Skip to main content
SpringerLink
Log in

Measurement of Transcripts Associated with Photorespiration and Related Redox Signaling

  • Protocol
  • First Online:
Photorespiration

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1653))

Abstract

To study photorespiration and to characterize related components, gene expression analysis is a central approach. An overview of the experimental setup, protocols, and methods we use to investigate photorespiration-associated gene expression is presented. Within this chapter, we describe simple procedures to experimentally alter the photorespiratory flux and provide protocols for transcriptomic analysis with a focus on genes encoding photorespiratory proteins as well as those induced by photorespiratory hydrogen peroxide (H2O2). Examples of typical results are presented and their significance to understanding redox signaling is discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Foyer CH, Bloom AJ, Queval G et al (2009) Photorespiratory metabolism: genes, mutants, energetics, and redox signaling. Annu Rev Plant Biol 60:455–484

    Article  CAS  PubMed  Google Scholar 

  2. Obata T, Florian A, Timm S, Bauwe H, Fernie AR (2016) On the metabolic interactions of (photo)respiration. J Exp Bot 67:3003–3014

    Article  CAS  PubMed  Google Scholar 

  3. Somerville CR (1986) Analysis of photosynthesis with mutants of higher plants and algae. Annu Rev Plant Physiol 37:467–507

    Article  CAS  Google Scholar 

  4. Leegood RC, Lea PJ, Adcock MD et al (1995) The regulation and control of photorespiration. J Exp Bot 46:1397–1414

    Article  CAS  Google Scholar 

  5. Blackwell RD, Murray AJS, Lea PJ (1987) Inhibition of photosynthesis in barley with decreased levels of chloroplastic glutamine synthetase. J Exp Bot 38:1799–1809

    Article  CAS  Google Scholar 

  6. Engel N, Ewald R, Gupta KJ, Zrenner R, Hagemann M, Bauwe H (2011) The presequence of Arabidopsis serine hydroxymethyltransferase SHM2 selectively prevents import into mesophyll mitochondria. Plant Physiol 157:1711–1720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Queval G, Issakidis-Bourguet E, Hoeberichts FA et al (2007) Conditional oxidative stress responses in the Arabidopsis photorespiratory mutant cat2 demonstrate that redox state is a key modulator of daylength-dependent gene expression and define photoperiod as a crucial factor in the regulation of H2O2-induced cell death. Plant J 52:640–657

    Article  CAS  PubMed  Google Scholar 

  8. Kerchev P, Waszczak C, Lewandowska A et al (2016) Lack of GLYCOLATE OXIDASE1, but not GLYCOLATE OXIDASE2, attenuates the photorespiratory phenotype of CATALASE2-deficient Arabidopsis. Plant Physiol 171:1704–1719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Queval G, Neukermans J, Vanderauwera S et al (2012) Day length is a key regulator of transcriptomic responses to both CO2 and H2O2 in Arabidopsis. Plant Cell Environ 35:374–387

    Article  CAS  PubMed  Google Scholar 

  10. Kangasjärvi S, Neukermans J, Li S et al (2012) Photosynthesis, photorespiration, and light signalling in defence responses. J Exp Bot 63:1619–1636

    Article  PubMed  Google Scholar 

  11. Noctor G, Veljovic-Jovanovic S, Driscoll S et al (2002) Drought and oxidative load in the leaves of C3 plants: a predominant role for photorespiration? Ann Bot 89:841–850

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chaouch S, Queval G, Vanderauwera S et al (2010) Peroxisomal hydrogen peroxide is coupled to biotic defense responses by ISOCHORISMATE SYNTHASE1 in a daylength-related manner. Plant Physiol 153:1692–1705

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Rojas CM, Senthil-Kumar M, Wang K et al (2012) Glycolate oxidase modulates reactive oxygen species-mediated signal transduction during nonhost resistance in Nicotiana benthamiana and Arabidopsis. Plant Cell 24:336–352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Vanderauwera S, Zimmermann P, Rombauts S et al (2005) Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol 139:806–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kerchev P, Mühlenbock P, Denecker J et al (2015) Activation of auxin signalling counteracts photorespiratory H2O2-dependent cell death. Plant Cell Environ 38:253–265

    Article  CAS  PubMed  Google Scholar 

  16. Mhamdi A, Queval G, Chaouch S et al (2010) Catalase function in plants: a focus on Arabidopsis mutants as stress-mimic models. J Exp Bot 61:4197–4220

    Article  CAS  PubMed  Google Scholar 

  17. Mhamdi A, Hager J, Chaouch S et al (2010) Arabidopsis GLUTATHIONE REDUCTASE1 plays a crucial role in leaf responses to intracellular hydrogen peroxide and in ensuring appropriate gene expression through both salicylic acid and jasmonic acid signaling pathways. Plant Physiol 153:1144–1160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Tognetti VB, Van Aken O, Morreel K et al (2010) Perturbation of indole-3-butyric acid homeostasis by the UDP-glucosyltransferase UGT74E2 modulates Arabidopsis architecture and water stress tolerance. Plant Cell 22:2660–2679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Vanderauwera S, Suzuki N, Miller G et al (2011) Extranuclear protection of chromosomal DNA from oxidative stress. Proc Natl Acad Sci U S A 108:1711–1716

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bolstad BM, Irizarry RA, Åstrand M et al (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185–193

    Article  CAS  PubMed  Google Scholar 

  21. Irizarry RA, Hobbs B, Collin F et al (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249–264

    Article  PubMed  Google Scholar 

  22. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article 3

    Article  Google Scholar 

  23. Dai M, Thompson RC, Maher C et al (2010) NGSQC: cross-platform quality analysis pipeline for deep sequencing data. BMC Genomics 11(Suppl 4):S7

    Article  PubMed  PubMed Central  Google Scholar 

  24. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Dobin A, Davis CA, Schlesinger F et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21

    Article  CAS  PubMed  Google Scholar 

  27. Anders S, Pyl PT, Huber W (2015) HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169

    Article  CAS  PubMed  Google Scholar 

  28. Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930

    Article  CAS  PubMed  Google Scholar 

  29. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    Article  CAS  PubMed  Google Scholar 

  30. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550

    Article  PubMed  PubMed Central  Google Scholar 

  31. Davletova S, Rizhsky L, Liang H et al (2005) Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis. Plant Cell 17:268–281

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Mhamdi A, Noctor G (2016) High CO2 primes plant biotic stress defences through redox-linked pathways. Plant Physiol 172:929–942

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Gadjev I, Vanderauwera S, Gechev TS et al (2006) Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis. Plant Physiol 141:436–445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Willems P, Mhamdi A, Stael S et al (2016) The ROS wheel: refining ROS transcriptional footprints. Plant Physiol 171:1720–1733

    Article  PubMed  PubMed Central  Google Scholar 

  35. Noctor G, Mhamdi A, Foyer CH (2016) Oxidative stress and antioxidative systems: recipes for successful data collection and interpretation. Plant Cell Environ 39:1140–1160

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Martine De Cock for help in preparing the revised version of the manuscript. This work was supported by the Agence Nationale de la Recherche project CYNTHIOL (no. ANR12–BSV6–0011) to G.N. and by grants from Ghent University Multidisciplinary Research Partnership “Sustainable BioEconomy” (project 01MRB510W), the Interuniversity Attraction Poles Program (IUAP P7/29), and the Research Foundation-Flanders (grant no. G0D7914N) to F.V.B., and also by the Scientific Exchange program Flanders-France (grant Tournesol T.2008.21) to G.N. and F.V.B.P.K. is a recipient of Omics@VIB Marie Curie COFUND fellowship.

Author information

Authors and Affiliations

  1. Department of Plant Systems Biology, VIB, 9052, Ghent, Belgium

    Amna Mhamdi, Pavel I. Kerchev, Patrick Willems & Frank Van Breusegem

  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium

    Amna Mhamdi, Pavel I. Kerchev, Patrick Willems & Frank Van Breusegem

  3. Medical Biotechnology Center, VIB, 9000, Ghent, Belgium

    Patrick Willems

  4. Department of Biochemistry, Ghent University, 9000, Ghent, Belgium

    Patrick Willems

  5. Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405, Orsay cedex, France

    Graham Noctor

  6. Unité Mixte de Recherche 9213/Unité Mixte de Recherche 1403, Université Paris-Sud, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France

    Graham Noctor

Authors
  1. Amna Mhamdi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pavel I. Kerchev
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Patrick Willems
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Graham Noctor
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Frank Van Breusegem
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Graham Noctor or Frank Van Breusegem .

Editor information

Editors and Affiliations

  1. Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany

    Alisdair R. Fernie

  2. Plant Physiology Department, University of Rostock, Rostock, Germany

    Hermann Bauwe

  3. Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Düsseldorf, Germany

    Andreas P.M. Weber

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Mhamdi, A., Kerchev, P.I., Willems, P., Noctor, G., Van Breusegem, F. (2017). Measurement of Transcripts Associated with Photorespiration and Related Redox Signaling. In: Fernie, A., Bauwe, H., Weber, A. (eds) Photorespiration. Methods in Molecular Biology, vol 1653. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7225-8_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7225-8_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7224-1

  • Online ISBN: 978-1-4939-7225-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation