Table 1.
Summary of Chlamydomonas pyrenoid–specific proteins whose localization has been confirmed.
| Protein name | Gene ID | Subpyrenoid localization | Localization reference | Reported or predicted functions | |
|---|---|---|---|---|---|
| ABCF6 | Cre06.g271850 | Matrix | ① | Lau et al. (2023) | Predicted ATP-binding cassette family F like protein |
| CPLD2 | Cre03.g206550 | Matrix | ① | Wang et al. (2022) | Homolog of the Arabidopsis XuBP phosphatase CbbY (At3g48420) |
| EPYC1/ LCI5 |
Cre10.g436550 | Matrix | ① | Mackinder et al. (2016) | Rubisco linker, phase-separates with Rubisco to form the pyrenoid matrix |
| HDA5 | Cre06.g290400 | Matrix | ① | Wang et al. (2022) | Predicted histone deacetylase |
| rbcL | CreCp.g802313 | Matrix | ① | Holdsworth (1971); Mackinder et al. (2017) | Large and small subunits of the Rubisco holoenzyme, which fixes CO2 and produces 3-PG and 2-PG |
| RBCS1 | Cre02.g120100 | ||||
| RBCS2 | Cre02.g120150 | ||||
| RCA1 | Cre04.g229300 | Matrix | ① | Vladimirova et al. (1982); Lacoste-Royal (1987); McKay et al. (1991); Mackinder et al. (2017) | Rubisco activase |
| STR16 | Cre13.g573250 | Matrix | ① | Wang et al. (2022); Lau et al. (2023) | Predicted thiosulfate sulfurtransferase containing a rhodanese domain |
| STR18 | Cre16.g663150 | Matrix | ① | Wang et al. (2022); Lau et al. (2023) | Predicted thiosulfate sulfurtransferase containing a rhodanese domain |
| – | Cre16.g648400 | Matrix | ① | Wang et al. (2022) | – |
| – | Cre02.g143635 | Matrix | ① | Wang et al. (2022) | – |
| CAH3 | Cre09.g415700 | Tubules | ② | Sinetova et al. (2012) | Alpha-type carbonic anhydrase |
| CAS1 | Cre12.g497300 | Tubules | ② | Wang et al. (2016) | Calcium-mediated regulator of the expression of some CCM-related genes |
| CYN7 | Cre12.g544150 | Tubules | ② | Wang et al. (2022) | Predicted peptidyl-prolyl cis-trans isomerase |
| CYN20-6 | Cre12.g544114 | Tubules | ② | Wang et al. (2022) | Predicted peptidyl-prolyl cis-trans isomerase |
| DEG8 | Cre01.g028350 | Tubules | ② | Wang et al. (2022) | Predicted DegP-type protease, Arabidopsis homolog is involved in the degradation of photodamaged PSII reaction center protein D1 |
| HCF136 | Cre06. g273700 | Tubules | ② | Wang et al. (2022) | PS II stability/assembly factor HCF136 |
| PSAH | Cre07. g330250 | Tubules | ② | Mackinder et al. (2017) | PSI subunit |
| PSBP1 | Cre12.g550850 | Tubules | ② | Wang et al. (2022) | Predicted oxygen-evolving enhancer protein 2 of PS II |
| RBMP1 | Cre06. g261750 | Tubules | ② | Meyer et al. (2020b) | Proposed to mediate pyrenoid matrix connection to tubules |
| TEF14 | Cre06.g256250 | Tubules | ② | Wang et al. (2022) | Predicted thylakoid-luminal protein, no labeled domains |
| - | Cre03.g172700 | Tubules | ② | Lau et al. (2023) | Protein with multiple predicted Rubisco-binding motifs |
| CGLD14 | Cre10.g446350 | Pyrenoid center (reticulated region) | ⑤ | Wang et al. (2022) | PSBP domain-containing protein 3, conserved in the green lineage and diatoms |
| PNU1 | Cre03.g183550 | Pyrenoid center (reticulated region) | ⑤ | Wang et al. (2022) | PROTEIN F23H11.5, has a bifunctional nuclease domain |
| RBMP2 | Cre09.g416850 | Tubules (reticulated region) | ⑤ | Meyer et al. (2020b) | Proposed to mediate pyrenoid matrix connection to tubules |
| PSBP4 | Cre08.g362900 | Thylakoid lumen puncta | ⑨ | Mackinder et al. (2017) | Luminal PsbP-like protein, Arabidopsis homolog is essential for PS I assembly and function |
| SAGA1 | Cre11.g467712 | Puncta surrounding the matrix | ④ | Itakura et al. (2019); Meyer et al. (2020b) | Proposed to mediate adherence of the starch sheath to the matrix |
| SAGA2 | Cre09.g394621 | Interface between matrix and starch sheath | ④ | Meyer et al. (2020b) | Proposed to mediate adherence of the starch sheath to the matrix |
| SMC7 | Cre17.g720450 | Puncta surrounding the matrix | ④ | Lau et al. (2023) | Proposed to have a similar function as SAGA1 |
| SBE3 | Cre10.g444700 | Starch sheath | ③ | Mackinder et al. (2017) | Conserved starch-branching enzyme |
| STA2 | Cre17.g721500 | Starch sheath | ③ | Mackinder et al. (2017) | Granule-bound starch synthase involved in amylose biosynthesis and the biosynthesis of long chains in amylopectin |
| – | Cre09.g394547 | Starch sheath | ③ | Wang et al. (2022) | Predicted cyclomaltodextrin glucanotransferase/cyclodextrin glycosyltransferase |
| – | Cre09.g415600 | Starch sheath | ③ | Wang et al. (2022) | Predicted glucan 1,4-alpha-glucosidase/Lysosomal alpha-glucosidase; has a starch-binding domain |
| LCI9 | Cre09.g394473 | Gaps between starch plates | ⑦ | Mackinder et al. (2017) | Contains 2 starch-binding domains; may help ensure a close fit for adjacent starch plates |
| LCIB | Cre10.g452800 | Gaps between starch plates and tubules (very low CO2) | ⑧ | Yamano et al. (2010); Wang and Spalding (2014b); Mackinder et al. (2017) | Beta-type carbonic anhydrase |
| LCIC | Cre06.g307500 | Gaps between starch plates and tubules (very low CO2) | ⑧ | Yamano et al. (2010); Mackinder et al. (2017) | Beta-type carbonic anhydrase |
| – | Cre09.g394510 | Starch-matrix interface and gaps between starch plates | ④⑦⑧ | Lau et al. (2023) | Contains a CBM20 starch-binding domain and a t-SNARE domain; proposed to be involved in membrane remodeling of the pyrenoid tubules; could be involved in membrane remodeling of the pyrenoid tubules |
| MDH1 | Cre03.g194850 | Pyrenoid periphery | – | Wang et al. (2022) | Malate dehydrogenase |
| MIND1 | Cre12.g522950 | Pyrenoid periphery | – | Wang et al. (2022) | Homolog of the Arabidopsis chloroplast division site regulator MinD1 |
The circled numbers indicating the subpyrenoid localizations are coordinated with the circled numbers in Fig. 1C.