Datum: 19.08.2022

Mitochondrial PEP Carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations

Photosynthetic carbon fixation is often limited by CO2 availability, which led to the evolution of CO2 concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C4 plants, but whether biochemical CCMs are commonly found in diatoms is a subject of debate.

  • In the diatom Phaeodactylum tricornutum, phosphoenolpyruvate carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative polymerase chain reaction, Western blots, and enzymatic assays to examine PEPC expression and PEPC activity, under low and high concentrations of dissolved inorganic carbon (DIC).
  • We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability conditions showed reduced growth and photosynthetic affinity for DIC while behaving similarly to wild-type (WT) cells at high DIC concentrations. These mutants furthermore exhibited significantly lower 13C/12C ratios compared to the WT.
  • Our data imply that in P. tricornutum at least parts of the CCM rely on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.


Diatoms are an important part of the marine phytoplankton and are responsible for a significant portion of oceanic primary production (Nelson et al., 1995; Falkowski & Raven, 1997). Photosynthesis is a fundamental process for primary productivity, and ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco) is the key enzyme for CO2 fixation in the vast majority of oxygenic photosynthetic organisms, including photosynthetic Proteobacteria, and some Chloroflexi (Andersson & Backlund, 2008). Rubisco catalyzes the carboxylation reaction of ribulose-1,5-bisphosphate (RuBP), producing two molecules of the C3 compound 3-phosphoglycerate, the primary product of carbon fixation in most photosynthetic organisms. However, the dissolved inorganic carbon (DIC) in seawater corresponds to a CO2 concentration of 10–15 μM at pH 8.2 (Riebesell et al., 1993), which is much lower than the value of the Michaelis–Menten constant (Km = 20–60 μM) for CO2 concentration in the proximity of the diatom Rubisco enzyme (Badger et al., 1998; Whitney et al., 2011; Young et al., 2016). To circumvent CO2 limitation, diatoms, as well as many other phytoplankton, use CO2 concentrating mechanisms (CCMs) that comprise the active uptake and transport of inorganic carbon to increase the CO2 concentration in the proximity of Rubisco, improving photosynthetic efficiency, especially in a carbon-limited environment (Kaplan & Reinhold, 1999; Burkhardt et al., 2001; Matsuda et al., 20012017; Giordano et al., 2005; Reinfelder, 2010; Hopkinson et al., 2011; Kikutani et al., 2016; Clement et al., 2017; Shen et al., 2017; Jensen et al., 2019; Launay et al., 2020). There are also phytoplankton that lack CCMs (e.g. Chrysophytes (Maberly et al., 2009)).


Yu G., Nakajima K., Gruber A., Río Bártulos C., Schober A.F., Lepetit B., Yohannes E., Matsuda Y., Kroth P.G. 2022: Mitochondrial PEP Carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations. New Phytologist 235: 1379–1393 [IF=10.152] DOI: 10.1111/nph.18268





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