose-1,5-bisphosphate carboxylase/oxygenase (TSZrbcII) in

716 eight arbitrarily defined regions of the outer mantle (OM R1-8) of T. squamosa

717 (N=3). The eight regions of the outer mantle are defined in the supplementary

718 material, Fig. S2.

TSZrbcII transcript level (x106)

Clam A Clam B Clam C

OM R1 1.95 1.21 0.78

OM R2 0.62 1.05 0.57

OM R3 1.12 0.99 0.89

OM R4 0.90 1.10 1.35

OM R5 1.06 1.50 1.42

OM R6 0.90 1.53 1.12

OM R7 1.26 2.05 0.30

OM R8 0.91 1.60 0.67

Mean ± SD 1.09 ± 0.39 1.38 ± 0.36 0.89 ± 0.39

719

28 720 Fig. 1. The detection of zooxanthellae in five organs of Tridacna squamosa by alcohol

721 treatment. A visual comparison of the coloration of a colorful outer mantle (OM), b

722 whitish inner mantle (IM), c ctenidium, d hepatopancreas, and e foot muscle of T.

723 squamosa immersed in formaldehyde fixative (left panel) followed with overnight

724 dehydration with alcohol (right panel). Arrowheads show the regions of organs that are

725 concentrated with zooxanthellae. Note that there is a change in color from brown to

726 green (representing zooxanthellae) during pre- and post-alcohol treatments.

727 Fig. 2. Differential interference contrast (DIC) and fluorescence microscopy of the five organs

728 of Tridacna squamosa. Zooxanthellae (ZX) appear in red (autofluorescence) in a the

729 inner fold of outer mantle facing the sun (OM), b the whitish region (WR) of inner

730 mantle (IM, WR), c the zooxanthellae-concentrated region (ZR) of IM (IM, ZR), d the

731 middle ctenidial suspensory ligament (MCL) of ctenidium (CT), e the hepatopancreas

732 (HP), f the whitish region (WR) of foot muscle (FM, WR), and g the zooxanthellae-

733 concentrated region (ZR) of FM (FM, ZR) of T. squamosa. h Composite image of DIC

734 with corresponding red (autofluorescence) and green (immunolabelling of TSZRBCII

735 using the custom-made anti-RBCII antibody) channels of OM. Arrowheads show the

736 presence of whole zooxanthellae in the organs; asterisks show partially degraded

737 zooxanthellae specifically in the HP; and open arrowheads show immunostaining of

738 TSZRBCII in the pyrenoid of ZX. Abbreviations: CF: ctenidial filament, DT: digestive

739 tubules, EP: epithelium; EPF: extrapallial fluid, EBV: efferent branchial vein, HL:

740 hemolymph; MC: macrophage centre, SW: seawater, SWC: secondary water channel,

741 TWC: tertiary water channels, ZT: zooxanthellae tubules. Scale bar: 50 µm for a-g, 20

742 µm for h, 20 µm for all insets.

743 Fig. 3. Transcript levels (copies of transcript per ng total RNA) of Tridacna squamosa

744 zooxanthellal form II ribulose-1,5-bisphosphate carboxylase/oxygenase (TSZrbcII) in

745 various organs of T. squamosa. a Transcript levels (x106 copies of transcript per ng 29 746 total RNA) of TSZrbcII in five organs of T. squamosa. Results represent means +

747 S.E.M. (N=10). One way analysis of variance (ANOVA), followed by Dunnett’s T3

748 test, were conducted to analyze the differences between the means. Significantly

749 different means are indicated with different letters (P<0.05). b Transcript levels (x106

750 copies of transcript per ng total RNA) of TSZrbcII in the inner mantle and the foot

751 muscle of T. squamosa. The black and white bars represent the transcript levels of

752 TSZrbcII obtained from the brown and white regions, respectively, of the organ.

753 Results represent means + S.E.M. (N=5). An independent t-test was conducted to

754 analyze the differences between the means. Significantly different means between the

755 brown regions and the white regions are indicated with asterisks (P<0.05).

756 Fig. 4. Effects of light on the mRNA expression of Tridacna squamosa zooxanthellal form II

757 ribulose-1,5-bisphosphate carboxylase/oxygenase (TSZrbcII) in the outer mantle of T.

758 squamosa. Transcript levels (x106 copies of transcript per ng total RNA) of TSZrbcII

759 in the outer mantle of T. squamosa exposed to 12 h of darkness (control) or 3, 6 or 12 h

760 of light. Results represent means + S.E.M. (N=6). One way analysis of variance

761 (ANOVA), followed by Tukey’s test, were conducted to analyze the differences

762 among the means.

763 Fig. 5. Effects of light on the protein abundance of Tridacna squamosa zooxanthellal form II

764 ribulose-1,5-bisphosphate carboxylase/oxygenase (TSZRBCII) in the outer mantle of

765 T. squamosa exposed to 12 h of darkness (control) or 3, 6 or 12 h of light. a An

766 immunoblot of TSZRBCII. b TSZRBCII protein abundance expressed as arbitrary

767 densitometric units (a.u.) per 20 μg protein from the outer mantle. Results represent

768 means + S.E.M. (N=5). One way analysis of variance (ANOVA), followed by Tukey’s

769 test, were conducted to analyze the differences among the means. Significantly

770 different means are indicated with different letters (P<0.05).

30 771 Fig. 6. Effects of light on the protein abundance of Tridacna squamosa zooxanthellal form II

772 ribulose-1,5-bisphosphate carboxylase/oxygenase (TSZRBCII) in the a inner mantle, b

773 ctenidium, c hepatopancreas, and d foot muscle of T. squamosa exposed to 12 h of

774 darkness (control) or 3, 6 or 12 h of light. An immunoblot of TSZRBCII is presented

775 for each of the four organs. TSZRBCII protein abundance is expressed as arbitrary

776 densitometric units (a.u.) per 100 μg protein. Results represent means + S.E.M. (N=5).

777 One way analysis of variance (ANOVA), followed by Tukey’s test, were conducted to

778 analyze the differences among the means.

31 779 Fig. 1

780

32 781 Fig. 2

782

0 783 Fig. 3

784

0 785 Fig. 4

786

1 787 Fig. 5

788

0 789 Fig. 6

790

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