Skip to main content

Laser Microdissection as a Useful Tool to Study Gene Expression in Plant and Fungal Partners in AM Symbiosis

  • Protocol
  • First Online:
Arbuscular Mycorrhizal Fungi

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2146))

Abstract

Laser microdissection (LMD) technology has been widely applied to plant tissues, offering novel information on the role of different cell-type populations during plant–microbe interactions. In this chapter, protocols to apply the LMD approach to study plant and fungal transcript profiles in different cell-type populations from arbuscular mycorrhizal (AM) roots are described in detail, starting from the biological material preparation to gene expression analyses by RT-PCR and RT-qPCR.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 149.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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. Athman A, Tanz SK, Conn VM et al (2014) Protocol: a fast and simple in situ PCR method for localising gene expression in plant tissue. Plant Methods 10:29

    Article  PubMed  PubMed Central  Google Scholar 

  2. Balestrini R, Bonfante P (2008) Laser microdissection (LM): applications to plant materials. Plant Biosyst 142:331–336

    Article  Google Scholar 

  3. Fiorilli V, Volpe V, Balestrini R (2019) Microscopic techniques coupled to molecular and genetic approaches to highlight cell-type specific differences in mycorrhizal symbiosis. In: Reinhardt D, Sharma AK (eds) Methods in Rhizosphere biology research. Springer, New York

    Google Scholar 

  4. Emmert-Buck MR, Bonner RF, Smith PD et al (1996) Laser capture microdissection. Science 274:998–1001

    Article  CAS  PubMed  Google Scholar 

  5. Birnbaum K, Shasha DE, Wang JY et al (2003) A gene expression map of the Arabidopsis root. Science 302:1956–1960

    Article  CAS  PubMed  Google Scholar 

  6. Nelson T, Tausta SL, Gandotra N, Liu T (2006) Laser microdissection of plant tissue: what you see is what you get. Annu Rev Plant Biol 57:181–201

    Article  CAS  PubMed  Google Scholar 

  7. Day RC, Grossniklaus U, Macknight RC (2005) Be more specific! Laser-assisted microdissection of plant cells. Trends Plant Sci 10:397–406

    Article  CAS  PubMed  Google Scholar 

  8. Day RC, McNoe LA, Macknight RC (2007) Transcript analysis of laser microdissected plant cells. Physiol Plant 129:267–282

    Article  CAS  Google Scholar 

  9. Ramsay K, Jones MGK, Wang Z (2006) Laser capture microdissection: a novel approach to microanalysis of plant–microbe interactions. Mol Plant Pathol 7:429–435

    Article  CAS  PubMed  Google Scholar 

  10. Balestrini R, Gómez-Ariza J, Klink VP, Bonfante P (2009) Application of laser microdissection to plant pathogenic and symbiotic interaction. J Plant Interact 4:81–92

    Article  CAS  Google Scholar 

  11. Millar JL, Becker MG, Belmonte MF (2015) Laser microdissection of plant tissues. In: Yeung ECT, Stasolla C, Sumner MJ, Huang BQ (eds) Plant microtechniques and protocols. Springer International Publishing Switzerland, Cham

    Google Scholar 

  12. Hacquard S, Delaruelle C, Legué V et al (2010) Laser capture microdissection of Uredinia formed by Melampsora larici-populina revealed a transcriptional switch between biotrophy and sporulation. Mol Plant-Microbe Interact 23:1275–1286

    Article  CAS  PubMed  Google Scholar 

  13. Chandran D, Inada N, Hather G et al (2010) Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proc Natl Acad Sci U S A 107:460–465

    Article  CAS  PubMed  Google Scholar 

  14. Santi S, Grisan S, Pierasco A et al (2013) Laser microdissection of grapevine leaf phloem infected by stolbur reveals site-specific gene responses associated to sucrose transport and metabolism. Planr Cell Environ 36:343–355

    Article  CAS  Google Scholar 

  15. Rossi M, Pesando M, Vallino M et al (2018) Application of laser microdissection to study phytoplasma site-specific gene expression in the model plant Arabidopsis thaliana. Microbiol Res 217:60–68

    Article  CAS  PubMed  Google Scholar 

  16. Honaas LA, Wafula EK, Yang Z et al (2013) Functional genomics of a generalist parasitic plant: laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biol 13:9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Asano T, Masumura T, Kusano H et al (2002) Construction of specialized cDNA library from plant cells isolated by laser capture microdissection: toward comprehensive analysis of the genes expressed in the rice phloem. Plant J 32:401–408

    Article  CAS  PubMed  Google Scholar 

  18. Kerk NM, Ceserani T, Tausta SL et al (2003) Laser capture microdissection of cells from plant tissues. Plant Physiol 132:27–35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Inada N, Wildermuth MC (2005) Novel tissue preparation method and cell-specific marker for laser microdissection of Arabidopsis mature leaf. Planta 221:9–16

    Article  CAS  PubMed  Google Scholar 

  20. Cai S, Lashbrook CC (2006) Laser capture microdissection of plant cells from tape transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling. Plant J 48:628–637

    Article  CAS  PubMed  Google Scholar 

  21. Tang W, Coughlan S, Crane E et al (2006) The application of laser microdissection to in planta gene expression profiling of the maize anthracnose stalk rot fungus Colletotrichum graminicola. Mol Plant-Microbe Interact 19:1240–1250

    Article  CAS  PubMed  Google Scholar 

  22. Gomez SK, Harrison MJ (2009) Laser microdissection and its application to analyze gene expression in arbuscular mycorrhizal symbiosis. Pest Manag Sci 65:504–511

    Article  CAS  PubMed  Google Scholar 

  23. Gaude N, Bortfeld S, Duensing N et al (2012) Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo extensive and specific reprogramming during arbuscular mycorrhizal development. Plant J 69:510–528

    Article  CAS  PubMed  Google Scholar 

  24. Nakazono M, Qiu F, Borsuk LA, Schable PS (2003) Laser capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissue of maize. Plant Cell 15:583–596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Klink VP, Overall CC, Alkharouf NW et al (2007) Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). Planta 226:1389–1409

    Article  CAS  PubMed  Google Scholar 

  26. Ithal N, Recknor J, Nettleton D et al (2007) Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Mol Plant-Microbe Interact 20:293–305

    Article  CAS  PubMed  Google Scholar 

  27. Tsuji H, Aya K, Ueguchi-Tanaka M et al (2006) GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anthers. Plant J 47:427–444

    Article  CAS  PubMed  Google Scholar 

  28. Smith SE, Read D (2008) Mycorrhizal Symbiosis, 3rd edn. Academic Press, New York

    Google Scholar 

  29. Bucher M, Hause B, Krajinski F, Küster H (2014) Through the doors of perception to function in arbuscular mycorrhizal symbioses. New Phytol 204:833–840

    Article  CAS  PubMed  Google Scholar 

  30. Balestrini R, Lumini E (2018) Focus on mycorrhizal symbioses. Appl Soil Ecol 123:299–304

    Article  Google Scholar 

  31. Balestrini R, Bonfante P (2014) Cell wall remodeling in mycorrhizal symbiosis: a way towards biotrophism. Front Plant Sci 5:237

    Article  PubMed  PubMed Central  Google Scholar 

  32. Lanfranco L, Fiorilli V, Gutjahr C (2018) Partner communication and role of nutrients in the arbuscular mycorrhizal symbiosis. New Phytol 220:1031–1046

    Article  PubMed  Google Scholar 

  33. Balestrini R, Fochi V, Lopa A, Perotto S (2018) The use of laser microdissection to investigate cell specific gene expression in orchid tissues. In: Lee Y-I, Chee-Tak Yeung E (eds) Orchid propagation: from laboratories to greenhouses - methods and protocols. Humana Press, Springer Protocols Handbooks, New York

    Google Scholar 

  34. Hacquard S, Tisserant E, Brun A et al (2013) Laser microdissection and microarray analysis of Tuber malanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Harting net compartments. Environ Microbiol 15:1853–1869

    Article  CAS  PubMed  Google Scholar 

  35. Fochi V, Chitarra W, Kohler A et al (2017) Fungal and plant gene expression in the Tulasnella calosporaSerapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas. New Phytol 213:365–379

    Article  CAS  PubMed  Google Scholar 

  36. Fochi V, Falla N, Girlanda M et al (2017) Cell-specific expression of plant nutrient transporter genes in orchid mycorrhizae. Plant Sci 263:39–45

    Article  CAS  PubMed  Google Scholar 

  37. Spatafora JW, Chang Y, Benny GL et al (2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108(5):1028–1046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Giovannetti M, Sbrana C, Logi C (1994) Early processes involved in host recognition by arbuscular mycorrhizal fungi. New Phytol 127:703–709

    Article  Google Scholar 

  39. Gutjahr C, Paszkowski U (2013) Multiple control levels of root system remodelling in arbuscular mycorrhizal symbiosis. Front Plant Sci 4:204

    Article  PubMed  PubMed Central  Google Scholar 

  40. Gutjahr C, Parniske M (2013) Cell and developmental biology of arbuscular mycorrhiza symbiosis. Annu Rev Cell Dev Biol 29:593–617

    Article  CAS  PubMed  Google Scholar 

  41. Gaude N, Schulze WX, Franken P, Krajinski F (2012) Cell type-specific protein and transcription profiles implicate periarbuscular membrane synthesis as an important carbon sink in the mycorrhizal symbiosis. Plant Signal Behav 7:461–464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Gaude N, Bortfeld S, Erban A et al (2015) Symbiosis dependent accumulation of primary metabolites in arbuscule-containing cells. BMC Plant Biol 15:234

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Balestrini R, Gomez-Ariza J, Lanfranco L, Bonfante P (2007) Laser microdissection reveals that transcripts for five plant and one fungal phosphate transporter genes are contemporaneously present in arbusculated cells. Mol Plant-Microbe Interact 20:1055–106210

    Article  CAS  PubMed  Google Scholar 

  44. Fiorilli V, Catoni M, Miozzi L et al (2009) Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus. New Phytol 184:975–987

    Article  CAS  PubMed  Google Scholar 

  45. Guether M, Neuhäuser B, Balestrini R et al (2009) A mycorrhizal specific ammonium transporter from Lotus japonicus acquires nitrogen. Plant Physiol 150:73–83

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Gomez KS, Javot H, Deewatthanawong P et al (2009) Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis. BMC Plant Biol 9:10

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Guether M, Balestrini R, Hannah M et al (2009) Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus. New Phytol 182:200–212

    Article  CAS  PubMed  Google Scholar 

  48. Hogekamp C, Arndt D, Pareira PA et al (2011) Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread. Plant Physiol 157:2023–2043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Guether M, Volpe V, Balestrini R et al (2011) LjLHT1.2-a mycorrhiza-inducible plant amino acid transporter from Lotus japonicus. Biol Fertil Soils 47:925–936

    Article  CAS  Google Scholar 

  50. Giovannetti M, Balestrini R, Volpe V et al (2012) Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus. BMC Plant Biol 12:186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Hogekamp C, Küster H (2013) A roadmap of cell-type specific gene expression during sequential stages of the arbuscular mycorrhiza symbiosis. BMC Genomics 14:306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Giovannetti M, Tolosano M, Volpe V et al (2014) Identification and functional characterization of a sulfate transporter induced by both sulfur starvation and mycorrhiza formation in Lotus japonicus. New Phytol 204:609–619

    Article  CAS  PubMed  Google Scholar 

  53. Recchia GH, Konzen ER, Cassieri F et al (2018) Arbuscular mycorrhizal symbiosis leads to differential regulation of drought-responsive genes in tissue-specific root cells of common bean. Front Microbiol 9:1339

    Article  PubMed  PubMed Central  Google Scholar 

  54. Pérez-Tienda J, Testillano PS, Balestrini R et al (2011) GintAMT2, a new member of the ammonium transporter family in the arbuscular mycorrhizal fungus Glomus intraradices. Fungal Genet Biol 48:1044–1055

    Article  PubMed  CAS  Google Scholar 

  55. Fiorilli V, Lanfranco L, Bonfante P (2013) The expression of GintPT, the phosphate transporter of Rhizophagus irregularis, depends on the symbiotic status and phosphate availability. Planta 237:1267–1277

    Article  CAS  PubMed  Google Scholar 

  56. Tisserant E, Kohler A, Dozolme-Seddas P et al (2012) The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont. New Phytol 193:755–769

    Article  CAS  PubMed  Google Scholar 

  57. Belmondo S, Fiorilli V, Pérez-Tienda J et al (2014) A dipeptide transporter from the arbuscular mycorrhizal fungus Rhizophagus irregularis is upregulated in the intraradical phase. Front Plant Sci 5:436

    Article  PubMed  PubMed Central  Google Scholar 

  58. Fiorilli V, Belmondo S, Khouja AR et al (2016) RiPEIP1, a gene from the arbuscular mycorrhizal fungus Rhizophagus irregularis, is preferentially expressed in planta and may be involved in root colonization. Mycorrhiza 26:609–621

    Article  CAS  PubMed  Google Scholar 

  59. Zeng T, Holmer R, Hontelez J et al (2018) Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis. Plant J 94:411–425

    Article  CAS  PubMed  Google Scholar 

  60. Gómez-Ariza J, Balestrini R, Novero M, Bonfante P (2009) Cell-specific gene expression of phosphate transporters in mycorrhizal tomato roots. Biol Fertil Soils 45:845–853

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank Jorge Gómez-Ariza and Marco Giovannetti for their help to optimize the described protocols and the helpful discussion during the experiments.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Raffaella Balestrini or Valentina Fiorilli .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Balestrini, R., Fiorilli, V. (2020). Laser Microdissection as a Useful Tool to Study Gene Expression in Plant and Fungal Partners in AM Symbiosis. In: Ferrol, N., Lanfranco, L. (eds) Arbuscular Mycorrhizal Fungi. Methods in Molecular Biology, vol 2146. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0603-2_13

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0603-2_13

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0602-5

  • Online ISBN: 978-1-0716-0603-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics