The carbonate concentration mechanism of Pyropia yezoensis (Rhodophyta): evidence from transcriptomics and biochemical data

Abstract

Background Pyropia yezoensis (Rhodophyta) is widely cultivated in East Asia and plays important economic, ecological and research roles. Although inorganic carbon utilization of P. yezoensis has been investigated from a physiological aspect, the carbon concentration mechanism (CCM) of P. yezoensis remains unclear. To explore the CCM of P. yezoensis, especially during its different life stages, we tracked changes in the transcriptome, photosynthetic efficiency and in key enzyme activities under different inorganic carbon concentrations. Results Photosynthetic efficiency demonstrated that sporophytes were more sensitive to low carbon (LC) than gametophytes, with increased photosynthesis rate during both life stages under high carbon (HC) compared to normal carbon (NC) conditions. The amount of starch and number of plastoglobuli in cells corresponded with the growth reaction to different inorganic carbon (Ci) concentrations. We constructed 18 cDNA libraries from 18 samples (three biological replicates per Ci treatment at two life cycles stages) and sequenced these using the Illumina platform. De novo assembly generated 182,564 unigenes, including approximately 275 unigenes related to CCM. Most genes encoding internal carbonic anhydrase (CA) and bicarbonate transporters involved in the biophysical CCM pathway were induced under LC in comparison with NC, with transcript abundance of some PyCAs in gametophytes typically higher than that in sporophytes. We identified all key genes participating in the C4 pathway and showed that their RNA abundances changed with varying Ci conditions. High decarboxylating activity of PEPCKase and low PEPCase activity were observed in P. yezoensis. Activities of other key enzymes involved in the C4-like pathway were higher under HC than under the other two conditions. Pyruvate carboxylase (PYC) showed higher carboxylation activity than PEPC under these Ci conditions. Isocitrate lyase (ICL) showed high activity, but the activity of malate synthase (MS) was very low. Conclusion We elucidated the CCM of P. yezoensis from transcriptome and enzyme activity levels. All results indicated at least two types of CCM in P. yezoensis, one involving CA and an anion exchanger (transporter), and a second, C4-like pathway belonging to the PEPCK subtype. PYC may play the main carboxylation role in this C4-like pathway, which functions in both the sporophyte and gametophyte life cycles.

Carbonic Anhydrase Isoforms of Pyropia Yezoensis: Intracellular Location and Expression Profiles in Response to Inorganic Carbon Concentration and Life Stage

“…PyCA1 is localized exclusively in the chloroplast and shows higher transcript abundance during the two life stages, with a RPKM value under NC above 2000 and above 600 in leafy thalli and lamentous thalli, respectively. Furthermore, PyCA1 is up-regulated under LC conditions [9]. On the basis of its subcellular localization and transcript abundance, we suggest that PyCA1 plays important roles in the CCM of P. yezoensis during the two life stages.…”

“…PyCA1, PyCA2, PyCA4, PyCA5 and PyCA6 correspond to DN38784_c0_g1, DN99529_c0_g1, DN84778_c0_g1, DN105259_c0_g1 and DN50495_c0_g1, respectively, and the transcript abundance of these ve CA genes in response to different Ci concentrations during the two life stages of P. yezoensis has been demonstrated and discussed in previous work [9]. We therefore determined the transcript abundance of the remaining six CA genes under different Ci conditions during the two life stages by using transcriptomic data (Fig.…”

“…The mitochondrial PyCAs, PyCA6 and three γCAs, had relatively high transcript abundance, especially PyCA6, showing the second highest transcript abundance among the 11 CA genes in leafy thalli at approximately half that of PyCA1 [9]. Previous work has shown that pyruvate carboxylase in mitochondria has high carboxylation activity, using CO 2 to produce oxaloacetate (OAA), an important TCA cycle substrate [9].…”

“…Identi cation and cloning of putative carbonic anhydrase genes in P. yezoensis Candidate CA genes were screened from the P. yezoensis transcriptome and genome database (https://db.cngb.org/cnsa/ with accession number CNP0000880; BioProject PRJNA589917 in NCBI)[9,21]. Putative sequences were analyzed with NCBI BLASTX (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to con rm inclusion of the conserved CA domain.…”

“…Because of its economic and ecological importance, and its research value, P. yezoensis is becoming a model macroalga among the Rhodophyta [5, 6].To adapt to the low CO 2 concentrations in seawater, Pyropia have evolved a CO 2 concentrating mechanism (CCM) [7, 8]. Our previous research has indicated that P. yezoensis possesses biophysical CCM and biochemical CCM capabilities [9]. Carbonic anhydrase (CA), the key component of biophysical CCM, catalyzes the reversible dehydration of HCO 3 − to CO 2 , and also plays key roles in photosynthesis and respiration in many organisms [10,11,12].…”