Spatial distribution of organelles in leaf cells and soybean root nodules revealed by focused ion beam-scanning electron microscopy
Brandon C. Reagan A , Paul J. -Y. Kim A , Preston D. Perry A , John R. Dunlap B and Tessa M. Burch-Smith A CA Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA.
B Advanced Microscopy and Imaging Center, University of Tennessee, Knoxville, 1499 Circle Dr Knoxville, TN 37996, USA.
C Corresponding author. Email: tburchsm@utk.edu
This paper originates from a presentation at the Fourth International Symposium on Plant Signaling and Behavior, Komarov Botanical Institute RAS/Russian Science Foundation, Saint Petersburg, Russia, 19–23 June 2016.
Functional Plant Biology 45(2) 180-191 https://doi.org/10.1071/FP16347
Submitted: 2 October 2016 Accepted: 23 December 2016 Published: 13 February 2017
Abstract
Analysis of cellular ultrastructure has been dominated by transmission electron microscopy (TEM), so images collected by this technique have shaped our current understanding of cellular structure. More recently, three-dimensional (3D) analysis of organelle structures has typically been conducted using TEM tomography. However, TEM tomography application is limited by sample thickness. Focused ion beam-scanning electron microscopy (FIB-SEM) uses a dual beam system to perform serial sectioning and imaging of a sample. Thus FIB-SEM is an excellent alternative to TEM tomography and serial section TEM tomography. Animal tissue samples have been more intensively investigated by this technique than plant tissues. Here, we show that FIB-SEM can be used to study the 3D ultrastructure of plant tissues in samples previously prepared for TEM via commonly used fixation and embedding protocols. Reconstruction of FIB-SEM sections revealed ultra-structural details of the plant tissues examined. We observed that organelles packed tightly together in Nicotiana benthamiana Domin leaf cells may form membrane contacts. 3D models of soybean nodule cells suggest that the bacteroids in infected cells are contained within one large membrane-bound structure and not the many individual symbiosomes that TEM thin-sections suggest. We consider the implications of these organelle arrangements for intercellular signalling.
Additional keywords: FIB-SEM, HPF-FS, membrane continuity, plasmodesmata, root nodules, tomogram.
References
Bammes BE, Rochat RH, Jakana J, Chen DH, Chiu W (2012) Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. Journal of Structural Biology 177, 589–601.| Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency.Crossref | GoogleScholarGoogle Scholar |
Bapaume L, Reinhardt D (2012) How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza. Frontiers in Plant Science 3, 223
| How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza.Crossref | GoogleScholarGoogle Scholar |
Bergersen FJ (1997) Regulation of nitrogen fixation in infected cells of leguminous root nodules in relation to O2 supply. Plant and Soil 191, 189–203.
| Regulation of nitrogen fixation in infected cells of leguminous root nodules in relation to O2 supply.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2sXmt1Kksbw%3D&md5=0e3f457786a847c876cbab7a08884fe3CAS |
Bhawana , Miller JL, Cahoon AB (2014) 3D Plant cell architecture of Arabidopsis thaliana (Brassicaceae) using focused ion beam-scanning electron microscopy. Applications in Plant Sciences 2, 1300090
| 3D Plant cell architecture of Arabidopsis thaliana (Brassicaceae) using focused ion beam-scanning electron microscopy.Crossref | GoogleScholarGoogle Scholar |
Bobik K, Dunlap JR, Burch-Smith TM (2014) Tandem high-pressure freezing and quick freeze substitution of plant tissues for transmission electron microscopy. Journal of Visualized Experiments 92, 51844
Burch-Smith TM, Zambryski PC (2010) Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the formation of secondary plasmodesmata. Current Biology 20, 989–993.
| Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the formation of secondary plasmodesmata.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXnsVarsrY%3D&md5=873007b7a5c56adb1c8cc1d72f1055acCAS |
Burch-Smith TM, Zambryski PC (2012) Plasmodesmata paradigm shift: regulation from without versus within. Annual Review of Plant Biology 63, 239–260.
| Plasmodesmata paradigm shift: regulation from without versus within.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xos1ams7Y%3D&md5=2619b897ecc858813a9c6f9622ce5b50CAS |
Burch-Smith TM, Brunkard JO, Choi YG, Zambryski PC (2011) Organelle-nucleus cross-talk regulates plant intercellular communication via plasmodesmata. Proceedings of the National Academy of Sciences of the United States of America 108, E1451–E1460.
| Organelle-nucleus cross-talk regulates plant intercellular communication via plasmodesmata.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XjvFOmsw%3D%3D&md5=c13f90b30772ddf91e3ca46b5d5923b1CAS |
Cran DG, Dyer AF (1973) Membrane continuity and associations in the fern, Dryopteris borreri. Protoplasma 76, 103–108.
| Membrane continuity and associations in the fern, Dryopteris borreri.Crossref | GoogleScholarGoogle Scholar |
Cretoiu D, Gherghiceanu M, Hummel E, Zimmermann H, Simionescu O, Popescu LM (2015) FIB-SEM tomography of human skin telocytes and their extracellular vesicles. Journal of Cellular and Molecular Medicine 19, 714–722.
| FIB-SEM tomography of human skin telocytes and their extracellular vesicles.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXlsVKjsrw%3D&md5=f5e9f63363e7bbdc737b1c2030073f24CAS |
Crotty WJ, Ledbetter MC (1973) Membrane continuities involving chloroplasts and other organelles in plant cells. Science 182, 839–841.
| Membrane continuities involving chloroplasts and other organelles in plant cells.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC3cvgsFCjsg%3D%3D&md5=465a58ff17231cb6f9ad9743a0c7221dCAS |
Crumpton-Taylor M, Grandison S, Png KM, Bushby AJ, Smith AM (2012) Control of starch granule numbers in Arabidopsis chloroplasts. Plant Physiology 158, 905–916.
| Control of starch granule numbers in Arabidopsis chloroplasts.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XltVOktbY%3D&md5=a9e151cd95945ba7e7d4fcb0cb89d844CAS |
Dahl R, Staehelin LA (1989) High-pressure freezing for the preservation of biological structure: theory and practice. Journal of Electron Microscopy Technique 13, 165–174.
| High-pressure freezing for the preservation of biological structure: theory and practice.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DyaK3c%2Fmtlyhtw%3D%3D&md5=267500f6cb9ea593a6c3ea744f0b6469CAS |
Ding B, Turgeon R, Parthasarathy MV (1992) Substructure of freeze-substituted plasmodesmata. Protoplasma 169, 28–41.
| Substructure of freeze-substituted plasmodesmata.Crossref | GoogleScholarGoogle Scholar |
Drobne D, Milani M, Zrimec A, Zrimec MB, Tatti F, Draslar K (2005) Focused ion beam/scanning electron microscopy studies of Porcellio scaber (Isopoda, Crustacea) digestive gland epithelium cells. Scanning 27, 30–34.
| Focused ion beam/scanning electron microscopy studies of Porcellio scaber (Isopoda, Crustacea) digestive gland epithelium cells.Crossref | GoogleScholarGoogle Scholar |
Hanks JF, Schubert K, Tolbert NE (1983) Isolation and characterization of infected and uninfected cells from soybean nodules: role of uninfected cells in ureide synthesis. Plant Physiology 71, 869–873.
| Isolation and characterization of infected and uninfected cells from soybean nodules: role of uninfected cells in ureide synthesis.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL3sXitFartLc%3D&md5=5d169728e0708a4ff434a918bb9425e6CAS |
Hayles MF, Stokes DJ, Phifer D, Findlay KC (2007) A technique for improved focused ion beam milling of cryo-prepared life science specimens. Journal of Microscopy 226, 263–269.
| A technique for improved focused ion beam milling of cryo-prepared life science specimens.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXnvVCiu7w%3D&md5=d95225a00ba9e38e2ca3251733f34210CAS |
House A, Balkwill K (2013) FIB-SEM: an additional technique for investigating internal structure of pollen walls. Microscopy and Microanalysis 19, 1535–1541.
| FIB-SEM: an additional technique for investigating internal structure of pollen walls.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhslKrs7zJ&md5=281c42b4e0328979a96b5766c56491a2CAS |
House A, Balkwill K (2016) Labyrinths, columns and cavities: new internal features of pollen grain walls in the Acanthaceae detected by FIB-SEM. Journal of Plant Research 129, 225–240.
| Labyrinths, columns and cavities: new internal features of pollen grain walls in the Acanthaceae detected by FIB-SEM.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XitVGiuw%3D%3D&md5=4fecd8219c491d31dca9ffca37d3e2a0CAS |
Iacovache I, De Carlo S, Cirauqui N, Dal Peraro M, van der Goot FG, Zuber B (2016) Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process. Nature Communications 7, 12062
| Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process.Crossref | GoogleScholarGoogle Scholar |
Kittelmann M, Hawes C, Hughes L (2016) Serial block face scanning electron microscopy and the reconstruction of plant cell membrane systems. Journal of Microscopy 263, 200–211.
| Serial block face scanning electron microscopy and the reconstruction of plant cell membrane systems.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XhtFOjt7fM&md5=ff5aa512d1ffc39f89d46a2eb5fec829CAS |
Kopek BG, Shtengel G, Xu CS, Clayton DA, Hess HF (2012) Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes. Proceedings of the National Academy of Sciences of the United States of America 109, 6136–6141.
| Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xmt12mtbg%3D&md5=ba18a6adba5613a12d414775659a762bCAS |
Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont JC, Mc Guire C, Nowack MK, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, VAN Brempt R, Visser Y, Guérin CJ (2015) Developing 3D SEM in a broad biological context. Journal of Microscopy 259, 80–96.
| Developing 3D SEM in a broad biological context.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC2Mvpsl2hug%3D%3D&md5=9d12c8d380cc89e57d0e26242ff485a1CAS |
Lütz-Meindl U, Luckner M, Andosch A, Wanner G (2016) Structural stress responses and degradation of dictyosomes in algae analysed by TEM and FIB-SEM tomography. Journal of Microscopy 263, 129–141.
| Structural stress responses and degradation of dictyosomes in algae analysed by TEM and FIB-SEM tomography.Crossref | GoogleScholarGoogle Scholar |
McDonald K (1999) High-pressure freezing for preservation of high resolution fine structure and antigenicity for immunolabeling. Methods in Molecular Biology 117, 77–97.
McDonald KL, Webb RI (2011) Freeze substitution in 3 hours or less. Journal of Microscopy 243, 227–233.
| Freeze substitution in 3 hours or less.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC3MjkvFyiug%3D%3D&md5=6a4a95372ed82fbfcad064657f82e38bCAS |
McLean B, Whatley JM, Juniper BE (1988) Continuity of chloroplast and endoplasmic reticulum membranes in Chara and Equisetum. New Phytologist 109, 59–65.
| Continuity of chloroplast and endoplasmic reticulum membranes in Chara and Equisetum.Crossref | GoogleScholarGoogle Scholar |
Mehrshahi P, Stefano G, Andaloro JM, Brandizzi F, Froehlich JE, DellaPenna D (2013) Transorganellar complementation redefines the biochemical continuity of endoplasmic reticulum and chloroplasts. Proceedings of the National Academy of Sciences of the United States of America 110, 12126–12131.
| Transorganellar complementation redefines the biochemical continuity of endoplasmic reticulum and chloroplasts.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXht1emu77E&md5=b4b4ac283811070afa83779308b728dcCAS |
Mehrshahi P, Johnny C, DellaPenna D (2014) Redefining the metabolic continuity of chloroplasts and ER. Trends in Plant Science 19, 501–507.
| Redefining the metabolic continuity of chloroplasts and ER.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXkvFSjsL4%3D&md5=843cdb4c9c3e23d91920cb416b88de35CAS |
Melo RC, Morgan E, Monahan-Earley R, Dvorak AM, Weller PF (2014) Pre-embedding immunogold labeling to optimize protein localization at subcellular compartments and membrane microdomains of leukocytes. Nature Protocols 9, 2382–2394.
| Pre-embedding immunogold labeling to optimize protein localization at subcellular compartments and membrane microdomains of leukocytes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXhsFOlt77M&md5=7f1a737319d48ac113d0d818b3d6b8f6CAS |
Mersey B, McCully ME (1978) Monitoring of the course of fixation of plant cells. Journal of Microscopy 114, 49–76.
| Monitoring of the course of fixation of plant cells.Crossref | GoogleScholarGoogle Scholar |
Milne RG, Ramasso E, Lenzi R, Masenga V, Sarindu N, Clark MF (1995) Pre- and post-embedding immunogold labeling and electron microscopy in plant host tissues of three antigenically unrelated MLOs: primula yellows, tomato big bud and bermudagrass white leaf. European Journal of Plant Pathology 101, 57–67.
| Pre- and post-embedding immunogold labeling and electron microscopy in plant host tissues of three antigenically unrelated MLOs: primula yellows, tomato big bud and bermudagrass white leaf.Crossref | GoogleScholarGoogle Scholar |
Newcomb EH, Tandon SR (1981) Uninfected cells of soybean root nodules: ultrastructure suggests key role in ureide production. Science 212, 1394–1396.
| Uninfected cells of soybean root nodules: ultrastructure suggests key role in ureide production.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL3MXktl2jsLk%3D&md5=8cd53fe915b9d395b8d2a8863d5a662dCAS |
Okamoto N, Keeling PJ (2014) The 3D structure of the apical complex and association with the flagellar apparatus revealed by serial TEM tomography in Psammosa pacifica, a distant relative of the Apicomplexa. PLoS One 9, e84653
| The 3D structure of the apical complex and association with the flagellar apparatus revealed by serial TEM tomography in Psammosa pacifica, a distant relative of the Apicomplexa.Crossref | GoogleScholarGoogle Scholar |
Otegui MS, Mastronarde DN, Kang BH, Bednarek SY, Staehelin LA (2001) Three-dimensional analysis of syncytial-type cell plates during endosperm cellularization visualized by high resolution electron tomography. The Plant Cell 13, 2033–2051.
| Three-dimensional analysis of syncytial-type cell plates during endosperm cellularization visualized by high resolution electron tomography.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3MXnt12ht7o%3D&md5=65861f40a4de7366bf2456310453d551CAS |
Overall RL, Wolfe J, Gunning BES (1982) Intercellular communication in Azolla roots: I. Ultrastructure of plasmodesmata. Protoplasma 111, 134–150.
| Intercellular communication in Azolla roots: I. Ultrastructure of plasmodesmata.Crossref | GoogleScholarGoogle Scholar |
Park SJ, Schertel A, Lee KE, Han SS (2014) Ultra-structural analysis of the brain in a Drosophila model of Alzheimer’s disease using FIB/SEM microscopy. Microscopy 63, 3–13.
| Ultra-structural analysis of the brain in a Drosophila model of Alzheimer’s disease using FIB/SEM microscopy.Crossref | GoogleScholarGoogle Scholar |
Schertel A, Snaidero N, Han HM, Ruhwedel T, Laue M, Grabenbauer M, Mobius W (2013) Cryo FIB-SEM: volume imaging of cellular ultrastructure in native frozen specimens. Journal of Structural Biology 184, 355–360.
| Cryo FIB-SEM: volume imaging of cellular ultrastructure in native frozen specimens.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhslSmurbJ&md5=131e538f0ac766a1001382a7824f1921CAS |
Schmidt F, Kuhbacher M, Gross U, Kyriakopoulos A, Schubert H, Zehbe R (2011) From 2D slices to 3D volumes: image based reconstruction and morphological characterization of hippocampal cells on charged and uncharged surfaces using FIB/SEM serial sectioning. Ultramicroscopy 111, 259–266.
| From 2D slices to 3D volumes: image based reconstruction and morphological characterization of hippocampal cells on charged and uncharged surfaces using FIB/SEM serial sectioning.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXisVyrtL8%3D&md5=032dfeacc383381221e265c07148d100CAS |
Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9, 671–675.
| NIH Image to ImageJ: 25 years of image analysis.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhtVKntb7P&md5=d0e047c13797abd8a794b8b1e00e9cedCAS |
Selker JM, Newcomb EH (1985) Spatial relationships between uninfected and infected cells in root nodules of soybean. Planta 165, 446–454.
| Spatial relationships between uninfected and infected cells in root nodules of soybean.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC2c7ntlemsg%3D%3D&md5=a84c64f04c9c5b18621b62eb427be5f6CAS |
Sousa AA, Azari AA, Zhang G, Leapman RD (2011) Dual-axis electron tomography of biological specimens: extending the limits of specimen thickness with bright-field STEM imaging. Journal of Structural Biology 174, 107–114.
| Dual-axis electron tomography of biological specimens: extending the limits of specimen thickness with bright-field STEM imaging.Crossref | GoogleScholarGoogle Scholar |
Staehelin LA, Kang BH (2008) Nanoscale architecture of endoplasmic reticulum export sites and of Golgi membranes as determined by electron tomography. Plant Physiology 147, 1454–1468.
| Nanoscale architecture of endoplasmic reticulum export sites and of Golgi membranes as determined by electron tomography.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtVSrsbfL&md5=649b40b517a697fc8331adb1ba6ebb4cCAS |
Studer D, Hennecke H, Muller M (1992) High-pressure freezing of soybean nodules leads to an improved preservation of ultrastructure. Planta 188, 155–163.
| High-pressure freezing of soybean nodules leads to an improved preservation of ultrastructure.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC2c7hslChsQ%3D%3D&md5=e16c5cf2779ea68da31f9fc08067d932CAS |
Terauchi M, Nagasato C, Kajimura N, Mineyuki Y, Okuda K, Katsaros C, Motomura T (2012) Ultrastructural study of plasmodesmata in the brown alga Dictyota dichotoma (Dictyotales, Phaeophyceae). Planta 236, 1013–1026.
| Ultrastructural study of plasmodesmata in the brown alga Dictyota dichotoma (Dictyotales, Phaeophyceae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhsVWnsLvJ&md5=a36c8b780a1c1be49bcf11fc844cd801CAS |
Udvardi MK, Day DA (1997) Metabolite transport across symbiotic membranes of legume nodules. Annual Review of Plant Physiology and Plant Molecular Biology 48, 493–523.
| Metabolite transport across symbiotic membranes of legume nodules.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2sXjs1emt7g%3D&md5=469a96c7415332a89d150d3ee38b45ddCAS |
Vance CP (1983) Rhizobium infection and nodulation: a beneficial plant disease? Annual Review of Microbiology 37, 399–424.
| Rhizobium infection and nodulation: a beneficial plant disease?Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DyaL2c%2FltV2ktw%3D%3D&md5=fbef84f50f7d1ca8d46c7948b630ad5bCAS |
Vaughn KC, Campbell WH (1988) Immunogold localization of nitrate reductase in maize leaves. Plant Physiology 88, 1354–1357.
| Immunogold localization of nitrate reductase in maize leaves.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaL1MXnt1GgtA%3D%3D&md5=03dc350cf617145982b7582eba85d331CAS |
Villinger C, Gregorius H, Kranz C, Hohn K, Munzberg C, von Wichert G, Mizaikoff B, Wanner G, Walther P (2012) FIB/SEM tomography with TEM-like resolution for 3D imaging of high-pressure frozen cells. Histochemistry and Cell Biology 138, 549–556.
| FIB/SEM tomography with TEM-like resolution for 3D imaging of high-pressure frozen cells.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xht12mur3E&md5=4d9a8e8ec4a8173895b3d388b698d544CAS |
Wanner G, Schafer T, Lutz-Meindl U (2013) 3-D analysis of dictyosomes and multivesicular bodies in the green alga Micrasterias denticulata by FIB/SEM tomography. Journal of Structural Biology 184, 203–211.
| 3-D analysis of dictyosomes and multivesicular bodies in the green alga Micrasterias denticulata by FIB/SEM tomography.Crossref | GoogleScholarGoogle Scholar |
Wei D, Jacobs S, Modla S, Zhang S, Young CL, Cirino R, Caplan J, Czymmek K (2012) High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy. BioTechniques 53, 41–48.
White RG, Badelt K, Overall RL, Vesk M (1994) Actin associated with plasmodesmata. Protoplasma 180, 169–184.
| Actin associated with plasmodesmata.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2MXis1Ght7w%3D&md5=ec0f098bc3bdf10c78294ee3ef27a2a5CAS |
Young RJ, Dingle T, Robinson K, Pugh PJA (1993) An application of scanned focused ion beam milling to studies on the internal morphology of small arthropods. Journal of Microscopy 172, 81–88.
| An application of scanned focused ion beam milling to studies on the internal morphology of small arthropods.Crossref | GoogleScholarGoogle Scholar |