The role of Rubisco kinetics and pyrenoid morphology in shaping the CCM of haptophyte microalgae

Abstract

The haptophyte algae are a cosmopolitan group of primary producers that contribute significantly to the marine carbon cycle and play a major role in paleo-climate studies. Despite their global importance, little is known about carbon assimilation in haptophytes, in particular the kinetics of their Form 1D CO₂-fixing enzyme, Rubisco. Here we examine Rubisco properties of three haptophytes with a range of pyrenoid morphologies (Pleurochrysis carterae, Tisochrysis lutea, and Pavlova lutheri) and the diatom Phaeodactylum tricornutum that exhibit contrasting sensitivities to the trade-offs between substrate affinity (K_m) and turnover rate (k_cat) for both CO₂ and O₂. The pyrenoid-containing T. lutea and P. carterae showed lower Rubisco content and carboxylation properties (K_C and k^C_cat) comparable with those of Form 1D-containing non-green algae. In contrast, the pyrenoid-lacking P. lutheri produced Rubisco in 3-fold higher amounts, and displayed a Form 1B Rubisco k^C_cat–K_C relationship and increased CO₂/O₂ specificity that, when modeled in the context of a C₃ leaf, supported equivalent rates of photosynthesis to higher plant Rubisco. Correlation between the differing Rubisco properties and the occurrence and localization of pyrenoids with differing intracellular CO₂:O₂ microenvironments has probably influenced the divergent evolution of Form 1B and 1D Rubisco kinetics.

Introduction

The CO₂-fixing enzyme Rubisco (EC 4.1.1.39) evolved in the Archaean Eon when the atmosphere lacked O₂, and CO₂ was estimated to be 50-fold higher than current levels (Berner and Canfield, 1989; Berner, 2006; Tabita et al., 2008). With the evolution of O₂-producing photosynthesis around the early Proterozoic (2.5 Gya), atmospheric O₂ increased while the CO₂ concentration declined (Canfield, 2005) (Fig. 1). The diminishing atmospheric CO₂:O₂ ratio negatively influenced Rubisco catalysis, as its photosynthetic CO₂-fixing function is competitively inhibited by O₂ to produce 2-phosphoglycolate (2-PG) (Tcherkez et al., 2006; Whitney et al., 2011; Sharwood, 2017). Recycling of 2-PG to 3-phosphoglycerate (3-PGA) by photorespiration consumes energy and loses fixed CO₂. A further limitation to Rubisco function in the modern atmosphere is a low affinity for CO₂ and a slow catalytic rate that necessitates high Rubisco concentrations to support adequate rates of photosynthesis (Reinfelder, 2011; Whitney et al., 2011; Long et al., 2015; Sharwood et al., 2016b).

The catalytic limitations of Rubisco are exacerbated in aquatic ecosystems due to restraints on aqueous CO₂ availability because of slow rates of gas diffusion in water (~10000 times slower than in air) and reliance on mixing of the water column (Badger et al., 1998). In addition, increased partitioning of inorganic carbon to HCO₃^– with higher pH in aquatic systems diminishes aqueous CO₂ availability. There is evidence of catalytic adaptation by Rubisco in algae to the changing atmospheric CO₂ (and O₂) conditions over geological time scales (Young et al., 2012). Recent work, however, showed that the characteristic faster CO₂ fixation rates (k^C_cat) and lower CO₂ affinities (i.e. higher K_m for CO₂; K_C) observed in Form 1A and Form 1B Rubisco [e.g. in Chlamydomonas with a pyrenoid-based CO₂-concentrating mechanism (CCM)] (Badger et al., 1998; Ghannoum et al., 2005; Sharwood et al., 2016a) are not shared by diatom Form 1D Rubisco (Hanson, 2016; Young et al., 2016; see also Fig. 3A). This has led to calls for a more expansive analysis of Rubisco’s natural kinetic diversity so that we can fully understand the correlative interactions between specificity for CO₂ as opposed to O₂ (S_C/O), k^C_cat, and K_C. The one-dimensional, linear correlations previously proposed (Tcherkez et al., 2006; Savir et al., 2010) may actually vary with photosynthetic taxa (Tcherkez, 2013, 2016; Hanson, 2016; Sharwood, 2017).

In photosynthetic organisms, the CCM arose multiple times in response to a declining atmospheric CO₂:O₂ ratio as a means to increase the CO₂/O₂ environment around Rubisco (Fig. 1). Data on the anatomical, biochemical, and genomic detail for CCMs in vascular plants with C₄ and Crassulacean acid metabolism (CAM) physiologies are highly detailed (von Caemmerer and Furbank, 2016). The high CO₂ environment reduces Rubisco oxygenation and the associated energy costs of photorespiration, allowing the plant to work with lower stomatal conductance and reduced amounts of Rubisco (Sage et al., 2012). These features allow more efficient use of water, nitrogen, and light, and permit these plants to survive in more arid and nutrient-limited environments (Sage, 2002; Ghannoum et al., 2005; Lara and Andreo, 2011; Long et al., 2015). The CCM in plants also allowed Form 1B Rubisco to evolve a higher k^C_cat at the expense of a higher K_C (i.e. lower CO₂ affinity) with little or no effect on S_C/O (Sharwood et al., 2016a, b). Curiously this k^C_cat–K_C trade-off is not shared by Form 1D Rubisco from diatoms where relatively higher K_C values have been retained as a consequence of other environmental pressures (low nutrient and extracellular CO₂ availability) that pose limitations to resource investment into Rubisco (Young et al., 2016). It is likely that resources other than CO₂, such as nitrogen and light availability, have a strong influence on CCM evolution and regulation (Raven et al., 2008, 2012).

Understanding how microalgal Rubisco catalysis has differentially evolved remains limited by our understanding of the structural components and effectiveness of the CCM in microalgae. The last few years have seen significant advances in our understanding of CCM in the model freshwater green alga, Chlamydomonas reinhardtii (Engel et al., 2015; Wang et al., 2015; Yamano et al., 2015; Mackinder et al., 2016; Mangan et al., 2016; Wang et al., 2016). To what extent this knowledge is translatable to the CCM of the structurally differing and evolutionarily distinct marine microalgae (e.g. diatoms and haptophytes) remains unclear (Bedoshvili et al., 2009; Hopkinson et al., 2011, 2013). Currently a completed nuclear haptophyte genome is available for the Isochrysidale Emiliania huxleyi (Read et al., 2013) and a draft genome for the Prymnesiale Chrysochromulina tobin (Hovde et al., 2015). Although less understood, the CCMs of marine microalgae are known typically to employ a pyrenoid, Rubisco activase, carbonic anhydrase (CA), and inorganic carbon (C_i) transporters to elevate CO₂ levels around Rubisco (Hopkinson et al., 2011; Reinfelder, 2011; Loganathan et al., 2016). The pyrenoid is a proteinaceous body that appears electron dense when examined by TEM and contains most, sometimes all, of the cellular Rubisco (Engel et al., 2015; Mackinder et al., 2016).

In C. reinhardtii, HCO₃^– transport occurs via thylakoids and C_i transporters that work in association with pyrenoid CAs to elevate CO₂ around Rubisco (Karlsson et al., 1998; Trimborn et al., 2007; Lee et al., 2013; Wang et al., 2015; Yamano et al., 2015). Physiological and genetic evidence in model diatoms imply that HCO₃^– is pumped into the chloroplast stroma and diffuses into the pyrenoid where it is converted to CO₂ by CA to elevate the [CO₂] around Rubisco (Hopkinson et al., 2011, 2016). Recent identification of a thylakoid lumen-localized CA in P. tricornutum further suggests that the pyrenoid-penetrating thylakoids probably provide an important CO₂ supply within the pyrenoids (Kikutani et al., 2016).

What remains unclear is how the pyrenoid structure influences CCM efficiency. In C. reinhardtii, the pyrenoid contains a starch sheath (Moroney et al., 2011; Engel et al., 2015) while in diatoms it can comprise a lipid membrane (Bedoshvili et al., 2009), lack a delimiting structure (Bendif et al., 2011), vary in number and shape, and differ in the presence/structure of traversing thylakoids (Badger et al., 1998). To better understand the relationships between Rubisco kinetics, content, and pyrenoid biology in marine microalgae, we have expanded on our previous study of diatom Rubisco (Young et al., 2016) to include three marine haptophytes that contain bulging (Pleurochrysis carterae), immersed [Tisochrysis lutea, formerly Isocrysis sp. strain CS-177 (Bendif et al., 2013)], or no pyrenoid (Pavlova lutheri) within their chloroplast and varying numbers and location of pyrenoid-traversing thylakoids (Fig. 2A).

Materials and methods

Algae culturing

Cultures of the haptophytes P. lutheri (CS-182), P. carterae (CS-287), T. lutea [CS-177; original strain name Isochrysis sp. (Bendif et al., 2013)], and the diatom, Phaeodactylum tricornutum (CS-29) were obtained from the Australian National Algae Culture Collection CSIRO (https://www.csiro.au/en/Research/Collections/ANACC) and grown at 20 °C in 0.2 μm filtered and autoclaved seawater containing f/2 (Guillard and Ryther, 1962) or GSe (P. carterae; Blackburn et al., 2001) nutrients, vitamins, and trace metals. The cultures were grown in polycarbonate culture flasks under 150 ± 50 μmol photons m^–2 s^–1 illumination on a 16:8 h light:dark cycle.

Pyrenoid morphology and CCM characterization.

Details of pyrenoid morphology and estimates of C_i and CA pools for the microalgae were compiled from the literature (Manton and Peterfi, 1969; Billard and Gayral, 1972; Green, 1975; Green and Pienaar, 1977; Borowitzka and Volcani, 1978; Hori and Green, 1985; Badger et al., 1998; Bendif et al., 2011, 2013). A preliminary screen for putative δ-CA genes was carried out using PCR. δ-CA is a functional carbonic anhydrase, as demonstrated in vitro by Del Prete et al. (2014) and Lee et al. (2013). It is regulated by CO₂, and is thus important in inorganic carbon acquisition (Lane and Morel, 2000a).

Genomic DNA was extracted as described (Richlen and Barber, 2005) and candidate δ-CA genes were amplified by PCR using primers Δfwd (5'-GTTGGCGAGACGTACGAGGTGCACTGG-3') and Δrev (5'- GCGATCGACCTGCCAGGTGATGGG-3') that were designed to the conserved C-terminal amino acid sequences VGETYEVHW and PITWQVDR, respectively. The ~370 bp DNA product amplified from P. carterae and Isochrysis galbana (for comparison with T. lutea) was sequenced by Source BioScience (Oxford, UK). Confirmation that the absence of δ-CA from our P. tricornutum (strain CCAP1055/1 a monoclonal culture derived from a fusiform cell in May 2003 from strain CCMP632) was further supported by analysis for δ-CA homologs within the fully sequenced genome of P. tricornutum (Bowler et al., 2008) and its predicted protein products. Similarly, the absence of δ-CA was further confirmed by a search of the Pavlovales sp. CCMP2436 (JGI) genome sequence.

A BLAST search of the genomes was carried out using the δ-CA protein sequence from Thalassiosira pseudonana (BAO52718) and Thalassiosira weissflogii (AAV39532), both centric diatoms, and Fragilariopsis cylindrus CCMP1102 (OEU11320), a pennate diatom, as query sequences. The BLAST search yielded no hits. Together with our PCR, we concluded that there were no δ-CA homologs in this strain of P. tricornutum. A BLAST search was also carried out on the genome of Pavlovales sp. CCMP2436 (JGI), an environmental isolate using the δ-CA protein sequence from T. pseudonana (BA052718) and the haptophytes Emiliania huxleyi (ABG37687), I. galbana (EC146202, EC142695), and Chrysochromulina sp. CCMP291 (KO021563, KO028292). Although this genome is not fully curated and the culture has not been taxonomically described, the preliminary search yielded no hits.

Rubisco extraction and kinetic assessment

Algal cells were harvested via centrifugation (2000 g for 10 min) and the pelleted cells snap-frozen in liquid nitrogen and stored at –80 °C until assay. The crude soluble cell extracts were obtained by rupturing cells using a French press as described previously (Young et al., 2016). As detailed in the same study, Rubisco content was quantified by [¹⁴C]CABP (2-carboxyarabinitol 1,5-bisphosphate) binding within the crude extract and concentrations of soluble protein were quantified using the Bradford assay against BSA. Rubisco catalytic parameters: maximum carboxylation rate (k^C_cat) and half-saturation constants for CO₂ and O₂ (K_C and K_O, respectively) were measured at 25 °C using ¹⁴CO₂ fixation assays employing crude extract that had been activated for 10–15 min at 25 °C with 10 mM MgCl₂ and 10 mM NaHCO₃. The CO₂ concentrations in the ¹⁴CO₂ assays were calculated using the Henderson–Hasselbalch equation and the parameters detailed in (Sharwood et al., 2016a). Measurements of S_C/O were made using Rubisco rapidly purified from ~1 g of pelleted algal cells as described (Young et al., 2016).

Simulating the influence of microalgae Rubisco on C₃ plant photosynthesis

The carboxylase activity-limited assimilation rates were simulated according to Farquhar et al. (1980) using the equation:

assuming a CO₂ solubility in H₂O (s_c) of 0.0334M bar^–1, an O of 267 μM, a Rubisco content (B) of 20 µmol catalytic sites m^–2, and a non-photorespiratory CO₂ assimilation rate (R_d) of 2 µmol m^–2 s^–1. Under higher chloroplast CO₂ pressures (C_c), the photosynthetic rate becomes light- (or electron transport rate, ETR-) limited and is modeled according to the equation:

assuming an electron transport rate (J) of 150 µmol m^–2 s^–1.

Results and Discussion

The differing pyrenoid morphologies within the microalgae studied

A central objective of this study was to examine the correlations between pyrenoid morphology, evidence of a CCM, and the content and catalysis of Rubisco in microalgae. As summarized in Fig. 2A, T. lutea possesses a pyrenoid immersed in the center of the plastid with 1–2 thylakoids traversing the center of the pyrenoid (Bendif et al., 2013; Borowitzka and Volcani, 1978). In contrast, the pyrenoid in P. carterae bulges out from the plastid toward the center of the cell, with 5–6 continuous thylakoids traversing the plastid and pyrenoid (Manton and Peterfi, 1969; Beech and Wetherbee, 1988). Immersed versus bulging pyrenoids differ in the location within the cell, relative separation from the plastid (i.e. the presence of a lipid membrane has been suggested from TEM observations), and the connectivity to plastid thylakoids. A lipid membrane has been observed around the immersed/semi-immersed pyrenoids of two other members of the Isochrysidales—Chrysotila lamellosa (Billard and Gayral, 1972; Green and Parke, 1975) and Isochrysis galbana (Green and Pienaar, 1977). However, Bendif et al. (2013) did not detect a membrane around the pyrenoid of T. lutea nor has one been observed around pyrenoids of the bulging morphotype in any haptophyte species, including P. carterae. In the Pavlovophyceae, the pyrenoids are often bulging towards the exterior of the cell—albeit not in P. lutheri where no pyrenoid is apparent (Green, 1975; Burris, 1981; Bendif et al., 2011). Phaeodactylum tricornutum was included in this study and, like many members of the lineage, has pyrenoids that are fully immersed within the chloroplast with 1–2 pyrenoid-traversing thylakoids (Borowitzka and Volcani, 1978; Bedoshvili et al., 2009) (Fig. 2A).

Experimental evidence for a CCM

A key component of a CCM is the enzyme CA that catalyzes the rapid interconversion between CO₂ and HCO₃^–. In marine primary producers, the CA activity of a CCM is particularly beneficial for accessing CO₂ from the high oceanic HCO₃^– concentrations. The effects of two CA inhibitors, the membrane-permeable ethoxyzolamide (EZA) and the relatively impermeable acetazolamide (AZA), are commonly used to test for CCM activity (Okazaki et al., 1992). This is undertaken by examining the influence of EZA and AZA on the affinity of photosynthesis for plasma membrane-based inorganic carbon (C_i) (Okazaki et al., 1992; Badger et al., 1998) and light-stimulated CA activity (Burns and Beardall, 1987).

Using modern cell biology tools, there have been significant advances in understanding the CCM components in microalgae (Engel, 2015) which includes the discovery of novel CA isoforms and their intercellular localization (Jin et al., 2016; Kikutani et al., 2016). While a comparable detailed analysis of haptophyte CCM components is beyond the scope of this work, Fig. 2B summarizes the known CCM features in the microalgae studied here. EZA treatment reduces the affinity for C_i in photosynthesis for the pyrenoid-containing I. galbana (as a proxy for T. lutea), P. tricornutum, and P. carterae species, with the external CA inhibitor AZA also affecting the C_i affinity in P. carterae (Badger et al., 1998; Chen et al., 2006; Hopkinson et al., 2013). We note that other diatoms with fully immersed pyrenoids have been shown to be sensitive to AZA (Hopkinson et al., 2013). The influence of EZA or AZA on the photosynthetic carbon assimilation rate in P. lutheri, the species lacking a pyrenoid, remains untested. Similarly, the light-stimulated CA activity found in P. tricornutum and T. lutea has yet to be examined in P. carterae and P. lutheri (Fig. 2B). It is estimated that the CCMs associated with immersed pyrenoids can increase intracellular C_i pools ~6-fold higher than that permissible by passive diffusion (Fig. 2B (Burns and Beardall, 1987; Colman and Rotatore, 1995; Badger et al., 1998).

The δ isoform of CA (or TWCA1), whose expression in the diatom T. weissflogii is modulated by extracellular CO₂ levels (Morel et al., 1994; Lane and Morel, 2000a, b) and in marine dinoflagellates functions as an external CA (Lapointe et al., 2008), holds the potential as a key component of a CCM in microalgae. The catalytic activity and inhibition of δ-CA demonstrate the functionality of the CA in the diatom Thalassiosira pseudonana and the haptophyte Emiliania huxleyi (Soto et al., 2006; Lee et al., 2013; Del Prete et al., 2014). Using sequence homology searches, we were able to detect δ-CA homologs in genome data sets for P. carterae and T. lutea, but not in P. tricornutum or P. lutheri (using the Pavlovale sp. CCMP2436 genome as a proxy). Importantly the absence of detectable sequence homology does not disqualify these microalgae from producing δ-CA or alternative CA isoforms, especially considering that new CAs are still being discovered (Jin et al., 2016; Kitkanti et al., 2016). Indeed, a number of other CA types are expressed in P. tricornutum that include one localized in the pyrenoid (Tachibana et al., 2011), an extracellular CA (Hopkinson et al., 2013), and a θ-type CA located in the thylakoid lumen (Jin et al., 2016). Our BLAST search of the Pavlovale sp. CCMP2436 genome supports the absence of a δ-CA in P. lutheri; however, further investigation is required (e.g. whether P. lutheri contains other forms of CA). Overall, the existing evidence suggests that the presence of a pyrenoid coincides with the presence and activity of CA (Fig. 2B), consistent with their role in the microalgae CCM.

The carboxylation properties of haptophyte Rubisco

Form 1B Rubisco from organisms operating a CCM characteristically show higher rates of maximum carboxylation k^C_cat and a reduction in CO₂ affinity (i.e. an increase in K_C) than the Rubisco from their non-CCM relatives. For example, the Rubisco from C₄ plants typically have a higher k^C_cat and higher K_C than C₃ plant Rubisco (Sage, 2002; Savir et al., 2010; Sharwood et al., 2016a, c; Tcherkez, 2016). As shown in Fig. 3A, the K_C diversity among Form 1B vascular plant Rubisco spans a limited range in values relative to the Form 1D Rubisco from diatoms (Hanson, 2016; Young et al., 2016). Moreover, the relationship between K_C and k^C_cat at 25 °C for the Form 1D Rubisco differs from Form 1B Rubisco (Fig. 3A).

For comparison of different CCM effectiveness on Rubisco kinetics within organisms containing the 1D Rubisco, we examined the kinetics of the Form 1D Rubiscos from freshly lysed P. carterae, T. lutea, and P. lutheri cells. The Rubisco activity in the cellular extract was stable at 25 °C for at least 20 min following extraction (see Supplementary Fig. S1 at JXB online). The CO₂–Mg²⁺ activation status of the extracted Rubisco varied between 50% and 60%, comparable with that seen in the cellular extract of diatoms (Young et al., 2016). To ensure full activation of all eight catalytic sites in each L₈S₈ molecule, the cellular extract was incubated for 10–15 min at 25 °C in buffer containing 10 mM MgCl₂ and 10 mM NaHCO₃ before assaying k^C_cat under varying CO₂ concentrations by ¹⁴CO₂ fixation. By this approach, the values of k^C_cat and K_C extrapolated from fitting the data to the Michaelis–Menten equation were reproducible between replicate cellular preparations (Table 1).

Significant kinetic diversity at 25 °C was observed among each haptophyte Rubisco relative to P. tricornutum (model diatom species) and Nicotiana tabacum (tobacco, model plant Rubisco used in kinetic comparisons; Whitney et al., 2001; Sharwood et al., 2016a, b) (Table 1). The k^C_cat of P. carterae, P. tricornutum, and tobacco were similar and each ~50% higher than those of T. lutea and P. lutheri Rubisco. Comparable levels of variation in K_C were also observed among the haptophyte Rubiscos (14.5–24.1 μM) that are notably lower and spanning a smaller range than the K_C values of diatom Rubiscos (22–70 μM; Fig. 3A). This suggests haptophyte Rubisco may experience a lower CO₂ microenvironment relative to diatoms. This is probably the case for Rubisco in P. lutheri that lacks a pyrenoid (Burris, 1981; Bendif et al., 2011) and whose Rubisco has the lowest K_C and highest S_C/O (i.e. a greater selectivity for CO₂ over O₂; Table 1).

A correlative analysis of haptophyte Rubisco kinetics

A comparison of Rubisco kinetics of each haptophyte identified contrasting relationships when compared with the 25 °C properties of Form 1B and 1D L₈S₈ Rubisco from a range of eukaryotic phototrophs (Fig. 3A–E; data compiled in Supplementary Table S1). An examination of the K_C–k^C_cat relationship for ‘green’ Form 1B (vascular plants, CCM-positive green algae) and ‘non-green’ Form 1D (diatoms, haptophytes, and red algae) Rubisco suggests they follow differing trajectories (Fig. 3A). As suggested previously, this might arise from lineage-dependent variation in ribulose bisphosphate (RuBP) enolization energies and/or mechanistic differences in their multistep carboxylation chemistry (Tcherkez, 2013, 2016; Young et al., 2016).

With regard to haptophyte Rubisco, the K_C–k^C_cat relationship of P. lutheri and P. carterae Rubisco appeared to align more closely with Form 1B Rubisco (Fig. 3A). Consequently, their carboxylation efficiencies under both anaerobic (k^C_cat/K_C) and ambient O₂ (k^C_cat/K_C^21%O2) are higher than those of T. lutea Rubisco (Table 1) whose K_C–k^C_cat relationship closely aligns with red algae and diatom Form 1D Rubiscos (Fig. 3A), and lower carboxylation efficiency of P. tricornutum Rubisco (Table 1). These findings suggest that there may be differences in the CCM effectiveness between the bulging pyrenoids in P. carterae relative to the immersed pyrenoids of diatoms and T. lutea. It also raises questions regarding how differences in the CCM and/or cellular metabolism in phytoplankton with immersed pyrenoids have led to the evolution of atypical Form 1D Rubisco kinetics.

Somewhat analogous to their differing K_C–k^C_cat relationships, both Form 1B and 1D enzymes showed differing linear correlations between K_O and k^O_cat (Fig. 3B) but no identifiable correlations between their k^C_cat/k^O_cat (Fig. 3C) and K_C/K_O (Fig. 3D) relationships. This finding is consistent with increasing experimental evidence that changes in the carboxylation and oxygenation properties are not coupled in an obligatory manner (Savir et al., 2010; Whitney et al., 2011; Sharwood et al., 2016a; Sharwood, 2017). This unfastening of carboxylation and oxygenation has enabled significant Rubisco kinetic diversity to have evolved in nature, in particular with regard to CO₂/O₂ selectivity (S_C/O) whose correlative trade-off with k^C_cat follows a diffuse exponential relationship (Fig. 3E; Sharwood, 2017) rather than the linear response previously postulated (Tcherkez et al., 2006; Savir et al., 2010). Within the k^C_cat–S_C/O relationship, the haptophyte Rubisco localizes in a region comparable with diatom Rubisco between the high S_C/O, low k^C_cat of Form 1D red algae Rubisco and the lower S_C/O, higher k^C_cat of Form 1B Rubisco (Fig. 3E).

Interpreting the differing O₂ sensitivities of haptophyte Rubisco

While the CCMs of phototrophic organisms function to elevate the CO₂:O₂ ratio around Rubisco through increased CO₂ supply, it is unclear how the ratio is dependent on complementary mechanisms to lower O₂. In many organisms employing a CCM, the O₂-generating components are located away from Rubisco. For example, the Rubisco-containing bundle sheath cell (BSC) chloroplasts in C₄ plants within NADP-malic enxyme (NADP-ME) subtypes characteristically lack the O₂-evolving PSII complexes (Sage et al., 2014; von Caemmerer and Furbank, 2016). Similarly, the thylakoids traversing the pyrenoid of the red algae Porphyridium cruentum lack PSII (McKay and Gibbs, 1990), while in the dinoflagellate Gonyaulax polyedra during times of high carbon fixation the Rubisco is spatially relocated to pyrenoids near the cell center away from the O₂-evolving light-harvesting reactions (Nassoury et al., 2001). Similarly in cyanobacteria, the carboxysomes localize to the cell interior away from the PSII thylakoids lining the cell periphery (Liberton et al., 2011). These strategies for spatially separating O₂ production away from Rubisco appear to be key components of the CCM. Unfortunately, measuring the O₂ concentration in bundle sheath cell chloroplasts, cyanobacteria carboxysomes, or inside the pyrenoid of algae remains an insurmountable challenge.

As indicated above, the oxygenation properties of Rubisco show significant natural variation. Drawing correlations between their O₂ sensitivity (i.e. K_O) and CCM efficiency is therefore quite challenging. An additional complexity is that the extent of O₂ solubility is reduced by the highly proteinaceous matrix of pyrenoids, chloroplasts, and carboxysomes (Tcherkez, 2016) and by the increasing pressures experienced by microalgae down the water column. Interestingly the higher K_O of T. lutea, P. tricornutum, and P. lutheri Rubisco lend to limiting the influence of changing O₂ concentrations on carboxylation efficiency relative to Rubisco from tobacco and P. carterae (Fig. 4). This implies that the variable O₂ concentrations experienced by diatoms and haptophytes within the water column might have influenced their Rubisco kinetic evolution. Furthermore, pyrenoid morphology and ultrastructure may also have influenced the evolved oxygenase properties. For example, P. lutheri Rubisco exhibits a low affinity for O₂ (K_O ~1150 μM), implying that its Rubisco experiences higher O₂ concentrations than the Rubisco from algae possessing immersed (e.g. T. lutea, P. tricornutum, K_O ~650–800 μM) or bulging (P. carterae, K_O ~366 μM) pyrenoids (Table 1).

These observations could be interpreted to suggest that the pyrenoids, in particular those with a bulging morphology, might be lowering the O₂ environment to augment the CO₂:O₂ ratio around Rubisco. Possibly internally bulging pyrenoids may locate Rubisco closer to the reducing chemistry of the cytosol or the mitochondria and their respired CO₂. Other mechanisms for altering pyrenoid CO₂:O₂ include reducing thylakoid number within the pyrenoid, reducing the O₂-producing PSII activity (McKay and Gibbs, 1990), or employing pyrenoid tubules for diffusion (Engel et al., 2015). Challenging these hypotheses is the observed high K_O (~2000 μM, indicating an insensitivity to O₂) for Rubisco from the pyrenoid-containing diatom Thalassiosira weissflogii (Young et al., 2016) and that multiple thylakoids traverse the pyrenoid of P. carterae, albeit with untested levels of PSII activity (Manton and Peterfi, 1969).

The influence of a CCM on the Rubisco requirement in haptophytes

A characteristic feature of the CCM in C₄ plants is that it reduces the requirement for Rubisco, allowing for increased nitrogen use efficiency (Ghannoum et al., 2005). In diatoms, the Rubisco content was found to correlate with K_C, suggesting that the allocation of resources into the enzyme may depend on CCM efficiency (Young et al., 2016). For example, the low K_C of Rubisco from Phaeodactylum and Chaetoceros diatom species correlated with increased investment in Rubisco content, while in Thalassiosira and Skeletonema species it was hypothesized that resources were instead allocated to the CCM rather than Rubisco to saturate the enzymes low CO₂ affinity (Young et al., 2016).

Among the three haptophyte species examined here, we identified a negative relationship between increasing CO₂ affinity (i.e. reducing K_C) and increasing Rubisco content (dashed line, Fig. 5). The trajectory of this relationship poorly correlated with the Rubisco content and K_C of P. tricornutum. While it is known that Rubisco content in diatoms can be influenced by growth stage (Losh et al., 2013), our measurements comprised replicate algae samples from cultures growing under non-nutrient limiting conditions and resulted in reproducible measures of Rubisco content (Fig. 5). While future experiments are aimed at examining these properties from a wider range of microalgae species, it is apparent that in the pyrenoid-lacking P. lutheri cells there is ~3- to 4-fold higher investment of soluble cellular protein in Rubisco (Fig. 5). Likewise, the Rubisco content in hornworts also shows a comparable correlation with the presence/absence of pyrenoids (Hanson et al., 2002). Similarly, in C₃ plants, Rubisco comprises a larger resource investment [25–50% (w/w) total soluble protein] relative to C₄ plants where the CCM and higher k^C_cat reduces the amount of Rubisco required [i.e. 8–15% (w/w) of the soluble cellular protein (Ghannoum et al., 2005; Sharwood et al., 2016a, c)].

How suited is phytoplankton Rubisco to supporting photosynthesis in C₃ plants?

Improving the catalytic efficiency of Rubisco is a key target for improving the rate of photosynthesis and growth in key C₃ crops such as rice and wheat (Long et al., 2015; Sharwood et al., 2016b). This has led to considerable interest in identifying whether the natural catalytic diversity of Rubisco can be exploited to deliver improvements in crop Rubisco performance. The faster Rubisco from Synechococcus PCC7942 (cyanobacteria) and the photosynthetic bacterium Rhodospirillum rubrum are not able to support faster C₃ plant growth, even under elevated CO₂, due to their low carboxylation efficiencies under ambient O₂ (k^C_cat/K_C^21%O2) and their low S_C/O (Sharwood, 2017). In comparison, the higher k^C_cat/K_C^21%O2 and S_C/O of the Form 1D Rubisco from Griffithsia monilis (filamentous red algae) would support faster rates of photosynthesis in C₃ crops with the potential to improve productivity by up to 30% (Long et al., 2015). Realizing this benefit is impeded by the incompatible assembly requirements of Form 1D Rubisco in plant chloroplasts (Whitney et al., 2001). Nevertheless, it is hoped solutions to improving crop Rubisco may be achieved through increased understanding of natural kinetic diversity among all Rubisco forms (Whitney et al., 2011; Sharwood, 2017). We therefore used the modeling approach of Farquhar et al. (1980) to simulate how each microalga would influence C₃ photosyntesis under varying chloroplast CO₂ concentrations (C_c; Fig. 6). The low k^C_cat/K_C^21%O2 of T. lutea (and P. tricornutum) Rubisco (Table 1) impeded their simulated effect on C₃ photosythesis at 25 °C. In contrast, the high S_C/O of P. lutheri Rubisco improved the simulated photosynthetic rates relative to tobacco Rubisco under low C_c but not above 150 μbar of CO₂ due to its lower k^C_cat and k^C_cat/K_C^21%O2 (Table 1). This finding suggests hat future kinetic surveys to identify microalgae Rubisco better suited to operating in C₃ plant chloroplasts might best focus on microalgae that lack a pyrenoid and a CCM.

Conclusions and future directions

Due to their importance at the base of the marine food chain, global biogeochemical cycling, and interpretation of paleo-chemical signals in marine sediments, it is essential that we better understand the diversity and function of the algae CCMs. In this pilot study, we provide preliminary evidence for correlations between Rubisco content, kinetics, and pyrenoid morphology within the chloroplast of different haptophytes and the diatom P. tricornutum. Recent work has highlighted the lack of knowledge on the components and variable efficiency of the CCM across environmentally important microalgae (Hanson, 2016; Hopkinson et al., 2016; Young et al., 2016). Previous models of the algal CCM relied on correlations with distant photosynthetic organisms and limited Rubisco kinetic data. Elucidating the diversity and biological relevance of CCMs in these species will provide the groundwork necessary for understanding primary production in the world’s oceans.

Our study provides evidence for the potential to use the binding affinities of Rubisco as a probe to gauge the intracellular CO₂:O₂ ratio around Rubisco and which might include an oxygen exclusion function by the pyrenoid. Future correlative analyses of Form 1D and Form 1B Rubisco kinetics from microalgae lacking pyrenoids and with differing pyrenoid morphologies are needed to yield a more robust functional understanding of the intrapyrenoid microenvironment and the natural diversity in carbon fixation in both terrestrial and aquatic ecosystems. Although challenging to measure, these Rubisco analyses are essential for understanding both (i) the different evolutionary histories of Form I Rubisco whose kinetics appear to have divergently evolved and (ii) the extent to which the competing carboxylation and oxygenation properties can be decoupled. Refining the existing assumptions about diversity and trends in photosynthetic evolution are paramount. Included in such endeavors are whether the non-canonical correlation between K_C and k^C_cat is limited to Form 1D Rubisco from microalgae with immersed pyrenoids (Fig. 3A), if resource allocation to Rubisco is elevated in species with a less effective CCM (Fig. 5), and to what extent increases in k^C_cat/K_C^21%O2, S_C/O, and K_O (i.e. a reduced O₂ sensitivity) can be used as a proxy to gauge the effectiveness of microalgae CCMs.

Supplementary data

Supplementary data are available at JXB online.

Fig. S1. Measurement of Rubisco activation status and stability in vitro at 25 °C.

Table S1. Rubisco kinetics at 25 °C as shown in Fig. 3.

Acknowledgements

AMCH was funded through a Clarendon Scholarship, Oxford and ANU visiting scholar (CE140100015). Funding for JNY and SMW was provided through Australian Research Council Grant CE14010001. RES was funded through the ARC DECRA scheme (DE13010760) and REMR was funded through an ERC Starting Grant (SP2-GA-2008-200915).

References

Author notes