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Cited by 26Plant nutrient uptake and metabolismPhotosynthetic Processes and MechanismsBacterial Genetics and Biotechnology

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Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria

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Kraus, Alexander, Spät, Philipp, Timm, Stefan, Wilson, Amy, Schumann, Rhena, Hagemann, Martin, Maček, Boris, Hess, Wolfgang R.·2024·Nature Communications
DOI 10.1038/s41467-024-46253-4PMC PMC10907346

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Abstract

When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.

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  1. Biller, S. J., Berube, P. M., Lindell, D. & Chisholm, S. W. Prochlorococcus: the structure and function of collective diversity. Nat. Rev. Microbiol. 13, 13–27 (2015). · DOI
  2. Flombaum, P. et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc. Natl Acad. Sci. USA 110, 9824–9829 (2013). · DOI
  3. Partensky, F., Hess, W. R. & Vaulot, D. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbio. l Mol. Biol. Rev. 63, 106–127 (1999). · DOI
  4. Hagemann, M. & Hess, W. R. Systems and synthetic biology for the biotechnological application of cyanobacteria. Curr. Opin. Biotechnol. 49, 94–99 (2018). · DOI
  5. Vijay, D., Akhtar, M. K. & Hess, W. R. Genetic and metabolic advances in the engineering of cyanobacteria. Curr. Opin. Biotechnol. 59, 150–156 (2019). · DOI
  6. Berube, P. M., O’Keefe, T. J., Rasmussen, A., LeMaster, T. & Chisholm, S. W. Production and cross-feeding of nitrite within Prochlorococcus populations. mBio 14, e01236–23 (2023).
  7. Morris, J. J., Johnson, Z. I., Szul, M. J., Keller, M. & Zinser, E. R. Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean’s surface. PLoS ONE 6, e16805 (2011). · DOI
  8. Roth-Rosenberg, D. et al. Prochlorococcus cells rely on microbial interactions rather than on chlorotic resting stages to survive long-term nutrient starvation. mBio 11, e01846-20 (2020). · DOI
  9. Suzuki, I., Sugiyama, T. & Omata, T. Regulation of nitrite reductase activity under CO2 limitation in the cyanobacterium Synechococcus sp. PCC7942. Plant Physiol. 107, 791–796 (1995). · DOI
  10. Vázquez-Bermúdez, M. F., Herrero, A. & Flores, E. 2-Oxoglutarate increases the binding affinity of the NtcA (nitrogen control) transcription factor for the Synechococcus glnA promoter. FEBS Lett. 512, 71–74 (2002). · DOI
  11. Tanigawa, R. et al. Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC 7942 by 2-oxoglutarate in vitro. Proc. Natl Acad. Sci. USA 99, 4251–4255 (2002). · DOI
  12. Espinosa, J., Forchhammer, K., Burillo, S. & Contreras, A. Interaction network in cyanobacterial nitrogen regulation: PipX, a protein that interacts in a 2-oxoglutarate dependent manner with PII and NtcA. Mol. Microbiol. 61, 457–469 (2006). · DOI
  13. Espinosa, J. et al. PipX, the coactivator of NtcA, is a global regulator in cyanobacteria. Proc. Natl Acad. Sci. USA 111, E2423–E2430 (2014). · DOI
  14. Forcada-Nadal, A., Llácer, J. L., Contreras, A., Marco-Marín, C. & Rubio, V. The PII-NAGK-PipX-NtcA regulatory axis of cyanobacteria: a tale of changing partners, allosteric effectors and non-covalent interactions. Front. Mol. Biosci. 5, 91 (2018). · DOI
  15. Muro-Pastor, M. I., Reyes, J. C. & Florencio, F. J. Cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate levels. J. Biol. Chem. 276, 38320–38328 (2001). · DOI
  16. Giner-Lamia, J. et al. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res. 45, 11800–11820 (2017). · DOI
  17. García-Domínguez, M., Reyes, J. C. & Florencio, F. J. NtcA represses transcription of gifA and gifB, genes that encode inhibitors of glutamine synthetase type I from Synechocystis sp. PCC 6803. Mol. Microbiol. 35, 1192–1201 (2000). · DOI
  18. Bolay, P. et al. The novel PII-interacting protein PirA controls flux into the cyanobacterial ornithine-ammonia cycle. mBio 12, e00229-21 (2021). · DOI
  19. Bolay, P. et al. The sRNA NsiR4 fine-tunes arginine synthesis in the cyanobacterium Synechocystis sp. PCC 6803 by post-transcriptional regulation of PirA. RNA Biol. 19, 811–818 (2022). · DOI
  20. Orthwein, T. et al. The novel PII-interactor PirC identifies phosphoglycerate mutase as key control point of carbon storage metabolism in cyanobacteria. Proc. Natl Acad. Sci. USA 118, e2019988118 (2021). · DOI
  21. Kopf, M. et al. Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803. DNA Res. 21, 527–539 (2014). · DOI
  22. Kopf, M., Klähn, S., Scholz, I., Hess, W. R. & Voß, B. Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria. Sci. Rep. 5, 9560 (2015). · DOI
  23. Mitschke, J. et al. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc. Natl Acad. Sci. USA 108, 2124–2129 (2011). · DOI
  24. Baumgartner, D., Kopf, M., Klähn, S., Steglich, C. & Hess, W. R. Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome. BMC Microbiol. 16, 285 (2016). · DOI
  25. Krauspe, V. et al. Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria. Proc. Natl Acad. Sci. USA 118, e2012277118 (2021). · DOI · Paper page
  26. Song, K. et al. AtpΘ is an inhibitor of F0F1 ATP synthase to arrest ATP hydrolysis during low-energy conditions in cyanobacteria. Curr. Biol. 32, 136–148.e5 (2022). · DOI
  27. Spät, P., Krauspe, V., Hess, W. R., Maček, B. & Nalpas, N. Deep proteogenomics of a photosynthetic cyanobacterium. J. Proteome Res. 22, 1969–19 (2023). · DOI
  28. Rippka, R., Deruelles, J., Waterbury, J. B., Herdman, M. & Stanier, R. Y. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology 111, 1–61 (1979). · DOI · Paper page
  29. Bombar, D., Heller, P., Sanchez-Baracaldo, P., Carter, B. J. & Zehr, J. P. Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria. ISME J. 8, 2530–2542 (2014). · DOI
  30. Zehr, J. P. et al. Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II. Science 322, 1110–1112 (2008). · DOI
  31. Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022). · DOI · Paper page
  32. Lin, S., Li, S., Ouyang, T. & Chen, G. Site-2 protease Slr1821 regulates carbon/nitrogen homeostasis during ammonium stress acclimation in cyanobacterium Synechocystis sp. PCC 6803. Int. J. Mol. Sci. 24, 6606 (2023). · DOI
  33. Gründel, M., Scheunemann, R., Lockau, W. & Zilliges, Y. Impaired glycogen synthesis causes metabolic overflow reactions and affects stress responses in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology 158, 3032–3043 (2012). · DOI
  34. Zhang, H. et al. The cyanobacterial ornithine-ammonia cycle involves an arginine dihydrolase. Nat. Chem. Biol. 14, 575–581 (2018). · DOI
  35. Alvarenga-Lucius, L. V. et al. The high-light-induced protein SliP4 binds to NDH1 and photosystems facilitating cyclic electron transport and state transition in Synechocystis sp. PCC 6803. N. Phytol. 239, 1083–1097 (2023). · DOI
  36. Schwarz, R. & Forchhammer, K. Acclimation of unicellular cyanobacteria to macronutrient deficiency: emergence of a complex network of cellular responses. Microbiology 151, 2503–2514 (2005). · DOI
  37. Flores, E. & Herrero, A. Nitrogen assimilation and nitrogen control in cyanobacteria. Biochem. Soc. Trans. 33, 164–167 (2005). · DOI
  38. Zhang, X. et al. The acceptor side of photosystem II i the initial target of nitrite stress inSynechocystis sp. strain PCC 6803. Appl. Environ. Microbiol. 83, e02952–16 (2017). · DOI
  39. Hirasawa, M. et al. Complex formation between ferredoxin and Synechococcus ferredoxin:nitrate oxidoreductase. Biochim. Biophys. Acta 1608, 155–162 (2004). · DOI
  40. Reyes, J. C., Chávez, S., Muro-Pastor, M. I., Candau, P. & Florencio, F. J. Effect of glucose utilization on nitrite excretion by the unicellular cyanobacterium Synechocystis sp. strain PCC 6803. Appl. Environ. Microbiol. 59, 3161–3163 (1993). · DOI
  41. Kloft, N., Rasch, G. & Forchhammer, K. Protein phosphatase PphA from Synechocystis sp. PCC 6803: the physiological framework of PII-P dephosphorylation. Microbiol. Read. Engl. 151, 1275–1283 (2005). · DOI
  42. Biller, S. J. et al. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. Sci. Data 1, 140034 (2014). · DOI
  43. Dufresne, A. et al. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc. Natl Acad. Sci. USA 100, 10020–10025 (2003). · DOI
  44. Rocap, G. et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042–1047 (2003). · DOI
  45. Trautmann, D., Voß, B., Wilde, A., Al-Babili, S. & Hess, W. R. Microevolution in cyanobacteria: re-sequencing a motile substrain of Synechocystis sp. PCC 6803. DNA Res. 19, 435–448 (2012). · DOI
  46. Hollingshead, S. & Vapnek, D. Nucleotide sequence analysis of a gene encoding a streptomycin/spectinomycin adenyltransferase. Plasmid 13, 17–30 (1985). · DOI
  47. Beyer, H. M. et al. AQUA cloning: a versatile and simple enzyme-free cloning approach. PLoS ONE 10, e0137652 (2015). · DOI
  48. Ludwig, A., Heimbucher, T., Gregor, W., Czerny, T. & Schmetterer, G. Transformation and gene replacement in the facultatively chemoheterotrophic, unicellular cyanobacterium Synechocystis sp. PCC6714 by electroporation. Appl. Microbiol. Biotechnol. 78, 729–735 (2008). · DOI
  49. Pinto, F. L., Thapper, A., Sontheim, W. & Lindblad, P. Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria. BMC Mol. Biol. 10, 79–79 (2009). · DOI
  50. Klähn, S. et al. Alkane biosynthesis genes in cyanobacteria and their transcriptional organization. Front. Bioeng. Biotechnol. 2, 24 (2014). · DOI
  51. Spät, P., Maček, B. & Forchhammer, K. Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation. Front. Microbiol. 6, 248 (2015). · DOI
  52. Ishihama, Y., Rappsilber, J. & Mann, M. Modular stop and go extraction tips with stacked disks for parallel and multidimensional peptide fractionation in proteomics. J. Proteome Res. 5, 988–994 (2006). · DOI
  53. Spät, P., Barske, T., Maček, B. & Hagemann, M. Alterations in the CO2 availability induce alterations in the phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803. N. Phytol. 231, 1123–1137 (2021). · DOI
  54. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008). · DOI · Paper page
  55. Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016). · DOI · Paper page
  56. Methods of Seawater Analysis https://doi.org/10.1002/9783527613984 (Wiley, 1999). · DOI
  57. Reinholdt, O. et al. Redox-regulation of photorespiration through mitochondrial thioredoxin o1. Plant Physiol. 181, 442–457 (2019). · DOI
  58. Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022). · DOI · Paper page

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Metadata

Authors
Kraus, A., Spät, P., Timm, S., Wilson, A., Schumann, R., Hagemann, M., Maček, B., & Hess, W. R.
Affiliations
  • University of Freiburg (DE)
  • University of Tübingen (DE)
  • University of Rostock (DE)
Corresponding author
Hess, Wolfgang R.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-03-01
Volume
15
Issue
1
Pages
1911-1911
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-46253-4
PMC
PMC10907346
OpenAlex
W4392387309
Cited by
26
References
1
Citations by year
2026: 6 · 2025: 11 · 2024: 9
FWCI
6.31
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion)
Funders
Deutsche Forschungsgemeinschaft (HE 2544/15-2, HA 2002/23-2)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant nutrient uptake and metabolism
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Photosynthetic Processes and Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
nitrite reductase, nitrite excretion, cyanobacteria, nitrogen metabolism, carbon limitation, Synechocystis sp. PCC 6803, protein-protein interaction, ammonium assimilation, amino acid pool, chlorosis
MeSH terms
Ammonia, Bacterial Proteins, Carbon, Nitrates, Nitrite Reductases, Nitrites, Nitrogen, Gene Expression Regulation, Bacterial, Synechocystis, Nitrate Reductase

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