Pyrenoid
Pyrenoids are sub-cellular micro-compartments found in
Algae are restricted to aqueous environments, even in aquatic habitats, and this has implications for their ability to access CO2 for photosynthesis. CO2 diffuses 10,000 times slower in water than in air, and is also slow to equilibrate. The result of this is that water, as a medium, is often easily depleted of CO2 and is slow to gain CO2 from the air. Finally, CO2 equilibrates with bicarbonate (HCO3−) when dissolved in water, and does so on a pH-dependent basis. In sea water for example, the pH is such that dissolved inorganic carbon (DIC) is mainly found in the form of HCO3−. The net result of this is a low concentration of free CO2 that is barely sufficient for an algal RuBisCO to run at a quarter of its maximum velocity, and thus, CO2 availability may sometimes represent a major limitation of algal photosynthesis.
Discovery
Pyrenoids were first described in 1803 by
In the following half-century, phycologists often used the pyrenoid as a taxonomic marker, but physiologists long failed to appreciate the importance of pyrenoids in aquatic photosynthesis. The classical paradigm, which prevailed until the early 1980s, was that the pyrenoid was the site of starch synthesis.[7] Microscopic observations were easily misleading as a starch sheath often encloses pyrenoids. The discovery of pyrenoid deficient mutants with normal starch grains in the green alga Chlamydomonas reinhardtii,[8] as well as starchless mutants with perfectly formed pyrenoids,[9] eventually discredited this hypothesis.
It was not before the early 1970s that the proteinaceous nature of the pyrenoid was elucidated, when pyrenoids were successfully isolated from a green alga,[10] and showed that up to 90% of it was composed of biochemically active RuBisCO. In the following decade, more and more evidence emerged that algae were capable of accumulating intracellular pools of DIC, and converting these to CO2, in concentrations far exceeding that of the surrounding medium. Badger and Price first suggested the function of the pyrenoid to be analogous to that of the carboxysome in cyanobacteria, in being associated with CCM activity.[11] CCM activity in algal and cyanobacterial photobionts of lichen associations was also identified using gas exchange and carbon isotope discrimination[12] and associated with the pyrenoid by Palmqvist[13] and Badger et al.[14] The Hornwort CCM was later characterized by Smith and Griffiths.[15]
From there on, the pyrenoid was studied in the wider context of carbon acquisition in algae, but has yet to be given a precise molecular definition.
Structure
There is substantial diversity in pyrenoid morphology and ultrastructure between algal species. The common feature of all pyrenoids is a spheroidal matrix, composed primarily of RuBisCO.[10] In most pyrenoid-containing organisms, the pyrenoid matrix is traversed by thylakoid membranes, which are in continuity with stromal thylakoids. In the unicellular red alga Porphyridium purpureum, individual thylakoid membranes appear to traverse the pyrenoid;[16] in the green alga Chlamydomonas reinhardtii, multiple thylakoids merge at the periphery of the pyrenoid to form larger tubules that traverse the matrix.[17][18] Unlike carboxysomes, pyrenoids are not delineated by a protein shell (or membrane). A starch sheath is often formed or deposited at the periphery of pyrenoids, even when that starch is synthesised in the cytosol rather than in the chloroplast.[19]
When examined with transmission electron microscopy, the pyrenoid matrix appears as a roughly circular electron dense granular structure within the chloroplast. Early studies suggested that RuBisCO is arranged in crystalline arrays in the pyrenoids of the diatom Achnanthes brevipes[20] and the dinoflagellate Prorocentrum micans.[21] However, recent work has shown that RuBisCO in the pyrenoid matrix of the green alga Chlamydomonas is not in a crystalline lattice and instead the matrix behaves as a phase-separated, liquid-like organelle.[22]
Mutagenic work on Chlamydomonas has shown that the RuBisCO small subunit is important for pyrenoid matrix assembly,[23] and that two solvent exposed alpha-helices of the RuBisCO small subunit are key to the process.[24] Assembly of RuBisCO into a pyrenoid was shown to require the intrinsically disordered RuBisCO-binding repeat protein EPYC1, which was proposed to "link" multiple RuBisCO holoenzymes together to form the pyrenoid matrix.[25] EPYC1 and Rubisco together were shown to be sufficient to reconstitute phase-separated droplets that show similar properties to C. reinhardtii pyrenoids in vivo, further supporting a "linker" role for EPYC1.[26]
The proteome of the Chlamydomonas pyrenoid has been characterized,[27] and the localizations and protein-protein interactions of dozens of pyrenoid-associated proteins were systematically determined.[28] Proteins localized to the pyrenoid include RuBisCO activase,[29] nitrate reductase[30] and nitrite reductase.[31]
In Chlamydomonas, a high-molecular weight complex of two proteins (LCIB/LCIC) forms an additional concentric layer around the pyrenoid, outside the starch sheath, and this is currently hypothesised to act as a barrier to CO2-leakage or to recapture CO2 that escapes from the pyrenoid.[32]
In Porphyridium and in Chlamydomonas, there is a single highly conspicuous pyrenoid in a single chloroplast, visible using light microscopy. By contrast, in diatoms and dinoflagellates, there can be multiple pyrenoids. The Chlamydomonas pyrenoid has been observed to divide by fission during chloroplast division.[33][22] In rare cases where fission did not occur, a pyrenoid appeared to form de novo.[22] Pyrenoids partially dissolved into the chloroplast stroma during every cell division, and this pool of dissolved components may condense into a new pyrenoid in cases where one is not inherited by fission.
Role of Pyrenoids in the CCM
The confinement of the CO2-fixing enzyme into a subcellular micro-compartment, in association with a mechanism to deliver CO2 to that site, is believed to enhance the efficacy of photosynthesis in an aqueous environment. Having a CCM favours carboxylation over wasteful oxygenation by RuBisCO. The molecular basis of the pyrenoid and the CCM have been characterised to some detail in the model green alga Chlamydomonas reinhardtii.
The current model of the biophysical CCM reliant upon a pyrenoid
Pyrenoids are highly plastic structures and the degree of RuBisCO packaging correlates with the state of induction of the CCM. In Chlamydomonas, when the CCM is repressed, for example when cells are maintained in a CO2-rich environment, the pyrenoid is small and the matrix is unstructured.[36] In the dinoflagellate Gonyaulax, the localisation of RuBisCO to the pyrenoid is under circadian control: when cells are photosynthetically active during the day, RuBisCO assembles into multiple chloroplasts at the centre of the cells; at night, these structures disappear.[37]
Physiology and regulation of the CCM
The algal CCM is inducible, and induction of the CCM is generally the result of low CO2 conditions. Induction and regulation of the Chlamydomonas CCM was recently studied by transcriptomic analysis, revealing that one out of three genes are up- or down-regulated in response to changed levels of CO2 in the environment.[38] Sensing of CO2 in Chlamydomonas involves a “master switch”, which was co-discovered by two laboratories.[39][40] This gene, Cia5/Ccm1, affects over 1,000 CO2-responsive genes[41] and also conditions the degree of packing of RuBisCO into the pyrenoid.
Origin
The CCM is only induced during periods of low CO2 levels, and it was the existence of these trigger levels of CO2 below which CCMs are induced that led researchers to speculate on the likely timing of origin of mechanisms like the pyrenoid.
There are several
However, alternative hypotheses have been proposed. Predictions of past CO2 levels suggest that they may have previously dropped as precipitously low as that seen during the expansion of land plants: approximately 300 MYA, during the Proterozoic Era.[43] This being the case, there might have been a similar evolutionary pressure that resulted in the development of the pyrenoid, though in this case, a pyrenoid or pyrenoid-like structure could have developed, and have been lost as CO2 levels then rose, only to be gained or developed again during the period of land colonisation by plants. Evidence of multiple gains and losses of pyrenoids over relatively short geological time spans was found in hornworts.[2]
Diversity
Pyrenoids are found in algal lineages,
References
- ^ PMID 15862091
- ^ PMID 23115334
- ^ Vaucher, J.-P. (1803). Histoire des conferves d'eau douce, contenant leurs différens modes de reproduction, et la description de leurs principales espèces, suivie de l'histoire des trémelles et des ulves d'eau douce. Geneva: J. J. Paschoud.
- ^ Brown, R.M., Arnott, H.J., Bisalputra, T., and Hoffman, L.R. (1967). The pyrenoid: Its structure, distribution, and function. Journal of Phycology, 3(Suppl. 1), 5-7.
- ^ Schmitz, F. (1882). Die Chromatophoren der Algen. Vergleichende untersuchungen über Bau und Entwicklung der Chlorophyllkörper und der analogen Farbstoffkörper der Algen. M. Cohen & Sohn (F. Cohen), Bonn, Germany.
- ^ Schimper, A.F.W. (1883). Über die Entwicklung der Chlorophyllkörner und Farbkörper. Botanische Zeitung , 41, 105-120, 126-131, 137-160.
- ^ Griffiths, D.J. (1980). The pyrenoid and its role in algal metabolism. Science Progress, 66, 537-553.
- ^ Goodenough, U.W. and Levine, R.P. (1970). Chloroplast structure and function in AC-20, a mutant strain of Chlamydomonas reinhardtii. III. Chloroplast ribosomes and membrane organization. J Cell Biol , 44, 547-562.
- ^ Villarejo, A., Plumed, M., and Ramazanov, Z. (1996). The induction of the CO2 concentrating mechanism in a starch-less mutant of Chlamydomonas reinhardtii. Physiol Plant, 98, 798-802.
- ^ a b Holdsworth, R.H. (1971). The isolation and partial characterization of the pyrenoid protein of Eremosphaera viridis. J Cell Biol, 51, 499-513.
- ^ Badger, M. R., & Price, G. D. (1992). The CO2 concentrating mechanism in cyanobacteria and microalgae. Physiologia Plantarum, 84(4), 606-615.
- ^ Máguas, C., Griffiths, H., Ehleringer, J., & Serodio, J. (1993). Characterization of photobiont associations in lichens using carbon isotope discrimination techniques. Stable Isotopes and Plant Carbon-Water Relations, 201-212.
- ^ Palmqvist, K. (1993). Photosynthetic CO2-use efficiency in lichens and their isolated photobionts: the possible role of a CO2-concentrating mechanism. Planta, 191(1), 48-56.
- ^ Badger, M. R., Pfanz, H., Büdel, B., Heber, U., & Lange, O. L. (1993). Evidence for the functioning of photosynthetic CO2-concentrating mechanisms in lichens containing green algal and cyanobacterial photobionts. Planta,191(1), 57-70.
- ^ Smith, E. C., & Griffiths, H. (1996). A pyrenoid-based carbon-concentrating mechanism is present in terrestrial bryophytes of the class Anthocerotae. Planta, 200(2), 203-212.
- PMID 13654450
- PMID 13438931
- PMID 25584625.
- ^ Wilson, S., West, J., Pickett‐Heaps, J., Yokoyama, A., & Hara, Y. (2002). Chloroplast rotation and morphological plasticity of the unicellular alga Rhodosorus (Rhodophyta, Stylonematales). Phycological research, 50(3), 183-191.
- PMID 11905213.
- PMID 5353655.
- ^ PMID 28938114.
- PMID 20424165
- PMID 23112177
- PMID 27166422.
- PMID 30498228.
- PMID 29481573.
- PMID 28938113.
- ^ McKay, R. M. L., Gibbs, S. P., & Vaughn, K. C. (1991). RuBisCo activase is present in the pyrenoid of green algae. Protoplasma, 162(1), 38-45.
- ^ Lopez-Ruiz, A., Verbelen, J. P., Roldan, J. M., & Diez, J. (1985). Nitrate reductase of green algae is located in the pyrenoid. Plant Physiology, 79(4), 1006-1010.
- ^ López-Ruiz, A., Verbelen, J. P., Bocanegra, J. A., & Diez, J. (1991). Immunocytochemical localization of nitrite reductase in green algae. Plant Physiology, 96(3), 699-704.
- PMID 20660228
- S2CID 84245338.
- PMID 17557885
- PMID 17291820
- ^ Rawat, M., Henk, M. C., Lavigne, L. L., & Moroney, J. V. (1996). Chlamydomonas reinhardtii mutants without ribulose-1, 5-bisphosphate carboxylase-oxygenase lack a detectable pyrenoid. Planta, 198(2), 263-270.
- PMID 15941407
- PMID 22634764
- PMID 11309511
- PMID 11287669
- PMID 22634760
- PMID 12554074
- ^ Riding, R. (2006). Cyanobacterial calcification, carbon dioxide concentrating mechanisms, and Proterozoic–Cambrian changes in atmospheric composition.Geobiology, 4(4), 299-316.
- ^ A phylogenomically informed five-order system for the closest relatives of land plants
- PMID 23345319.