A Spatial Interactome Reveals the Protein Organization of the Algal CO2-Concentrating Mechanism

Luke C.M. Mackinder, Chris Chen, Ryan D. Leib, Weronika Patena, Sean R. Blum, Matthew Rodman, Silvia Ramundo, Christopher M. Adams, Martin C. Jonikas

Research output: Contribution to journalArticlepeer-review

184 Scopus citations


Approximately one-third of global CO2 fixation is performed by eukaryotic algae. Nearly all algae enhance their carbon assimilation by operating a CO2-concentrating mechanism (CCM) built around an organelle called the pyrenoid, whose protein composition is largely unknown. Here, we developed tools in the model alga Chlamydomonas reinhardtii to determine the localizations of 135 candidate CCM proteins and physical interactors of 38 of these proteins. Our data reveal the identity of 89 pyrenoid proteins, including Rubisco-interacting proteins, photosystem I assembly factor candidates, and inorganic carbon flux components. We identify three previously undescribed protein layers of the pyrenoid: a plate-like layer, a mesh layer, and a punctate layer. We find that the carbonic anhydrase CAH6 is in the flagella, not in the stroma that surrounds the pyrenoid as in current models. These results provide an overview of proteins operating in the eukaryotic algal CCM, a key process that drives global carbon fixation.

Original languageEnglish (US)
Pages (from-to)133-147.e14
Issue number1
StatePublished - Sep 21 2017

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology


  • CCM
  • CO-concentrating mechanism
  • Chlamydomonas reinhardtii
  • Rubisco
  • affinity purification mass spectrometry
  • carbon fixation
  • high-throughput fluorescence protein tagging
  • photosynthesis
  • pyrenoid


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