Physiological and molecular evidence for phycobilisome degradation in maintaining carbon and nitrogen balance of cyanobacteria

Abstract

Phycobilisomes (PBS), the primary light-harvesting complexes in cyanobacteria, are degraded under nitrogen starvation to provide nitrogen for cell growth. This study reveals that carbon supply is a critical prerequisite for PBS degradation under nitrogen deficiency in Synechococcus sp. PCC 7002. Even under nitrogen-deficient conditions, PBS degradation is inhibited in the absence of sufficient carbon. We demonstrate that both the nblAB-mediated PBS-degradation pathway and the ccmLMNK operon-mediated CO₂-concentrating mechanism are essential for PBS degradation. Furthermore, our findings highlight the critical role of PBS degradation in cyanobacterial adaptation to high C/N conditions. Mutant strains (Mut-nblA and Mut-nblB) deficient in PBS degradation exhibited impaired adaptation to high C/N conditions, as evidenced by their inability to thrive in high NaHCO₃ (nitrogen-free) or CO₂ (low-nitrogen) environments. While these mutants displayed a greener phenotype under high C/N conditions compared to the wild type, they exhibited extensive cellular damage, and significant downregulation of photosynthesis-related genes. These results provide novel insights into the carbon-dependent regulation of PBS degradation and its essential role in cyanobacterial C/N balance, highlighting its significance for their adaptation to fluctuating environmental conditions.

Keywords

Cyanobacteria / NblA / CCM / Gene knockout / Carbon/nitrogen balance / Biological Sciences / Biochemistry and Cell Biology / Plant Biology

References

[1] BaierK, LehmannH, StephanDP, LockauW. NblA is essential for phycobilisome degradation in Anabaena sp. strain PCC 7120 but not for development of functional heterocysts. Microbiology, 2004, 150: 2739-2749.

[2] DaiGZ, QiuBS, ForchhammerK. Ammonium tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803 and the role of the multigene family. Plant Cell Environ, 2014, 37: 840-851.

[3] Damrow R, Maldener I, Zilliges Y (2016) The multiple functions of common microbial carbon polymers, glycogen and PHB, during stress responses in the non-diazotrophic cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 7:966

[4] Domínguez-MartínMA, SauerPV, KirstH, SutterM, BínaD, GreberBJ, NogalesE, PolívkaT, KerfeldCA. Structures of a phycobilisome in light-harvesting and photoprotected states. Nature, 2022, 609: 835-845.

[5] FloresE, FríasJE, RubioLM, HerreroA. Photosynthetic nitrate assimilation in cyanobacteria. Photosynth Res, 2005, 83: 117-133.

[6] ForchhammerK, SchwarzR. Nitrogen chlorosis in unicellular cyanobacteria—a developmental program for surviving nitrogen deprivation. Environ Microbiol, 2019, 21: 1173-1184.

[7] ForchhammerK, SelimKA. Carbon/nitrogen homeostasis control in cyanobacteria. FEMS Microbiol Rev, 2020, 44: 33-53.

[8] Giner-LamiaJ, Robles-RengelR, Hernández-PrietoMA, Muro-PastorMI, FlorencioFJ, FutschikME. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res, 2017, 45: 11800-11820.

[9] Gollan PJ, Muth-Pawlak D, Aro E-M (2020) Rapid transcriptional reprogramming triggered by alteration of the carbon/nitrogen balance has an impact on energy metabolism in Nostoc sp. PCC 7120. Life 10:297

[10] GründelM, ScheunemannR, LockauW, ZilligesY. Impaired glycogen synthesis causes metabolic overflow reactions and affects stress responses in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology, 2012, 158: 3032-3043.

[11] HerreroA, FloresE. Genetic responses to carbon and nitrogen availability in Anabaena. Environ Microbiol, 2019, 21: 1-17.

[12] HerreroA, Muro-PastorAM, ValladaresA, FloresE. Cellular differentiation and the NtcA transcription factor in filamentous cyanobacteria. FEMS Microbiol Rev, 2004, 28: 469-487.

[13] HouS, ZhouF, PengS, GaoH, XuX. The HetR-binding site that activates expression of patA in vegetative cells is required for normal heterocyst patterning in Anabaena sp. PCC 7120. Sci Bull, 2015, 60: 192-201.

[14] HuP, HouJ, XuY, NiuN, ZhaoC, LuL, ZhouM, ScheerH, ZhaoK. The role of lyases, NblA and NblB proteins and bilin chromophore transfer in restructuring the cyanobacterial light-harvesting complex. Plant J, 2020, 102: 529-540.

[15] JacksonSA, Eaton-RyeJJ, BryantDA, PosewitzMC, DaviesFK. Dynamics of photosynthesis in a glycogen-deficient glgC mutant of Synechococcus sp. strain PCC 7002. Appl Environ Microbiol, 2015, 81: 6210-6222.

[16] JiangHW, WuHY, WangCH, YangCH, KoJT, HoHC, TsaiMD, BryantDA, LiF-W, HoM-C, HoM-Y. A structure of the relict phycobilisome from a thylakoid-free cyanobacterium. Nat Commun, 2023, 14: 8009.

[17] JiangYL, WangXP, SunH, HanSJ, LiWF, CuiN, LinGM, ZhangJY, ChengW, CaoDD, ZhangZY, ZhangCC, ChenY, ZhouCZ. Coordinating carbon and nitrogen metabolic signaling through the cyanobacterial global repressor NdhR. Proc Natl Acad Sci, 2018, 115: 403-408.

[18] KiyotaH, HiraiMY, IkeuchiM. NblA1/A2-dependent homeostasis of amino acid pools during nitrogen starvation in Synechocystis sp. PCC 6803. Metabolites, 2014, 4: 517-531.

[19] KlotzA, GeorgJ, BučinskáL, WatanabeS, ReimannV, JanuszewskiW, SobotkaR, JendrossekD, HessWR, ForchhammerK. Awakening of a dormant cyanobacterium from nitrogen chlorosis reveals a genetically determined program. Curr Biol, 2016, 26: 2862-2872.

[20] KlotzA, ReinholdE, DoelloS, ForchhammerK. Nitrogen starvation acclimation in Synechococcus elongatus: redox-control and the role of nitrate reduction as an electron sink. Life, 2015, 5: 888-904.

[21] KomendaJ, SobotkaR, NixonPJ. Assembling and maintaining the Photosystem II complex in chloroplasts and cyanobacteria. Curr Opin Plant Biol, 2012, 15: 245-251.

[22] KrasikovV, Aguirre von WobeserE, DekkerHL, HuismanJ, MatthijsHCP. Time-series resolution of gradual nitrogen starvation and its impact on photosynthesis in the cyanobacterium Synechocystis PCC 6803. Physiol Plant, 2012, 145: 426-439.

[23] KrauspeV, FahrnerM, SpätP, SteglichC, Frankenberg-DinkelN, MačekB, SchillingO, HessWR. Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria. Proc Natl Acad Sci, 2021, 118. e2012277118

[24] LeviM, SenderskyE, SchwarzR. Decomposition of cyanobacterial light harvesting complexes: NblA-dependent role of the bilin lyase homolog NblB. Plant J, 2018, 94: 813-821.

[25] Liu H, Zhang MM, Weisz DA, Cheng M, Pakrasi HB, Blankenship RE (2021) Structure of cyanobacterial phycobilisome core revealed by structural modeling and chemical cross-linking. Sci Adv 7:eaba5743

[26] LiuLM, LiDL, DengB, WangXW, JiangHB. Special roles for efflux systems in iron homeostasis of non-siderophore-producing cyanobacteria. Environ Microbiol, 2022, 24: 551-565.

[27] LiuS, JuneauP, QiuB. Effects of iron on the growth and minimal fluorescence yield of three marine Synechococcus strains (Cyanophyceae). Phycol Res, 2012, 60: 61-69.

[28] Ludwig M, Bryant DA (2012) Acclimation of the global transcriptome of the cyanobacterium Synechococcus sp. strain PCC 7002 to nutrient limitations and different nitrogen sources. Front Microbiol 3:145

[29] MontgomeryBL. Spatiotemporal phytochrome signaling during photomorphogenesis: from physiology to molecular mechanisms and back. Front Plant Sci, 2016, 7: 480.

[30] NagarajanA, ZhouM, NguyenAY, LibertonM, KediaK, ShiT, PiehowskiP, ShuklaA, FillmoreTL, NicoraC, SmithRD, KoppenaalDW, JacobsJM, PakrasiHB. Proteomic insights into phycobilisome degradation, a selective and tightly controlled process in the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. Biomolecules, 2019, 9: 374.

[31] RabouilleS, CampbellDA, MasudaT, ZavřelT, BernátG, PolereckyL, HalseyK, EichnerM, KotabováE, StephanS, LukešM, ClaquinP, Bonomi-BarufiJ, LombardiAT, ČervenýJ, SuggettDJ, GiordanoM, KromkampJC, PrášilO. Electron & biomass dynamics of Cyanothece under interacting nitrogen & carbon limitations. Front Microbiol, 2021, 12. 617802

[32] RuanZ, PrášilO, GiordanoM. The phycobilisomes of Synechococcus sp. are constructed to minimize nitrogen use in nitrogen-limited cells and to maximize energy capture in energy-limited cells. Environ Exp Bot, 2018, 150: 152-160.

[33] SakamotoT, DelgaizoVB, BryantDA. Growth on urea can trigger death and peroxidation of the cyanobacterium Synechococcus sp. strain PCC 7002. Appl Environ Microbiol, 1998, 64: 2361-2366.

[34] SalomonE, Bar-EyalL, SharonS, KerenN. Balancing photosynthetic electron flow is critical for cyanobacterial acclimation to nitrogen limitation. Biochim Biophys Acta Bioenerg, 2013, 1827: 340-347.

[35] SanfilippoJE, GarczarekL, PartenskyF, KehoeDM. Chromatic acclimation in cyanobacteria: a diverse and widespread process for optimizing photosynthesis. Annu Rev Microbiol, 2019, 73: 407-433.

[36] SenderskyE, KozerN, LeviM, MoizikM, GariniY, Shav-TalY, SchwarzR. The proteolysis adaptor, NblA, is essential for degradation of the core pigment of the cyanobacterial light-harvesting complex. Plant J, 2015, 83: 845-852.

[37] SenderskyE, LahmiR, ShaltielJ, PerelmanA, SchwarzR. NblC, a novel component required for pigment degradation during starvation in Synechococcus PCC 7942. Mol Microbiol, 2005, 58: 659-668.

[38] ShimmoriY, KanesakiY, NozawaM, YoshikawaH, EhiraS. Transcriptional activation of glycogen catabolism and the oxidative pentose phosphate pathway by NrrA facilitates cell survival under nitrogen starvation in the cyanobacterium Synechococcus sp. strain PCC 7002. Plant Cell Physiol, 2018, 59: 1225-1233.

[39] TakahashiM, MikamiK. Blue-red chromatic acclimation in the red alga Pyropia yezoensis. Algal Res, 2021, 58. 102428

[40] TanigawaR, ShirokaneM, MaedaS, OmataT, TanakaK, TakahashiH. Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC 7942 by 2-oxoglutarate in vitro. Proc Natl Acad Sci, 2002, 99: 4251-4255.

[41] UlloaO, Henríquez-CastilloC, Ramírez-FlandesS, PlominskyAM, MurilloAA, Morgan-LangC, HallamSJ, StepanauskasR. The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean. Proc Natl Acad Sci, 2021, 118. e2025638118

[42] Vidal R, Venegas-Calerón M (2019) Simple, fast and accurate method for the determination of glycogen in the model unicellular cyanobacterium Synechocystis sp. PCC 6803. J Microbiol Methods 164:105686

[43] WangX, HeY, ZhouY, ZhuB, XuJ, PanK, LiY. An attempt to simultaneously quantify the polysaccharide, total lipid, protein and pigment in single Cyclotella cryptica cell by Raman spectroscopy. Biotechnol Biofuels, 2023, 16: 63.

[44] WatanabeM, IkeuchiM. Phycobilisome: architecture of a light-harvesting supercomplex. Phycol Res, 2013, 116: 265-276

[45] YoshiharaA, KobayashiK. Photosynthesis and cell growth trigger degradation of phycobilisomes during nitrogen limitation. Plant Cell Physiol, 2022, 63: 189-199.

[46] ZengX, ZhangCC. The making of a heterocyst in cyanobacteria. Annu Rev Microbiol, 2022, 76: 597-618.

[47] ZhangCC, ZhouCZ, BurnapRL, PengL. Carbon and nitrogen metabolic balance: lessons from cyanobacteria. Trends Plant Sci, 2018, 23: 1116-1130.

[48] ZhangJ, MaJ, LiuD, QinS, SunS, ZhaoJ, SuiSF. Structure of phycobilisome from the red alga Griffithsia pacifica. Nature, 2017, 551: 57-63.

[49] ZhengL, ZhengZ, LiX, WangG, ZhangK, WeiP, ZhaoJ, GaoN. Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes. Nat Commun, 2021, 12: 5497.

RIGHTS & PERMISSIONS

The Author(s)