A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii.
Journal
The Plant cell
ISSN: 1532-298X
Titre abrégé: Plant Cell
Pays: England
ID NLM: 9208688
Informations de publication
Date de publication:
01 09 2023
01 09 2023
Historique:
received:
08
12
2022
accepted:
07
04
2023
medline:
4
9
2023
pubmed:
17
5
2023
entrez:
17
5
2023
Statut:
ppublish
Résumé
Phase separation underpins many biologically important cellular events such as RNA metabolism, signaling, and CO2 fixation. However, determining the composition of a phase-separated organelle is often challenging due to its sensitivity to environmental conditions, which limits the application of traditional proteomic techniques like organellar purification or affinity purification mass spectrometry to understand their composition. In Chlamydomonas reinhardtii, Rubisco is condensed into a crucial phase-separated organelle called the pyrenoid that improves photosynthetic performance by supplying Rubisco with elevated concentrations of CO2. Here, we developed a TurboID-based proximity labeling technique in which proximal proteins in Chlamydomonas chloroplasts are labeled by biotin radicals generated from the TurboID-tagged protein. By fusing 2 core pyrenoid components with the TurboID tag, we generated a high-confidence pyrenoid proxiome that contains most known pyrenoid proteins, in addition to new pyrenoid candidates. Fluorescence protein tagging of 7 previously uncharacterized TurboID-identified proteins showed that 6 localized to a range of subpyrenoid regions. The resulting proxiome also suggests new secondary functions for the pyrenoid in RNA-associated processes and redox-sensitive iron-sulfur cluster metabolism. This developed pipeline can be used to investigate a broad range of biological processes in Chlamydomonas, especially at a temporally resolved suborganellar resolution.
Identifiants
pubmed: 37195994
pii: 7169368
doi: 10.1093/plcell/koad131
pmc: PMC10473203
doi:
Substances chimiques
Proteome
0
Carbon Dioxide
142M471B3J
Ribulose-Bisphosphate Carboxylase
EC 4.1.1.39
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3260-3279Subventions
Organisme : Medical Research Council
ID : MR/T020679/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/T017589/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S015337/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R001014/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/X003035/1
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.
Déclaration de conflit d'intérêts
Conflict of interest statement. None declared.
Références
Science. 2013 Mar 15;339(6125):1328-1331
pubmed: 23371551
J Cell Sci. 2015 Nov 15;128(22):4210-9
pubmed: 26449969
Nucleic Acids Res. 2000 Jan 1;28(1):292
pubmed: 10592250
Mol Biol Cell. 2016 Apr 15;27(8):1188-96
pubmed: 26912792
Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):E2453-61
pubmed: 24927568
Nat Plants. 2020 Dec;6(12):1480-1490
pubmed: 33230314
Mol Cell. 2017 Oct 5;68(1):144-157.e5
pubmed: 28965817
Plant Cell. 2012 May;24(5):1860-75
pubmed: 22634764
Elife. 2015 Jan 13;4:
pubmed: 25584625
Cell. 2017 Sep 21;171(1):148-162.e19
pubmed: 28938114
New Phytol. 2018 Jan;217(1):54-61
pubmed: 28833179
Elife. 2019 Sep 19;8:
pubmed: 31535972
Plant Cell Physiol. 2010 Sep;51(9):1453-68
pubmed: 20660228
Nat Biotechnol. 2019 Dec;37(12):1435-1445
pubmed: 31792412
Nat Commun. 2020 Dec 9;11(1):6303
pubmed: 33298923
Plant Cell. 2012 May;24(5):1876-93
pubmed: 22634760
Nat Rev Mol Cell Biol. 2017 May;18(5):285-298
pubmed: 28225081
Plant Physiol. 1998 Apr;116(4):1585-91
pubmed: 9536077
Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19474-9
pubmed: 23112177
Plant Physiol. 2022 Feb 4;188(2):756-768
pubmed: 34662401
Nat Plants. 2022 May;8(5):583-595
pubmed: 35596080
Mol Cell. 2018 Feb 1;69(3):517-532.e11
pubmed: 29395067
ACS Infect Dis. 2018 Jun 8;4(6):918-925
pubmed: 29708735
Cell. 2017 Sep 21;171(1):133-147.e14
pubmed: 28938113
Biochemistry. 2014 Sep 23;53(37):5834-47
pubmed: 25153801
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Elife. 2021 Feb 16;10:
pubmed: 33591270
Curr Opin Neurobiol. 2018 Jun;50:17-23
pubmed: 29125959
Nat Commun. 2019 Jul 19;10(1):3252
pubmed: 31324801
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Plant Physiol. 2022 Oct 27;190(3):1609-1627
pubmed: 35961043
Mol Biol Evol. 2012 Dec;29(12):3625-39
pubmed: 22826458
Plant Cell. 2016 Feb;28(2):367-87
pubmed: 26764374
ACS Synth Biol. 2018 Sep 21;7(9):2074-2086
pubmed: 30165733
Sci Adv. 2020 Nov 11;6(46):
pubmed: 33177094
Proc Natl Acad Sci U S A. 2016 May 24;113(21):5958-63
pubmed: 27166422
Cell Chem Biol. 2020 Jul 16;27(7):858-865.e8
pubmed: 32470320
Plant Cell. 2021 May 31;33(4):1161-1181
pubmed: 33723601
Nat Commun. 2018 Nov 29;9(1):5076
pubmed: 30498228
Plant J. 2015 May;82(3):504-522
pubmed: 25660108
J Exp Bot. 2015 Aug;66(15):4551-66
pubmed: 26022256
Mol Microbiol. 2012 Sep;85(5):996-1006
pubmed: 22809289
J Cell Biol. 2008 Aug 25;182(4):641-6
pubmed: 18710928
Annu Rev Cell Dev Biol. 2014;30:39-58
pubmed: 25288112
Nucleic Acids Res. 2018 Jul 27;46(13):6909-6919
pubmed: 30053227
Antioxidants (Basel). 2021 Oct 29;10(11):
pubmed: 34829609
Plant Physiol. 2020 Apr;182(4):1883-1893
pubmed: 32041908
Free Radic Biol Med. 2021 Dec;177:287-298
pubmed: 34748908
Biochem J. 2016 Aug 15;473(16):2463-9
pubmed: 27274088
Elife. 2021 Dec 22;10:
pubmed: 34936552
Nat Struct Mol Biol. 2014 Feb;21(2):143-51
pubmed: 24389466
Photosynth Res. 2021 Feb;147(2):177-195
pubmed: 33280076
Nat Rev Methods Primers. 2021;1:
pubmed: 34549195
Plant Cell. 2019 Dec;31(12):3057-3072
pubmed: 31591163
J Cell Biol. 2012 Mar 19;196(6):801-10
pubmed: 22412018
Genome Biol. 2002;3(2):REVIEWS3003
pubmed: 11864377
Front Physiol. 2017 Jan 20;8:5
pubmed: 28163686
PLoS One. 2013 Jun 19;8(6):e66428
pubmed: 23840465
Elife. 2018 Oct 11;7:
pubmed: 30306890
Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489
pubmed: 33237286
Methods Mol Biol. 2011;714:15-29
pubmed: 21431732
Nat Methods. 2015 Jan;12(1):51-4
pubmed: 25419960
Plant J. 2011 Jun;66(5):770-80
pubmed: 21309872
Curr Opin Chem Biol. 2021 Feb;60:30-38
pubmed: 32801087
Biochim Biophys Acta Mol Cell Res. 2021 Apr;1868(5):118949
pubmed: 33421532
Plant J. 2015 May;82(3):429-448
pubmed: 25765072
Nat Genet. 2019 Apr;51(4):627-635
pubmed: 30886426
Nat Biotechnol. 2018 Oct;36(9):880-887
pubmed: 30125270
FEBS Lett. 1977 Dec 1;84(1):149-52
pubmed: 590515
Proc Natl Acad Sci U S A. 2019 Sep 10;116(37):18445-18454
pubmed: 31455733
PLoS One. 2018 Feb 26;13(2):e0185039
pubmed: 29481573
Annu Rev Biophys. 2020 May 6;49:107-133
pubmed: 32004090