Abstract
Carbon concentrating mechanism (CCM) and photorespiration (PR) are interlinked and co-regulated in Chlamydomonas reinhardtii, but conditions where co-regulation alters are not sufficiently explored. Here, we uncover that PR gene transcripts, like CCM transcripts, are induced even in the dark when both processes are not active. Such diurnal cycles show that transcript levels peak in the middle of 12 h day, decline by early part of 12-h dark followed by their onset again at mid-dark. Interestingly, the onset in the mid-dark phase is sensitive to high CO2, implying that the active carbon sensing mechanism operates even in the dark. The rhythmic alterations of both CCM and PR transcript levels are unlinked to circadian clock: the “free-running state” reveals no discernible rhythmicity in transcript changes. Only continuous light leads to high transcript levels but no detectable transcripts were observed in continuous dark. Asynchronous continuous light cultures, upon shifting to low from high CO2 exhibit only transient induction of PR transcripts/proteins while CCM transcript induction is stable, indicating the loss of co-regulation between PR and CCM gene transcription. Lastly, we also describe that both CCM and PR transcripts/proteins are induced in low CO2 even in mixotrophic cultures, but only in high light, the same being attenuated in high CO2, implying that high light is a mandatory “trigger” for CCM and PR induction in low CO2 mixotrophy. Our study provides comprehensive analyses of conditions where CCM and PR were differently regulated, setting a paradigm for a detailed mechanistic probing of these responses.
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Abbreviations
- AAT1:
-
Alanine:α-ketoglutarate aminotransf erase
- CAH3:
-
Carbonic anhydrase 3
- CCM:
-
Carbon concentrating mechanism
- CCP1:
-
Chloroplast carrier protein 1
- D1:
-
Photosystem II protein D1
- GDCH:
-
Glycine decarboxylase H protein
- GDH:
-
Glycolate dehydrogenase
- HPR:
-
Hydroxypyruvate reductase
- LCIB:
-
Low CO2 inducible membrane protein
- LCI1:
-
Low CO2 inducible membrane protein
- LHCSR3:
-
Light harvesting complex stress-related chlorophyll a/b binding protein
- PGP1:
-
Phosphoglycolate phosphatase
- PR:
-
Photorespiration
- RuBisCO:
-
Ribulose-1,5-bisphosphate carboxylase-oxygenase
- SGAT:
-
Serine:glyoxylate aminotransferase
- TAP medium:
-
Tris acetate phosphate medium
TP medium
Tris phosphate medium
References
Ashworth J, Coesel S, Lee A, Armbrust EV, Orellana MV, Baliga NS (2013) Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc Natl Acad Sci U S A 110:7518–7523. https://doi.org/10.1073/pnas.1300962110
Atkinson N, Feike D, Mackinder LCM, Meyer MT, Griffiths H, Jonikas MC, Smith AM, Mc Cormick AJ (2016) Introducing an algal carbon concentrating mechanism into higher plants: location and incorporation of key components. Plant Biotechnol J 14:1302–1315. https://doi.org/10.1111/pbi.12497
Badger MR, John Andrews T, Whitney S, Ludwig M, Yellowlees DC, Leggat W, Dean Price G (1998) The diversity and coevolution of Rubisco, plastids, pyrenoids, and chloroplast-based CO 2 -concentrating mechanisms in algae 1. 76:1052–1071. doi: https://doi.org/10.1139/b98-074
Bauwe H, Hagemann M, Fernie AR (2010) Photorespiration: players, partners and origin. Trends Plant Sci 15:330–336. https://doi.org/10.1016/j.tplants.2010.03.006
Bauwe H, Hagemann M, Kern R, Timm S (2012) Photorespiration has a dual origin and manifold links to central metabolism. Curr Opin Plant Biol 15:269–275. https://doi.org/10.1016/j.pbi.2012.01.008
Becker B (2013) Snow ball earth and the split of Streptophyta and Chlorophyta. Trends Plant Sci 18:180–183. https://doi.org/10.1016/j.tplants.2012.09.010
Beezley BB, Gruber PJ, Frederick SE (1976) Cytochemical localization of Glycolate dehydrogenase in mitochondria of Chlamydomonas. Plant Physiol 58:315–319. https://doi.org/10.1104/pp.58.3.315
Bernstein E (1960) Synchronous division in Chlamydomonas moewusii. Science 131:1528–1529. https://doi.org/10.1126/science.131.3412.1528
Blackwell RD, Murray AJS, Lea PJ, Kendall AC, Hall NP, Turner JC, Wallsgrove RM (1988) The value of mutants unable to carry out photorespiration. Photosynth Res 16:155–176. https://doi.org/10.1007/BF00039491
Blasing OE (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. the Plant Cell Online 17:3257–3281. https://doi.org/10.1105/tpc.105.035261
Buchanan BB (1980) Role of light in the regulation of chloroplastic enzyms. Annu Rev Plant Physiol 31:341–374. https://doi.org/10.1146/annurev.pp.31.060180.002013
Chaudhari VR, Vyawahare A, Bhattacharjee SK, Rao BJ (2015) Enhanced excision repair and lack of PSII activity contribute to higher UV survival of Chlamydomonas reinhardtii cells in dark. Plant Physiol Biochem 88:60–69. https://doi.org/10.1016/j.plaphy.2015.02.001
Chen ZY, Burow MD, Mason CB, Moroney JV (1996) A low-CO2-inducible gene encoding an alanine: alpha-ketoglutarate aminotransferase in Chlamydomonas reinhardtii. Plant Physiol 112(2):677–684
Cross FR, Umen JG (2015) The Chlamydomonas cell cycle. Plant J 82:370–392. https://doi.org/10.1111/tpj.12795
Duanmu D, Miller AR, Horken KM, Weeks DP, Spalding MH (2009) Knockdown of limiting- CO2 –induced gene HLA3 decreases HCO 3- transport and photosynthetic Ci affinity in Chlamydomonas reinhardtii. doi: https://doi.org/10.1073/pnas.0812885106
Eisenhut M, Ruth W, Haimovich M, Bauwe H, Kaplan A, Hagemann M (2008) The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants. Proc Natl Acad Sci U S A 105:17199–17204. https://doi.org/10.1073/pnas.0807043105
Espinoza C, Degenkolbe T, Caldana C, Zuther E, Leisse A, Willmitzer L, Hincha DK, Hannah MA (2010) Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in arabidopsis. PLoS One 5:e14101. https://doi.org/10.1371/journal.pone.0014101
Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH (2012) Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell 24:1876–1893. https://doi.org/10.1105/tpc.112.097949
Fernie AR, Bauwe H, Eisenhut M, Florian A, Hanson DT, Hagemann M, Keech O, Mielewczik M, Nikoloski Z, Peterhänsel C, Roje S, Sage R, Timm S, von Cammerer S, Weber APM, Westhoff P (2013) Perspectives on plant photorespiratory metabolism. Plant Biol 15:748–753. https://doi.org/10.1111/j.1438-8677.2012.00693.x
Foyer CH, Bloom AJ, Queval G, Noctor G (2009) Photorespiratory metabolism: genes, mutants, energetics, and redox signaling. Annu Rev Plant Biol 60:455–484. https://doi.org/10.1146/annurev.arplant.043008.091948
Foyer CH, Neukermans J, Queval G, Noctor G, Harbinson J (2012) Photosynthetic control of electron transport and the regulation of gene expression. J Exp Bot 63:1637–1661. https://doi.org/10.1093/jxb/ers013
Fujiwara S, Ishida N, Tsuzuki M (1996) Circadian expression of the carbonic anhydrase gene, Cah1, in Chlamydomonas reinhardtii. Plant Mol Biol 32:745–749. https://doi.org/10.1007/BF00020215
Fukuzawa H, Miura K, Ishizaki K, Kucho KI, Saito T, Kohinata T, Ohyama K (2001) Ccm1, a regulatory gene controlling the induction of a carbon-concentrating mechanism in Chlamydomonas reinhardtii by sensing CO2 availability. Proc Natl Acad Sci U S A 98:5347–5352. https://doi.org/10.1073/pnas.081593498
Gao H, Wang Y, Fei X, Wright DA, Spalding MH (2015) Expression activation and functional analysis of HLA3, a putative inorganic carbon transporter in Chlamydomonas reinhardtii. 1–11. doi: https://doi.org/10.1111/tpj.12788
Geiger DR, Servaites JC (1994) Diurnal regulation of photosynthetic carbon metabolism in C3 plants. Ann Rev Plant Physiol Plant Mol Biol 45:235–256. https://doi.org/10.1146/annurev.pp.45.060194.001315
Goldschmidt M, Rochaix JD (2006) EMBO Practical Course: Molecular Genetics of Chlamydomonas
Gorman SD, Levine RP, Gorman DS, Levine RP (1965) Cytochrome f and plastocyanin: their sequence in the photosynthetic electron transport chain of Chlamydomonas reinhardi. Proc Natl Acad Sci 54:1665–1669. https://doi.org/10.1073/pnas.54.6.1665
Govindjee DS (2011) Adventures with cyanobacteria: a personal perspective. Front Plant Sci 2:28. https://doi.org/10.3389/fpls.2011.00028
Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science (New York, NY) 290:2110–2113. https://doi.org/10.1126/science.290.5499.2110
Howell SH, Walker LL (1977) Transcription of the nuclear and chloroplast genomes during the vegetative cell cycle in Chlamydomonas reinhardi. Dev Biol 56:11–23. https://doi.org/10.1016/0012-1606(77)90151-8
Johnson CH, Stewart PL, Egli M (2011) The Cyanobacterial circadian system: from biophysics to bioevolution. Annu Rev Biophys 40:143–167. https://doi.org/10.1146/annurev-biophys-042910-155317
Kasting JF (1987) Theoretical constraints on oxygen and carbon dioxide concentrations in the Precambrian atmosphere. Precambrian Res 34:205–229. https://doi.org/10.1016/0301-9268(87)90001-5
Kinmonth-Schultz HA, Golembeski GS, Imaizumi T (2013) Circadian clock-regulated physiological outputs: dynamic responses in nature. Semin Cell Dev Biol 24:407–413. https://doi.org/10.1016/j.semcdb.2013.02.006
Kozaki A, Takeba G (1996) Photorespiration protects C3 plants from photooxidation. Nature 384:557–560. https://doi.org/10.1038/384557a0
Matsuo T, Ishiura M (2010) New insights into the circadian clock in chlamydomonas. Int Rev Cell Mol Biol 280:281–314. https://doi.org/10.1016/S1937-6448(10)80006-1
McClung CR, Hsu M, Painter JE, Gagne JM, Karlsberg SD, Salomé PA (2000) Integrated temporal regulation of the photorespiratory pathway. Circadian regulation of two Arabidopsis genes encoding serine hydroxymethyltransferase. Plant Physiol 123:381–392. https://doi.org/10.1104/pp.123.1.381
Mitchell MC, Meyer MT, Griffiths H (2014) Dynamics of carbon-concentrating mechanism induction and protein relocalization during the dark-to-light transition in synchronized Chlamydomonas reinhardtii. Plant Physiol 166:1073–1082. https://doi.org/10.1104/pp.114.246918
Mittag M, Kiaulehn S, Johnson CH (2005) Update on the circadian clock in Chlamydomonas reinhardtii. Plant Physiol 137:399–409. https://doi.org/10.1104/pp.104.052415
Miura K, Yamano T, Yoshioka S, Kohinata T, Inoue Y (2004) Expression Profiling-Based Identification of CO 2 -Responsive Genes Regulated by CCM1 Controlling a Carbon-Concentrating Mechanism in Chlamydomonas reinhardtii 1. 135:1595–1607. doi: https://doi.org/10.1104/pp.104.041400.1
Monnier A, Liverani S, Bouvet R, Jesson B, Smith JQ, Mosser J, Corellou F, Bouget F-Y (2010) Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles. BMC Genomics 11:192. https://doi.org/10.1186/1471-2164-11-192
Moroney JV, Wilson BJ, Tolbert NE (1986) Glycolate metabolism and excretion by Chlamydomonas reinhardtii. Plant Physiol 82:821–826. https://doi.org/10.1104/pp.82.3.821
Moroney JV, Husic HD, Tolbert NE, Kitayama M, Manuel LJ, Togasaki RK (1989) Isolation and characterization of a mutant of Chlamydomonas reinhardtii deficient in the CO2 concentrating mechanism. Plant Physiol 89:897–903. https://doi.org/10.1104/pp.89.3.897
Moroney JV, Jungnick N, DiMario RJ, Longstreth DJ (2013) Photorespiration and carbon concentrating mechanisms: two adaptations to high O2, low CO2 conditions. Photosynth Res 117:121–131. https://doi.org/10.1007/s11120-013-9865-7
Nakamura Y, Kanakagiri S, Van K, He W, Spalding MH (2005) Disruption of the glycolate dehydrogenase gene in the high-CO 2 -requiring mutant HCR89 of Chlamydomonas reinhardtii. Can J Bot 83:820–833. https://doi.org/10.1139/b05-067
Nelson B, Tolbert NE (1970) Glycolate Dehydrogenase in Green Algae. Arch Biochem Biophys 141:102–110. https://doi.org/10.1016/0003-9861(70)90112-8
Nisbet EG, Grassineau NV, Howe CJ, Abell PI, Regelous M, Nisbet RER (2007) The age of Rubisco: the evolution of oxygenic photosynthesis. Geobiology 5:311–335. https://doi.org/10.1111/j.1472-4669.2007.00127.x
Polukhina I, Fristedt R, Dinc E, Cardol P, Croce R (2016) Carbon supply and Photoacclimation cross talk in the green alga Chlamydomonas reinhardtii. Plant Physiol 172:1494–1505. https://doi.org/10.1104/pp.16.01310
Queval G, Foyer CH (2012) Redox regulation of photosynthetic gene expression. Philos Trans R Soc Lond Ser B Biol Sci 367:3475–3485. https://doi.org/10.1098/rstb.2012.0068
Rawat M, Moroney JV (1995) The regulation of carbonic anhydrase and Ribulose-1,5-Bisphosphate carboxylase/Oxygenase Activase by light and CO2 in Chlamydomonas reinhardtii. Plant Physiol 109:937–944
Reddy AB, Rey G (2014) Metabolic and nontranscriptional circadian clocks: eukaryotes. Annu Rev Biochem 83:165–189. https://doi.org/10.1146/annurev-biochem-060713-035623
Ruts T, Matsubara S, Wiese-Klinkenberg A, Walter A (2012) Diel patterns of leaf and root growth: endogenous rhythmicity or environmental response? J Exp Bot 63:3339–3351. https://doi.org/10.1093/jxb/err334
Sage RF (2004) The evolution of C 4 photosynthesis. New Phytol 161:341–370. https://doi.org/10.1046/j.1469-8137.2004.00974.x
Sage RF, Sage TL, Kocacinar F (2012) Photorespiration and the evolution of C 4 photosynthesis. Annu Rev Plant Biol 63:19–47. https://doi.org/10.1146/annurev-arplant-042811-105511
Sanders MA, Salisbury JL (1995) Immunofluorescence microscopy of cilia and flagella. Meth Cell Biol 47:163–169. https://doi.org/10.1016/S0091-679X(08)60805-5
Somerville CR, Ogren WL (1982) Genetic modification of photorespiration. Trends Biochem Sci 7:171–174. https://doi.org/10.1016/0968-0004(82)90130-X
Soon Im C, Grossman AR (2002) Identification and regulation of high light-induced genes in Chlamydomonas reinhardtii. Plant J 30:301–313. https://doi.org/10.1046/j.1365-313X.2001.01287.x
Spalding MH (1989) Photosynthesis and photorespiration in freshwater green algae. Aquat Bot 34:181–209. https://doi.org/10.1016/0304-3770(89)90056-9
Suzuki K, Marek LF, Spalding MH (1990) A Photorespiratory mutant of Chlamydomonas reinhardtii. Plant Physiol 93:231–237. https://doi.org/10.1104/pp.93.1.231
Thines B, Harmon FG, Li J, Chua N-H (2010) Four easy pieces: mechanisms underlying circadian regulation of growth and development this review comes from a themed issue on growth and development edited. Curr Opin Plant Biol 14:31–37. https://doi.org/10.1016/j.pbi.2010.09.009
Timm S, Florian A, Arrivault S, Stitt M, Fernie AR, Bauwe H (2012) Glycine decarboxylase controls photosynthesis and plant growth. FEBS Lett 586:3692–3697. https://doi.org/10.1016/j.febslet.2012.08.027
Timm S, Florian A, Wittmiß M, Jahnke K, Hagemann M, Fernie AR, Bauwe H (2013) Serine acts as a metabolic signal for the transcriptional control of photorespiration-related genes in Arabidopsis. Plant Physiol 162:379–389. https://doi.org/10.1104/pp.113.215970
Tirumani S, Kokkanti M, Chaudhari V, Shukla M, Rao BJ (2014) Regulation of CCM genes in Chlamydomonas reinhardtii during conditions of light-dark cycles in synchronous cultures. Plant Mol Biol 85:277–286. https://doi.org/10.1007/s11103-014-0183-z
Tolbert NE (1997) The C 2 oxidative photosynthetic carbon cycle. Annu Rev Plant Physiol Plant Mol Biol 48:1–25. https://doi.org/10.1146/annurev.arplant.48.1.1
Tolbert NE, Harrison M, Selph N (1983) Aminooxyacetate stimulation of glycolate formation and excretion by chlamydomonas. Plant Physiol 72:1075–1083
Tripathi U, Sarada R, Ravishankar GA (2001) A culture method for microalgal forms using two-tier vessel providing carbon-dioxide environment: studies on growth and carotenoid production. World J Microbiol Biotechnol 17:325–329. https://doi.org/10.1023/A:1016682120171
Tural B, Moroney JV (2005) Regulation of the expression of photorespiratory genes in Chlamydomonas reinhardtii. Can J Bot 83:810–819. https://doi.org/10.1139/b05-066
Wingler A, Lea PJ, Quick WP, Leegood RC (2000) Photorespiration: metabolic pathways and their role in stress protection. Philos Trans R Soc Lond Ser B Biol Sci 355:1517–1529. https://doi.org/10.1098/rstb.2000.0712
Xiang Y, Zhang J, Weeks DP (2001) The Cia5 gene controls formation of the carbon concentrating mechanism in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 98:5341–5346. https://doi.org/10.1073/pnas.101534498
Xie X, Huang A, Gu W, Zang Z, Pan G, Gao S, He L, Zhang B, Niu J, Lin A, Wang G (2016) Photorespiration participates in the assimilation of acetate in Chlorella sorokiniana under high light. New Phytol 209:987–998. https://doi.org/10.1111/nph.13659
Yamano T, Miura K, Fukuzawa H (2008) Expression analysis of genes associated with the induction of the carbonconcentrating mechanism in Chlamydomonas reinhardtii. Plant Physiol 147:340–354. https://doi.org/10.1104/pp.107.114652
Yamano T, Sato E, Iguchi H, Fukuda Y, Fukuzawa H, Buchanan BB (2015) Characterization of cooperative bicarbonate uptake into chloroplast stroma in the green alga Chlamydomonas reinhardtii. doi: https://doi.org/10.1073/pnas.1501659112
Zelitch I, Schultes NP, Peterson RB, Brown P, Brutnell TP (2009) High glycolate oxidase activity is required for survival of maize in normal air. Plant Physiol 149:195–204. https://doi.org/10.1104/pp.108.128439
Zhong HH, Young JC, Pease EA., Hangarter RP, McClung CR (1994) Interactions between Light and the Circadian Clock in the Regulation of CAT2 Expression in Arabidopsis Plant physiology 104:889–898
Acknowledgements
This work was supported by J.C. Bose Fellowship Grant, DST (10X-217) and Department of Atomic Energy Grant, Government of India (12P0123) to Prof. Basuthkar Jagadeeshwar Rao. We also thank Soumajit Saha for his help in microscopy imaging and valuable inputs throughout the project.
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BJ and TS conceived and designed the research. TS conducted the experiments. BJ contributed new reagents or analytical tools. BJ, TS, and KM analyzed the data. BJ wrote the manuscript. All authors read and approved the manuscript.
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Tirumani, S., Gothandam, K. & J Rao, B. Coordination between photorespiration and carbon concentrating mechanism in Chlamydomonas reinhardtii: transcript and protein changes during light-dark diurnal cycles and mixotrophy conditions. Protoplasma 256, 117–130 (2019). https://doi.org/10.1007/s00709-018-1283-4
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DOI: https://doi.org/10.1007/s00709-018-1283-4