View source for Pyrenoid

{{Short description|Organelle found within the chloroplasts of algae and hornworts}}
{{Hatnote|Not to be confused with [[pyrena]], a nutlet within a drupaceous fruit.}}
[[File:Cross section of a Chlamydomonas reinhardtii algae cell, a 3D representation.jpg|thumb|270px|Cross section of a ''Chlamydomonas reinhardtii'' algae cell, a 3D representation]]

'''Pyrenoids''' are sub-cellular phase-separated micro-compartments found in [[chloroplast]]s of many [[algae]],<ref name = king>{{cite journal | last1 = Giordano | first1 = M. | last2 = Beardall | first2 = J. | last3 = Raven | first3 = J. A. | year = 2005 | title = CO<sub>2</sub> concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution | url = | journal = Annu. Rev. Plant Biol. | volume = 56 | issue = | pages = 99–131 | doi = 10.1146/annurev.arplant.56.032604.144052 | pmid = 15862091 }}</ref> and in a single group of land plants, the [[hornwort]]s.<ref name=bop>{{cite journal | last1 = Villarreal | first1 = J. C. | last2 = Renner | first2 = S. S. | year = 2012 | title = Hornwort pyrenoids, carbon-concentrating structures, evolved and were lost at least five times during the last 100 million years | url = | journal = Proceedings of the National Academy of Sciences | volume = 109 | issue = 46| pages = 1873–1887 | pmid = 23115334 | doi = 10.1073/pnas.1213498109 | pmc = 3503201 | doi-access = free }}</ref><ref>{{cite journal | vauthors=Robison TA, Oh ZG, Lafferty D, Xu X, ((Villarreal JCA)), Gunn LH, Li FW| journal=Nature Plants | title=Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants | pages=63–73 | publisher=Nature Publishing Group | date=3 January 2025 | issn=2055-0278 | doi=10.1038/s41477-024-01871-0 | volume=11 | issue=1 | pmid=39753956 }}
</ref> Pyrenoids are associated with the operation of a carbon-concentrating mechanism (CCM). Their main function is to act as centres of carbon dioxide (CO<sub>2</sub>) fixation, by generating and maintaining a CO<sub>2</sub>-rich environment around the [[photosynthesis|photosynthetic]] [[enzyme]] [[ribulose-1,5-bisphosphate carboxylase/oxygenase]] (RuBisCO). Pyrenoids therefore seem to have a role analogous to that of [[carboxysomes]] in [[cyanobacteria]].

Algae are restricted to aqueous environments, even in aquatic habitats, and this has implications for their ability to access CO<sub>2</sub> for photosynthesis. CO<sub>2</sub> 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 CO<sub>2</sub> and is slow to gain CO<sub>2</sub> from the air. Finally, CO<sub>2</sub> equilibrates with bicarbonate ({{chem2|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 {{chem2|HCO3-}}. The net result of this is a low concentration of free CO<sub>2</sub> that is barely sufficient for an algal RuBisCO to run at a quarter of its [[enzyme kinetics|maximum velocity]], and thus, CO<sub>2</sub> availability may sometimes represent a major limitation of algal photosynthesis.

==Discovery==

Pyrenoids were first described in 1803 by [[Jean Pierre Étienne Vaucher|Vaucher]]<ref>{{cite book|author=Vaucher, J.-P.|year=1803|title=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|publisher=J. J. Paschoud|location=Geneva|url=https://www.biodiversitylibrary.org/item/43432#page/9/mode/1up}}</ref> (cited in Brown et al.<ref>{{cite journal | last1 = Brown | first1 = R.M. | last2 = Arnott | first2 = H.J. | last3 = Bisalputra | first3 = T. | last4 = Hoffman | first4 = L.R. | year = 1967 | title = The pyrenoid: Its structure, distribution, and function | url = | journal = Journal of Phycology | volume = 3 | issue = Suppl. 1 | pages = 5–7 }}</ref>). The term was first coined by Schmitz<ref>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.</ref> who also observed how algal chloroplasts formed de novo during cell division, leading [[Andreas Franz Wilhelm Schimper|Schimper]] to propose that chloroplasts were autonomous, and to surmise that all green plants had originated through the "unification of a colourless organism with one uniformly tinged with chlorophyll".<ref>{{cite journal | last1 = Schimper | first1 = A.F.W. | year = 1883 | title = Über die Entwicklung der Chlorophyllkörner und Farbkörper | url = | journal = Botanische Zeitung | volume = 41 | issue = | pages = 105–120, 126–131, 137–160 }}</ref> From these pioneering observations, [[Konstantin Mereschkowski|Mereschkowski]] eventually proposed, in the early 20th century, the [[endosymbiotic theory|symbiogenetic theory]] and the genetic independence of chloroplasts.

In the following half-century, [[phycology|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.<ref>{{cite journal | last1 = Griffiths | first1 = D.J. | year = 1980 | title = The pyrenoid and its role in algal metabolism | url = | journal = Science Progress | volume = 66 | issue = | pages = 537–553 }}</ref> 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'',<ref>{{cite journal | last1 = Goodenough | first1 = U.W. | last2 = Levine | first2 = R.P. | year = 1970 | title = Chloroplast structure and function in AC-20, a mutant strain of ''Chlamydomonas reinhardtii''. III. Chloroplast ribosomes and membrane organization | url = | journal = J Cell Biol | volume = 44 | issue = 3| pages = 547–562 | doi = 10.1083/jcb.44.3.547 | pmid = 5415236 | pmc = 2107979 }}</ref> as well as starchless mutants with perfectly formed pyrenoids,<ref>{{cite journal | last1 = Villarejo | first1 = A. | last2 = Plumed | first2 = M. | last3 = Ramazanov | first3 = Z. | year = 1996 | title = The induction of the CO<sub>2</sub> concentrating mechanism in a starch-less mutant of ''Chlamydomonas reinhardtii'' | url = | journal = Physiol Plant | volume = 98 | issue = 4| pages = 798–802 | doi = 10.1111/j.1399-3054.1996.tb06687.x }}</ref> 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,<ref name = bazinga>{{cite journal | last1 = Holdsworth | first1 = R.H. | year = 1971 | title = The isolation and partial characterization of the pyrenoid protein of ''Eremosphaera viridis'' | url = | journal = J Cell Biol | volume = 51 | issue = 21| pages = 499–513 | doi = 10.1083/jcb.51.2.499 | pmid = 5112653 | pmc = 2108136 }}</ref> 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 CO<sub>2</sub>, 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.<ref>{{cite journal | last1 = Badger | first1 = M. R. | last2 = Price | first2 = G. D. | year = 1992 | title = The CO<sub>2</sub> concentrating mechanism in cyanobacteria and microalgae | url = | journal = Physiologia Plantarum | volume = 84 | issue = 4| pages = 606–615 | doi = 10.1111/j.1399-3054.1992.tb04711.x }}</ref> CCM activity in algal and cyanobacterial photobionts of lichen associations was also identified using gas exchange and [[Biological carbon fixation#Carbon isotope discrimination|carbon isotope discrimination]]<ref>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.</ref> and associated with the pyrenoid by Palmqvist<ref>{{cite journal | last1 = Palmqvist | first1 = K | year = 1993 | title = Photosynthetic CO<sub>2</sub>-use efficiency in lichens and their isolated photobionts: the possible role of a CO<sub>2</sub>-concentrating mechanism | url = | journal = Planta | volume = 191 | issue = 1| pages = 48–56 | doi = 10.1007/BF00240895 }}</ref> and Badger et al.<ref>{{cite journal | last1 = Badger | first1 = M. R. | last2 = Pfanz | first2 = H. | last3 = Büdel | first3 = B. | last4 = Heber | first4 = U. | last5 = Lange | first5 = O. L. | year = 1993 | title = Evidence for the functioning of photosynthetic CO<sub>2</sub>-concentrating mechanisms in lichens containing green algal and cyanobacterial photobionts | url = | journal = Planta | volume = 191 | issue = 1| pages = 57–70 | doi = 10.1007/BF00240896 }}</ref> The Hornwort CCM was later characterized by Smith and Griffiths.<ref>{{cite journal | last1 = Smith | first1 = E. C. | last2 = Griffiths | first2 = H. | year = 1996 | title = A pyrenoid-based carbon-concentrating mechanism is present in terrestrial bryophytes of the class Anthocerotae | url = | journal = Planta | volume = 200 | issue = 2| pages = 203–212 | doi = 10.1007/BF00208310 }}</ref>

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.

[[File:Scenedesmus quadricauda close up DIC Image-1.tif|thumb|300px|right|Differential interference contrast micrograph of ''Scenedesmus quadricauda'' with the pyrenoid (central four circular structures) clearly visible.]]

==Structure==

=== Gross morphology and ultrastructure ===
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.<ref name = bazinga /> 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;<ref>{{cite journal | last1 = Brody | first1 = M. | last2 = Vatter | first2 = A. E. | year = 1959 | title = Observations on cellular structures of ''Porphyridium cruentum'' | journal = The Journal of Biophysical and Biochemical Cytology | volume = 5 | issue = 2| pages = 289–294 | doi = 10.1083/jcb.5.2.289 | pmid = 13654450 | pmc = 2224646 }}</ref> in the green alga ''[[Chlamydomonas reinhardtii]]'', multiple thylakoids merge at the periphery of the pyrenoid to form larger tubules that traverse the matrix.<ref>{{cite journal | last1 = Sager | first1 = R. | last2 = Palade | first2 = G. E. | year = 1957 | title = Structure and development of the chloroplast in ''Chlamydomonas'' I. The normal green cell | url = | journal = The Journal of Biophysical and Biochemical Cytology | volume = 3 | issue = 3| pages = 463–488 | doi = 10.1083/jcb.3.3.463 | pmid = 13438931 | pmc = 2224040 }}</ref><ref>{{Cite journal|last1=Engel|first1=Benjamin D|last2=Schaffer|first2=Miroslava|last3=Kuhn Cuellar|first3=Luis|last4=Villa|first4=Elizabeth|author-link4=Elizabeth Villa|last5=Plitzko|first5=Jürgen M|last6=Baumeister|first6=Wolfgang|date=2015-01-13|title=Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography|journal=eLife|language=en|volume=4|article-number=e04889|doi=10.7554/eLife.04889|issn=2050-084X|pmc=4292175|pmid=25584625 |doi-access=free }}</ref> 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.<ref>{{cite journal | last1 = Wilson | first1 = S. | last2 = West | first2 = J. | last3 = Pickett-Heaps | first3 = J. | last4 = Yokoyama | first4 = A. | last5 = Hara | first5 = Y. | year = 2002 | title = Chloroplast rotation and morphological plasticity of the unicellular alga Rhodosorus (Rhodophyta, Stylonematales) | url = | journal = Phycological Research | volume = 50 | issue = 3| pages = 183–191 | doi = 10.1111/j.1440-1835.2002.tb00150.x | doi-broken-date = 17 October 2025 }}</ref>

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''<ref>{{Cite journal|last=Holdsworth|first=Robert H.|title=The Presence of a Crystalline Matrix in Pyrenoids of the Diatom, Achnanthes Brevipes|date=1968-06-01|url=https://rupress.org/jcb/article/37/3/831/12498/THE-PRESENCE-OF-A-CRYSTALLINE-MATRIX-IN-PYRENOIDS|journal=Journal of Cell Biology|language=en|volume=37|issue=3|pages=831–837|doi=10.1083/jcb.37.3.831|issn=0021-9525|pmc=2107439|pmid=11905213}}</ref> and the dinoflagellate ''Prorocentrum micans''.<ref>{{Cite journal|last=Kowallik|first=K.|date=1969-07-01|title=The Crystal Lattice of the Pyrenoid Matrix of Prorocentrum Micans|url=https://jcs.biologists.org/content/5/1/251|journal=Journal of Cell Science|language=en|volume=5|issue=1|pages=251–269|doi=10.1242/jcs.5.1.251|issn=0021-9533|pmid=5353655|url-access=subscription}}</ref> 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.<ref name=":0">{{Cite journal|last1=Freeman Rosenzweig|first1=Elizabeth S.|last2=Xu|first2=Bin|last3=Kuhn Cuellar|first3=Luis|last4=Martinez-Sanchez|first4=Antonio|last5=Schaffer|first5=Miroslava|last6=Strauss|first6=Mike|last7=Cartwright|first7=Heather N.|last8=Ronceray|first8=Pierre|last9=Plitzko|first9=Jürgen M.|last10=Förster|first10=Friedrich|last11=Wingreen|first11=Ned S.|last12=Engel|first12=Benjamin D.|last13=Mackinder|first13=Luke C. M.|last14=Jonikas|first14=Martin C.|date=September 2017|title=The Eukaryotic CO2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization|journal=Cell|volume=171|issue=1|pages=148–162.e19|doi=10.1016/j.cell.2017.08.008|issn=0092-8674|pmc=5671343|pmid=28938114}}</ref>

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.<ref>{{Cite journal|last=Goodenough|first=Ursula W.|date=1970|title=Chloroplast Division and Pyrenoid Formation in Chlamydomonas Reinhardi1|url=https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.1970.tb02348.x|journal=Journal of Phycology|language=en|volume=6|issue=1|pages=1–6|doi=10.1111/j.1529-8817.1970.tb02348.x|bibcode=1970JPcgy...6....1G |s2cid=84245338|issn=1529-8817|url-access=subscription}}</ref><ref name=":0" /> In rare cases where fission did not occur, a pyrenoid appeared to form de novo.<ref name=":0" /> 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.

=== Molecular components ===

In ''Chlamydomonas'', specifically the model alga ''[[Chlamydomonas reinhardtii]]'':
* Mutagenic work has shown that the RuBisCO small subunit is important for pyrenoid matrix assembly,<ref>{{cite journal | last1 = Genkov | first1 = T. | last2 = Meyer | first2 = M. | last3 = Griffiths | first3 = H. | last4 = Spreitzer | first4 = R. J. | year = 2010 | title = Functional hybrid rubisco enzymes with plant small subunits and algal large subunits engineered ''RBCS'' cDNA for expression in ''Chlamydomonas'' | journal = Journal of Biological Chemistry | volume = 285 | issue = 26| pages = 19833–19841 | pmid = 20424165 | doi = 10.1074/jbc.M110.124230 | doi-access = free | pmc = 2888394 }}</ref> and that two solvent exposed alpha-helices of the RuBisCO small subunit are key to the process.<ref>{{cite journal | last1 = Meyer | first1 = M. T. | last2 = Genkov | first2 = T. | last3 = Skepper | first3 = J. N. | last4 = Jouhet | first4 = J. | last5 = Mitchell | first5 = M. C. | last6 = Spreitzer | first6 = R. J. | last7 = Griffiths | first7 = H. | year = 2012 | title = RuBisCO small-subunit α-helices control pyrenoid formation in ''Chlamydomonas'' | journal = Proceedings of the National Academy of Sciences | volume = 109 | issue = 47| pages = 19474–19479 | pmid = 23112177 | doi = 10.1073/pnas.1210993109 | doi-access = free | pmc = 3511088 }}</ref>
* 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.<ref>{{Cite journal|last1=Mackinder|first1=Luke C. M.|last2=Meyer|first2=Moritz T.|last3=Mettler-Altmann|first3=Tabea|last4=Chen|first4=Vivian K.|last5=Mitchell|first5=Madeline C.|last6=Caspari|first6=Oliver|last7=Rosenzweig|first7=Elizabeth S. Freeman|last8=Pallesen|first8=Leif|last9=Reeves|first9=Gregory|last10=Itakura|first10=Alan|last11=Roth|first11=Robyn|last12=Sommer|first12=Frederik|last13=Geimer|first13=Stefan|last14=Mühlhaus|first14=Timo|last15=Schroda|first15=Michael|last16=Goodenough|first16=Ursula|last17=Stitt|first17=Mark|last18=Griffiths|first18=Howard|last19=Martin C.|first19=Jonikas|date=2016-05-24|title=A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle|journal=Proceedings of the National Academy of Sciences|language=en|volume=113|issue=21|pages=5958–5963|doi=10.1073/pnas.1522866113|issn=0027-8424|pmc=4889370|pmid=27166422|doi-access=free|bibcode=2016PNAS..113.5958M }}</ref> 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.<ref>{{Cite journal|last1=Wunder|first1=Tobias|last2=Cheng|first2=Steven Le Hung|last3=Lai|first3=Soak-Kuan|last4=Li|first4=Hoi-Yeung|last5=Mueller-Cajar|first5=Oliver|date=2018-11-29|title=The phase separation underlying the pyrenoid-based microalgal Rubisco supercharger|journal=Nature Communications|language=en|volume=9|issue=1|page=5076|doi=10.1038/s41467-018-07624-w|issn=2041-1723|pmc=6265248|pmid=30498228|bibcode=2018NatCo...9.5076W}}</ref>
* SAGA1 and MITH1 are each necessary for the appearance of matrix-traversing membranes in the pyrenoid; combined they are sufficient for such membranes to appear, even when introduced into the model "higher" land plant ''[[Arabidopsis thaliana]]''. Without those matrix-traversing membrane "tubules", there would be no way for {{CO2}} to enter the pyrenoid.<ref>{{cite journal |last1=Hennacy |first1=Jessica H. |last2=Atkinson |first2=Nicky |last3=Kayser-Browne |first3=Angelo |last4=Ergun |first4=Sabrina L. |last5=Franklin |first5=Eric |last6=Wang |first6=Lianyong |last7=Eicke |first7=Simona |last8=Kazachkova |first8=Yana |last9=Kafri |first9=Moshe |last10=Fauser |first10=Friedrich |last11=Vilarrasa-Blasi |first11=Josep |last12=Jinkerson |first12=Robert E. |last13=Zeeman |first13=Samuel C. |last14=McCormick |first14=Alistair J. |last15=Jonikas |first15=Martin C. |title=SAGA1 and MITH1 produce matrix-traversing membranes in the CO2-fixing pyrenoid |journal=Nature Plants |date=15 November 2024 |doi=10.1038/s41477-024-01847-0 |doi-access=free|pmc=11649565 |pmid=39548241 |volume=10 |issue=12 |pages=2038–2051}}</ref>

The proteome of the ''Chlamydomonas'' pyrenoid has been characterized,<ref>{{Cite journal|last1=Zhan|first1=Yu|last2=Marchand|first2=Christophe H.|last3=Maes|first3=Alexandre|last4=Mauries|first4=Adeline|last5=Sun|first5=Yi|last6=Dhaliwal|first6=James S.|last7=Uniacke|first7=James|last8=Arragain|first8=Simon|last9=Jiang|first9=Heng|last10=Gold|first10=Nicholas D.|last11=Martin|first11=Vincent J. J.|date=2018-02-26|title=Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii|journal=PLOS ONE|language=en|volume=13|issue=2|article-number=e0185039|doi=10.1371/journal.pone.0185039|issn=1932-6203|pmc=5826530|pmid=29481573|doi-access=free|bibcode=2018PLoSO..1385039Z }}</ref> and the localizations and protein-protein interactions of dozens of pyrenoid-associated proteins were systematically determined.<ref>{{Cite journal|last1=Mackinder|first1=Luke C. M.|last2=Chen|first2=Chris|last3=Leib|first3=Ryan D.|last4=Patena|first4=Weronika|last5=Blum|first5=Sean R.|last6=Rodman|first6=Matthew|last7=Ramundo|first7=Silvia|last8=Adams|first8=Christopher M.|last9=Jonikas|first9=Martin C.|date=2017-09-21|title=A Spatial Interactome Reveals the Protein Organization of the Algal CO2-Concentrating Mechanism|journal=Cell|language=English|volume=171|issue=1|pages=133–147.e14|doi=10.1016/j.cell.2017.08.044|issn=0092-8674|pmid=28938113|pmc=5616186|doi-access=free}}</ref> Proteins localized to the pyrenoid include RuBisCO activase,<ref>{{cite journal | last1 = McKay | first1 = R. M. L. | last2 = Gibbs | first2 = S. P. | last3 = Vaughn | first3 = K. C. | year = 1991 | title = RuBisCo activase is present in the pyrenoid of green algae | url = | journal = Protoplasma | volume = 162 | issue = 1| pages = 38–45 | doi = 10.1007/BF01403899 }}</ref> nitrate reductase<ref>{{cite journal | last1 = Lopez-Ruiz | first1 = A. | last2 = Verbelen | first2 = J. P. | last3 = Roldan | first3 = J. M. | last4 = Diez | first4 = J. | year = 1985 | title = Nitrate reductase of green algae is located in the pyrenoid | url = | journal = Plant Physiology | volume = 79 | issue = 4| pages = 1006–1010 | doi = 10.1104/pp.79.4.1006 | pmid = 16664519 | pmc = 1075016 }}</ref> and nitrite reductase.<ref>{{cite journal | last1 = López-Ruiz | first1 = A. | last2 = Verbelen | first2 = J. P. | last3 = Bocanegra | first3 = J. A. | last4 = Diez | first4 = J. | year = 1991 | title = Immunocytochemical localization of nitrite reductase in green algae | url = | journal = Plant Physiology | volume = 96 | issue = 3| pages = 699–704 | doi = 10.1104/pp.96.3.699 | pmid = 16668245 | pmc = 1080833 }}</ref>

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 CO<sub>2</sub>-leakage or to recapture CO<sub>2</sub> that escapes from the pyrenoid.<ref>{{cite journal | last1 = Yamano | first1 = T. | last2 = Tsujikawa | first2 = T. | last3 = Hatano | first3 = K. | last4 = Ozawa | first4 = S. I. | last5 = Takahashi | first5 = Y. | last6 = Fukuzawa | first6 = H. | year = 2010 | title = Light and low-CO<sub>2</sub>-dependent LCIB–LCIC complex localization in the chloroplast supports the carbon-concentrating mechanism in ''Chlamydomonas reinhardtii'' | url = | journal = Plant and Cell Physiology | volume = 51 | issue = 9| pages = 1453–1468 | pmid = 20660228 | doi = 10.1093/pcp/pcq105 }}</ref>

==Role of pyrenoids in the CCM==

[[File:Carbon Concentrating Model for Chlamydomonas.png|thumb|300px| The currently hypothesised composition of the CCM found in ''Chlamydomonas reinhardtii''. 1= Extracellular environment. 2= Plasma membrane.
3= Cytoplasm. 4= Chloroplast membrane. 
5= Stroma. 6= Thylakoid membrane.
7= Thylakoid lumen. 8= Pyrenoid.]]

The confinement of the CO<sub>2</sub>-fixing enzyme into a subcellular micro-compartment, in association with a mechanism to deliver CO<sub>2</sub> to that site, is believed to enhance the efficacy of photosynthesis in an aqueous environment. Having a CCM favours carboxylation over [[photorespiration|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<ref>{{cite journal | pmid = 17557885 | doi=10.1128/EC.00064-07 | volume=6 | title=Proposed carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii | pmc=1951128 | year=2007 | journal=Eukaryot Cell | pages=1251–9  | last1 = Moroney | first1 = JV | last2 = Ynalvez | first2 = RA | issue=8 }}</ref><ref>{{cite journal | pmid = 17291820 | doi=10.1016/j.pbi.2007.01.012 | volume=10 | title=Novel metabolism in Chlamydomonas through the lens of genomics | year=2007 | journal=Curr Opin Plant Biol | pages=190–8  | last1 = Grossman | first1 = AR | last2 = Croft | first2 = M | last3 = Gladyshev | first3 = VN | last4 = Merchant | first4 = SS | last5 = Posewitz | first5 = MC | last6 = Prochnik | first6 = S | last7 = Spalding | first7 = MH | issue=2 }}</ref> considers active transport of bicarbonate from the extracellular environment to the vicinity of RuBisCO, via transporters at the [[cell membrane|plasma membrane]], the [[chloroplast membrane]], and [[thylakoid|thylakoid membranes]]. [[Carbonic anhydrases]] in the periplasm and also in the [[cytoplasm]] and [[stroma (fluid)|chloroplast stroma]] are thought to contribute to maintaining an intracellular pool of dissolved inorganic carbon, mainly in the form of bicarbonate. This bicarbonate is then thought to be pumped into the lumen of transpyrenoidal thylakoids, where a resident carbonic anhydrase is hypothesised to convert bicarbonate to CO<sub>2</sub>, and saturate RuBisCO with carboxylating substrate. It is likely that different algal groups evolved different types of CCMs, but it is generally taken that the algal CCM is articulated around a combination of carbonic anhydrases, inorganic carbon transporters, and some compartment to package RuBisCO.

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 CO<sub>2</sub>-rich environment, the pyrenoid is small and the matrix is unstructured.<ref>{{cite journal | last1 = Rawat | first1 = M. | last2 = Henk | first2 = M. C. | last3 = Lavigne | first3 = L. L. | last4 = Moroney | first4 = J. V. | year = 1996 | title = ''Chlamydomonas reinhardtii'' mutants without ribulose-1, 5-bisphosphate carboxylase-oxygenase lack a detectable pyrenoid | url = | journal = Planta | volume = 198 | issue = 2| pages = 263–270 | doi = 10.1007/BF00206252 }}</ref> 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.<ref>{{cite journal | last1 = Nassoury | first1 = N. | last2 = Wang | first2 = Y. | last3 = Morse | first3 = D. | year = 2005 | title = Brefeldin a inhibits circadian remodeling of chloroplast structure in the dinoflagellate Gonyaulax | url = | journal = Traffic | volume = 6 | issue = 7| pages = 548–561 | pmid = 15941407 | doi = 10.1111/j.1600-0854.2005.00296.x }}</ref>

==Physiology and regulation of the CCM==

The algal CCM is inducible, and induction of the CCM is generally the result of low CO<sub>2</sub> 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 CO<sub>2</sub> in the environment.<ref>{{cite journal | last1 = Brueggeman | first1 = A. J. | last2 = Gangadharaiah | first2 = D. S. | last3 = Cserhati | first3 = M. F. | last4 = Casero | first4 = D. | last5 = Weeks | first5 = D. P. | last6 = Ladunga | first6 = I. | year = 2012 | title = Activation of the carbon concentrating mechanism by CO<sub>2</sub> deprivation coincides with massive transcriptional restructuring in ''Chlamydomonas reinhardtii'' | journal = The Plant Cell | volume = 24 | issue = 5| pages = 1860–1875 | pmid = 22634764 | doi = 10.1105/tpc.111.093435 | pmc = 3442574 }}</ref> Sensing of CO<sub>2</sub> in ''Chlamydomonas'' involves a "master switch", which was co-discovered by two laboratories.<ref>{{cite journal | last1 = Xiang | first1 = Y. | last2 = Zhang | first2 = J. | last3 = Weeks | first3 = D. P. | year = 2001 | title = The Cia5 gene controls formation of the carbon concentrating mechanism in ''Chlamydomonas reinhardtii'' | journal = Proceedings of the National Academy of Sciences | volume = 98 | issue = 9| pages = 5341–5346 | pmid = 11309511 | doi = 10.1073/pnas.101534498 | doi-access = free | pmc = 33211 }}</ref><ref>{{cite journal | last1 = Fukuzawa | first1 = H. | last2 = Miura | first2 = K. | last3 = Ishizaki | first3 = K. | last4 = Kucho | first4 = K. I. | last5 = Saito | first5 = T. | last6 = Kohinata | first6 = T. | last7 = Ohyama | first7 = K. | year = 2001 | title = Ccm1, a regulatory gene controlling the induction of a carbon-concentrating mechanism in ''Chlamydomonas reinhardtii'' by sensing CO<sub>2</sub> availability | journal = Proceedings of the National Academy of Sciences | volume = 98 | issue = 9| pages = 5347–5352 | pmid = 11287669 | doi = 10.1073/pnas.081593498 | doi-access = free | pmc = 33212 }}</ref> This gene, Cia5/Ccm1, affects over 1,000 CO<sub>2</sub>-responsive genes<ref>{{cite journal | last1 = Fang | first1 = W. | last2 = Si | first2 = Y. | last3 = Douglass | first3 = S. | last4 = Casero | first4 = D. | last5 = Merchant | first5 = S. S. | last6 = Pellegrini | first6 = M. | last7 = Spalding | first7 = M. H. | year = 2012 | title = Transcriptome-wide changes in ''Chlamydomonas reinhardtii'' gene expression regulated by carbon dioxide and the CO<sub>2</sub>-concentrating mechanism regulator CIA5/CCM1 | journal = The Plant Cell | volume = 24 | issue = 5| pages = 1876–1893 | pmid = 22634760 | doi = 10.1105/tpc.112.097949 | pmc = 3442575 }}</ref> and also conditions the degree of packing of RuBisCO into the pyrenoid.

==Origin==

The CCM is only induced during periods of low CO<sub>2</sub> levels, and it was the existence of these trigger levels of CO<sub>2</sub> below which CCMs are induced that led researchers to speculate on the likely timing of origin of mechanisms like the pyrenoid.

There are several [[scientific hypothesis|hypotheses]] as to the origin of pyrenoids. With the rise of large terrestrial based flora following the colonisation of land by ancestors of [[charophyceae|Charophyte algae]], CO<sub>2</sub> levels dropped dramatically, with a concomitant increase in O<sub>2</sub> atmospheric concentration. It has been suggested that this sharp fall in CO<sub>2</sub> levels acted as an evolutionary driver of CCM development, and thus gave rise to pyrenoids<ref>{{cite journal | last1 = Badger | first1 = M. R. | last2 = Price | first2 = G. D. | year = 2003 | title = CO<sub>2</sub> concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution | url = | journal = Journal of Experimental Botany | volume = 54 | issue = 383| pages = 609–622 | doi = 10.1016/s0928-0987(02)00244-0 | pmid = 12554074 }}</ref> in doing so ensuring that rate of supply of CO<sub>2</sub> did not become a limiting factor for photosynthesis in the face of declining atmospheric CO<sub>2</sub> levels.

However, alternative hypotheses have been proposed. Predictions of past CO<sub>2</sub> 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|Proterozoic Era]].<ref>{{cite journal | last1 = Riding | first1 = R | year = 2006 | title = Cyanobacterial calcification, carbon dioxide concentrating mechanisms, and Proterozoic–Cambrian changes in atmospheric composition | url = | journal = Geobiology | volume = 4 | issue = 4| pages = 299–316 | doi = 10.1111/j.1472-4669.2006.00087.x }}</ref> 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 CO<sub>2</sub> 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.<ref name =bop />

==Diversity==

Pyrenoids are found in algal lineages,<ref name=king /> irrespective of whether the chloroplast was inherited from a single [[endosymbiotic theory|endosymbiotic event]] (e.g. [[archaeplastida|green and red algae]], but not in [[glaucophytes]]) or multiple endosymbiotic events ([[diatoms]], [[dinoflagellates]], [[coccolithophores]], [[cryptomonad|cryptophytes]], [[chlorarachniophytes]], and [[euglenozoa]]). Some algal groups, however, lack pyrenoids altogether: [[Florideophyceae|"higher" red algae]] and [[Cyanidiophyceae|extremophile red algae]], the green alga genera ''[[Chloromonas]]'' and ''[[Mougeotiopsis]]'',<ref>{{cite journal | pmc=9632326 | date=2022 | last1=Hess | first1=S. | last2=Williams | first2=S. K. | last3=Busch | first3=A. | last4=Irisarri | first4=I. | last5=Delwiche | first5=C. F. | last6=De Vries | first6=S. | last7=Darienko | first7=T. | last8=Roger | first8=A. J. | last9=Archibald | first9=J. M. | last10=Buschmann | first10=H. | last11=von Schwartzenberg | first11=K. | last12=De Vries | first12=J. | title=A phylogenomically informed five-order system for the closest relatives of land plants | journal=Current Biology  | volume=32 | issue=20 | pages=4473–4482.e7 | doi=10.1016/j.cub.2022.08.022 | pmid=36055238 | bibcode=2022CBio...32E4473H }}</ref> and "[[golden algae]]". Pyrenoids are usually considered to be poor [[taxonomy (biology)|taxonomic markers]] and may have evolved independently many times.<ref>{{cite journal|pmid=23345319 |date=2013 |last1=Meyer |first1=M. |last2=Griffiths |first2=H. |title=Origins and diversity of eukaryotic CO2-concentrating mechanisms: Lessons for the future |journal=Journal of Experimental Botany |volume=64 |issue=3 |pages=769–786 |doi=10.1093/jxb/ers390 }}.</ref>

==References==
{{Reflist}}

{{Protist}}

[[Category:Algae]]