The Pyrenoid: An Overlooked Organelle Comes out of Age

(1)

Article

Reference

The Pyrenoid: An Overlooked Organelle Comes out of Age

ROCHAIX, Jean-David

Abstract

The pyrenoid is a membrane-less organelle that exists in various photosynthetic organisms, such as algae, and wherein most global CO2 fixation occurs. Two papers from the Jonikas lab in this issue of Cell provide new insights into the structure, protein composition, and dynamics of this important organelle.

ROCHAIX, Jean-David. The Pyrenoid: An Overlooked Organelle Comes out of Age. Cell , 2017, vol. 171, no. 1, p. 28-29

DOI : 10.1016/j.cell.2017.09.012 PMID : 28938119

Available at:

http://archive-ouverte.unige.ch/unige:111401

Disclaimer: layout of this document may differ from the published version.

1 / 1

(2)

Leading Edge

Previews

The Pyrenoid: An Overlooked Organelle Comes out of Age

Jean-David Rochaix^1,*

1Departments of Molecular Biology and Plant Biology, University of Geneva, Geneva, Switzerland

*Correspondence:Jean-David.Rochaix@unige.ch http://dx.doi.org/10.1016/j.cell.2017.09.012

The pyrenoid is a membrane-less organelle that exists in various photosynthetic organisms, such as algae, and wherein most global CO

₂

fixation occurs. Two papers from the Jonikas lab in this issue of Cell provide new insights into the structure, protein composition, and dynamics of this important organelle.

Most life on Earth depends on photosyn- thesis, the process whereby inorganic carbon is fixed and converted into organic carbon metabolites using solar energy.

However, an important limitation in photo- synthesis is the poor performance of the CO2-fixing enzyme Rubisco (ribulose 1,5 bisphosphate carboxylase/oxygenase) due to its dual carboxylase and oxygenase activity. At ambient CO2 levels, the carboxylase and oxygenase activities compete with each other, leading to a significant decrease in carbon fixation through photorespiration. Nearly all freshwater and marine photoautotrophs, including cyanobacteria and algae, have solved this problem by increasing the level of CO2 in the vicinity of Rubisco through CO₂-concentrating mechanisms (CCM). In algae, CCM is mediated by several plasma and chloroplast-membrane inorganic carbon transporters, a set of carbonic anhydrases in strategic lo- cations, and the pyrenoid, a membrane- less organelle within chloroplasts, where approximately one-third of global CO₂ fixation is estimated to occur (Figure 1) (Wang et al., 2015). The pyrenoid contains a starch sheath and a matrix in which CO2

is concentrated together with Rubisco.

The matrix is traversed by membrane tubules that are continuous with the thylakoid membranes (Engel et al., 2015). The CCM is highly regulated by CO2 levels and by light and circadian signals (Mitchell et al., 2014), and many mutants affected in CCM have been identified based on their ability to grow photoauto- trophically under high-CO2but not under low-CO2conditions (Wang et al., 2015).

Although the pyrenoid and the CCM system have been studied in organisms

such as the model green algaChlamydo- monas reinhardtii, up until recently little was known about its protein composition, structure, and assembly. However, the situation has changed radically in recent years and spectacular advances are now reported in two studies from the group of Martin Jonikas in this issue of Cell (Mackinder et al., 2017; Freeman Rosenzweig et al., 2017). The Jonikas lab has invested a great deal of effort in establishing a reverse genetic system inChlamydomonasby generating an in- dexed mapped mutant library (Li et al., 2016). Screening of these mutants for a CCM phenotype revealed several novel genes involved in CCM that provide a rich source for further investigations (Mackinder et al., 2016).

In the first study, Jonikas and colleagues (Mackinder et al., 2017) develop high-throughput techniques involving fluorescent protein tagging and affinity purification mass spectrometry to identify additional components and to generate a spatially defined network of theChlamy- domonasCCM. Using this platform, they identify 135 candidate CCM-associated proteins and determine physical interac- tors for 38 of them. This work provides a wealth of new insights into the CCM ma- chinery, increasing the number of known pyrenoid proteins by more than 10-fold (from 7 to over 80). This set includes novel Rubisco-interacting proteins, photosystem I assembly factor candi- dates, and inorganic carbon flux components (Figure 1). This study also reveals that the pyrenoid structure is more complex than previously assumed, consisting of three distinct protein layers: a plate-like layer, a mesh layer, and a punctate layer.

In the second study, Jonikas and colleagues (Freeman Rosenzweig et al., 2017) further examine the structure and dynamics of the pyrenoid ofChlamydo- monasduring the cell cycle. Contrary to what was assumed earlier, the pyrenoid matrix is not crystalline or amorphous but appears to be liquid like, as revealed by the analysis of the Rubisco distribu- tion by cryoelectron microscopy and by FRAP experiments, mixing internally and dispersing into the surrounding stroma during cell division and in response to high CO2. Jonikas and colleagues also observe that proteins larger than 78 kDa are excluded from the pyrenoid matrix, which may be due to the surface tension generated by the proteins that produce the liquid phase (Bergeron-Sandoval et al., 2016). Previous work identified EPYC1 (essential pyrenoid component 1), a protein containing four nearly identical repeats that co-localizes with Rubisco throughout the pyrenoid matrix and interacts with its small subunit to form a lattice (Mackinder et al., 2016). EPYC1 is essential for normal pyrenoid size, number, morphology, Rubisco content, and efficient carbon fixation at low CO2.

Although the precise binding between Rubisco and EPYC1 is not yet known, this new study proposes that the liquid-like nature of the pyrenoid could be mediated through the binding of Ru- bisco to the repeats of EPYC1, forming a network with each EPYC1 binding four Rubiscos and each Rubisco binding eight EPYC1s. Thus, EPYC1 would act as a molecular glue holding Rubisco together in the pyrenoid.

Another fascinating aspect of the study by Freeman Rosenzweig et al., is

28 Cell171, September 21, 2017ª2017 Elsevier Inc.

(3)

the highly dynamic reorganization of the pyrenoid that occurs following changes in CO2 concentration and during the cell cycle. PossibIy, the relocalization of Rubisco from the pyrenoid to the stroma under high CO2 or in darkness could reflect a phase transition of the pyrenoid matrix from an aggregated to a soluble phase, allowing for rapid reorganization of Rubisco to optimize CO2fixation under changing environmental conditions. The fluidity of the pyrenoid matrix may also facilitate the access of Rubisco activase chaperones to the Rubisco active sites within the matrix. A similar phase transition may occur during cell division when the pyrenoid undergoes regression, i.e., reduction in size and/or fission. This study shows that both phenomena can occur simultaneously in the same cell.

These two papers not only significantly further our knowledge on the pyrenoid but also open widely the field of CCM to new investigations by raising a number of intriguing questions. How is the pyrenoid positioned within the cell, and how does it divide? What is the minimal requirement for assembling a functional pyrenoid?

Can the algal system be transferred to higher plants for improving crop productiv- ity? Introducing CCM into higher plants is predicted to increase yields by up to 60%

and to improve the efficiency of nitrogen and water use (Long et al., 2015). In this respect, it is encouraging that nearly all algal CCM proteins localize correctly in transgenic higher plants, indicating that the transfer of algal components is feasible (Atkinson et al., 2016). However, these en- gineering efforts were restricted because

only few components of the algal CCM were known. By providing a detailed blue- print of the algal CCM, the work of Jonikas and colleagues reveals new targets for transfer into crop plants that could improve carbon fixation. The finding that EPYC1 interacts with a kinase and two 14-3-3 proteins raises questions about the role of phosphorylation in the regulation of the in- teractions between EPYC1 and Rubisco, which could modulate the matrix phase.

Clearly, further functional studies of the pyrenoid are eagerly awaited and are likely to bring further surprises related to this rather unusual organelle.

REFERENCES

Atkinson, N., Feike, D., Mackinder, L.C., Meyer, M.T., Griffiths, H., Jonikas, M.C., Smith, A.M., and McCormick, A.J. (2016). Plant Biotechnol. J.

14, 1302–1315.

Bergeron-Sandoval, L.P., Safaee, N., and Mich- nick, S.W. (2016). Cell165, 1067–1079.

Engel, B.D., Schaffer, M., Kuhn Cuellar, L., Villa, E., Plitzko, J.M., and Baumeister, W. (2015). eLife4, e04889.

Freeman Rosenzweig, E.S., Xu, B., Kuhn Cuellar, L., Martinez-Sanchez, A., Schaffer, M., Strauss, M., Cartwright, H.N., Ronceray, P., Plitzko, J.M., Fo¨rster, F., et al. (2017). Cell 171, this issue, 148–162.

Li, X., Zhang, R., Patena, W., Gang, S.S., Blum, S.R., Ivanova, N., Yue, R., Robertson, J.M., Lefeb- vre, P.A., Fitz-Gibbon, S.T., et al. (2016). Plant Cell 28, 367–387.

Long, S.P., Marshall-Colon, A., and Zhu, X.G.

(2015). Cell161, 56–66.

Mackinder, L.C., Meyer, M.T., Mettler-Altmann, T., Chen, V.K., Mitchell, M.C., Caspari, O., Freeman Rosenzweig, E.S., Pallesen, L., Reeves, G., Ita- kura, A., et al. (2016). Proc. Natl. Acad. Sci. USA 113, 5958–5963.

Mackinder, L.C.M., Chen, C., Leib, R.D., Patena, W., Blum, S.R., Rodman, M., Ramundo, S., Adams, C.M., and Jonikas, M.C. (2017). Cell171, this issue, 133–147.

Mitchell, M.C., Meyer, M.T., and Griffiths, H.

(2014). Plant Physiol.166, 1073–1082.

Wang, Y., Stessman, D.J., and Spalding, M.H.

(2015). Plant J.82, 429–448.

Figure 1. Simplified Model for CO₂-Concentrating Mechanisms in the Pyrenoid ofChlamy- domonas

The liquid-like matrix of the pyrenoid is shown as a network of Rubisco aggregates held together by EPYC1 in which each EPYC1 protein (black sphere) binds four Rubiscos (brown sphere). Inorganic carbon is imported as HCO3 into the cell by the bicarbonate transporters LCI1 and HLA3, which form a complex on the plasma membrane. Alternatively, CO2may also enter the cell and be converted to HCO3 possibly by LCIB. Entry of HCO3 into the chloroplast is mediated by LCIA on the chloroplast envelope and into the thylakoid lumen by an unknown transporter. Finally HCO3 diffuses into the pyrenoid through the membrane tubules connected to the thylakoid network (dark green), where it is converted to CO2by CAH3 (orange square) and available for CO2fixation by Rubisco. The white layer around the pyrenoid represents the starch sheath. The cytosol and stroma are indicated. CBB, Calvin-Benson cycle; CX, putative shuttle for Rubisco substrates and products.

Cell171, September 21, 2017 29