Plant cell types: reporting and sampling with new technologies

Current Opinion in Plant Biology

Volumn 11, Issue 5, 2008, Pages 567-573

  Nelson, Timothy ^a   Gandotra, Neeru ^a   Tausta, S Lori ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SEPARATION; CHEMISTRY; CYTOLOGY; GENE EXPRESSION PROFILING; HISTOLOGY; METABOLISM; METHODOLOGY; PLANT; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW;

CELL SEPARATION; GENE EXPRESSION PROFILING; HISTOCYTOLOGICAL PREPARATION TECHNIQUES; PLANTS; PROTEOMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 51649097830     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2008.06.006     Document Type: Review

References (94)

1. Brandt S.P. Microgenomics: gene expression analysis at the tissue-specific and single-cell levels. J Exp Bot 56 (2005) 495-505
2. Fernie A.R. The future of metabolic phytochemistry: larger numbers of metabolites, higher resolution, greater understanding. Phytochemistry 68 (2007) 2861-2880
3. Gutstein H.B., Morris J.S., Annangudi S.P., and Sweedler J.V. Microproteomics: analysis of protein diversity in small samples. Mass Spectrom Rev 27 (2008) 316-330
4. Jilkine K., Gough K.M., Julian R., and Kaminskyj S.G. A sensitive method for examining whole-cell biochemical composition in single cells of filamentous fungi using synchrotron FTIR spectromicroscopy. J Inorg Biochem 102 (2008) 540-546
5. Jorrin J.V., Maldonado A.M., and Castillejo M.A. Plant proteome analysis: a 2006 update. Proteomics 7 (2007) 2947-2962
6. Kajiyama S., Harada K., Fukusaki E., and Kobayashi A. Single cell-based analysis of torenia petal pigments by a combination of ArF excimer laser micro sampling and nano-high performance liquid chromatography (HPLC)-mass spectrometry. J Biosci Bioeng 102 (2006) 575-578
7. Lange B.M. Single-cell genomics. Curr Opin Plant Biol 8 (2005) 236-241
8. Last R.L., Jones A.D., and Shachar-Hill Y. Towards the plant metabolome and beyond. Nat Rev Mol Cell Biol 8 (2007) 167-174
9. Lee J.Y., Levesque M., and Benfey P.N. High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems. Plant Physiol 138 (2005) 585-590
10. Li C., Yi H., Tan Y.X., Ai J.H., Zhou H., Li S.J., Zhang L., Xia Q.C., Wu J.R., Wang H.Y., et al. Analysis of microdissected cells by two-dimensional LC-MS approaches. Methods Mol Biol 428 (2007) 193-208
11. Mustafa D., Kros J.M., and Luider T. Combining laser capture microdissection and proteomics techniques. Methods Mol Biol 428 (2007) 159-178
12. Ohtsu K., Takahashi H., Schnable P.S., and Nakazono M. Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies. Plant Cell Physiol 48 (2007) 3-7
13. Schad M., Lipton M.S., Giavalisco P., Smith R.D., and Kehr J. Evaluation of two-dimensional electrophoresis and liquid chromatography-tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples. Electrophoresis 26 (2005) 2729-2738
14. Schad M., Mungur R., Fiehn O., and Kehr J. Metabolic profiling of laser microdissected vascular bundles of Arabidopsis thaliana. Plant Methods 1 (2005) 2
15. Shoemaker G.K., Lorieau J., Lau L.H., Gillmor C.S., and Palcic M.M. Multiple sampling in single-cell enzyme assays using CE-laser-induced fluorescence to monitor reaction progress. Anal Chem 77 (2005) 3132-3137
16. Casson S.A., Spencer M.W.B., and Lindsey K. Laser-capture microdissection to study global transcriptional changes during plant embryogenesis. Methods Mol Biol 427 (2008) 111-120
17. Verscht J., Tomos D., and Komor E. Sugar concentrations along and across the Ricinus communis L. hypocotyl measured by single cell sampling analysis. Planta 224 (2006) 1303-1314
18. Wang H., Qian W.J., Mottaz H.M., Clauss T.R., Anderson D.J., Moore R.J., Camp II D.G., Khan A.H., Sforza D.M., Pallavicini M., et al. Development and evaluation of a micro- and nanoscale proteomic sample preparation method. J Proteome Res 4 (2005) 2397-2403
19. Weckwerth W. Integration of metabolomics and proteomics in molecular plant physiology-coping with the complexity by data-dimensionality reduction. Physiol Plant 132 (2008) 176-189
20. Xia F., Jin W., Yin X., and Fang Z. Single-cell analysis by electrochemical detection with a microfluidic device. J Chromatogr A 1063 (2005) 227-233
21. Meyers B.C., Galbraith D.W., Nelson T., and Agrawal V. Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol 135 (2004) 637-652
22. Hennig L. Patterns of beauty-omics meets plant development. Trends Plant Sci 12 (2007) 287-293. The author gives an inspiring vision of ways in which new technologies and systems analysis can aid developmental biology.
23. Rensink W.A., and Buell C.R. Microarray expression profiling resources for plant genomics. Trends Plant Sci 10 (2005) 603-609
24. Nobuta K., Venu R.C., Lu C., Belo A., Vemaraju K., Kulkarni K., Wang W., Pillay M., Green P.J., Wang G.L., et al. An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25 (2007) 473-477. Although not at the cell type level, the authors set a high standard for a data atlas, consisting of rigorously comparable datasets from a variety of plant parts, treatments and stages. A valuable reference for those making cell type comparisons.
25. ••]
26. •,27,29], the authors use a variety of system approaches to mine patterns and relationships from the first comprehensive database of Arabidopsis root cell type transcriptomes. Cell types were obtained using FACS on lines with transgenes producing cell-specific GFP markers.
27. Dinneny J.R., Long T.A., Wang J.Y., Jung J.W., Mace D., Pointer S., Barron C., Brady S.M., Schiefelbein J., and Benfey P.N. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320 (2008) 942-945
28. Gifford M.L., Dean A., Gutierrez R.A., Coruzzi G.M., and Birnbaum K.D. Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A 105 (2008) 803-808
29. Nawy T., Lee J.-Y., Colinas J., Wang J.Y., Thongrod S.C., Malamy J.E., Birnbaum K., and Benfey P.N. Transcriptional profile of the Arabidopsis root quiescent center. The Plant Cell 17 (2005) 1908-1925
30. Breaker R.R. Engineered allosteric ribozymes as biosensor components. Curr Opin Biotechnol 13 (2002) 31-39
31. Breaker R.R. Natural and engineered nucleic acids as tools to explore biology. Nature 432 (2004) 838-845
32. Li I.T., Pham E., and Truong K. Protein biosensors based on the principle of fluorescence resonance energy transfer for monitoring cellular dynamics. Biotechnol Lett 28 (2006) 1971-1982
33. Berg R.H., and Beachy R.N. Fluorescent protein applications in plants. Methods Cell Biol 85 (2008) 153-177
34. Wild E., Dent J., Thomas G.O., and Jones K.C. Use of two-photon excitation microscopy and autofluorescence for visualizing the fate and behavior of semivolatile organic chemicals within living vegetation. Environ Toxicol Chem 26 (2007) 2486-2493
35. Ehrhardt D. GFP technology for live cell imaging. Curr Opin Plant Biol 6 (2003) 622-628
36. Houben A., Orford S.J., and Timmis J.N. In situ hybridization to plant tissues and chromosomes. Methods Mol Biol 326 (2006) 203-218
37. Aki T., Shigyo M., Nakano R., Yoneyama T., and Yanagisawa S. Nano scale proteomics revealed the presence of regulatory proteins including three FT-like proteins in phloem and xylem saps from rice. Plant Cell Physiol (2008) in press
38. Alvarez S., Marsh E.L., Schroeder S.G., and Schachtman D.P. Metabolomic and proteomic changes in the xylem sap of maize under drought. Plant Cell Environ 31 (2008) 325-340
39. Doering-Saad C., Newbury H.J., Bale J.S., and Pritchard J. Use of aphid stylectomy and RT-PCR for the detection of transporter mRNAs in sieve elements. J Exp Bot 53 (2002) 631-637
40. Doering-Saad C., Newbury H.J., Couldridge C.E., Bale J.S., and Pritchard J. A phloem-enriched cDNA library from Ricinus: insights into phloem function. J Exp Bot 57 (2006) 3183-3193
41. Gaupels F., Knauer T., and van Bel A.J. A combinatory approach for analysis of protein sets in barley sieve-tube samples using EDTA-facilitated exudation and aphid stylectomy. J Plant Physiol 165 (2008) 95-103
42. Kehr J., and Rep M. Protein extraction from xylem and phloem sap. Methods Mol Biol 355 (2007) 27-35
43. Brandt S., Kloska S., Altmann T., and Kehr J. Using array hybridization to monitor gene expression at the single cell level. J Exp Bot 53 (2002) 2315-2323
44. Karrer E.E., Lincoln J.E., Hogenhout S., Bennett A.B., Bostock R.M., Martineau B., Lucas W.J., Gilchrist D.G., and Alexander D. In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proc Natl Acad Sci U S A 92 (1995) 3814-3818
45. Wienkoop S., Zoeller D., Ebert B., Simon-Rosin U., Fisahn J., Glinski M., and Weckwerth W. Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification. Phytochemistry 65 (2004) 1641-1649
46. Raps A., Kehr J., Gugerli P., Moar W.J., Bigler F., and Hilbeck A. Immunological analysis of phloem sap of Bacillus thuringiensis corn and of the nontarget herbivore Rhopalosiphum padi (Homoptera: Aphididae) for the presence of Cry1Ab. Mol Ecol 10 (2001) 525-533
47. Tomos A.D., and Sharrock R.A. Cell sampling and analysis (SiCSA): metabolites measured at single cell resolution. J Exp Bot 52 (2001) 623-630
48. Brandt S., Kehr J., Walz C., Imlau A., Willmitzer L., and Fisahn J. Technical advance: a rapid method for detection of plant gene transcripts from single epidermal, mesophyll and companion cells of intact leaves. Plant J 20 (1999) 245-250
49. Matsuoka H., Komazaki T., Mukai Y., Shibusawa M., Akane H., Chaki A., Uetake N., and Saito M. High throughput easy microinjection with a single-cell manipulation supporting robot. J Biotechnol 116 (2005) 185-194
50. Zhao C., Craig J.C., Petzold H.E., Dickerman A.W., and Beers E.P. The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl. Plant Physiol 138 (2005) 803-818. The authors use mechanical microdissection to permit the comparison of xylem- and phloem-enriched transcriptomes. Information emerging from comparisons enabled gene discovery and subsequent characterization.
51. Thome M., Skrablin M.D., and Brandt S.P. Tissue-specific mechanical microdissection of higher plants. Physiologia Plantarum 128 (2006) 383-390
52. •], the authors employ comparison of bundle sheath and mesophyll transcriptomes and proteomes from maize leaves to investigate the basis for the cooperation of these cell types for C4 biology.
53. ••]
54. ••]
55. Demura T., Tashiro G., Horiguchi G., Kishimoto N., Kubo M., Matsuoka N., Minami A., Nagata-Hiwatashi M., Nakamura K., Okamura Y., et al. Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc Natl Acad Sci U S A 99 (2002) 15794-15799
56. Milioni D., Sado P.E., Stacey N.J., Roberts K., and McCann M.C. Early gene expression associated with the commitment and differentiation of a plant tracheary element is revealed by cDNA-amplified fragment length polymorphism analysis. Plant Cell 14 (2002) 2813-2824
57. Davey M.R., Anthony P., Power J.B., and Lowe K.C. Plant protoplasts: status and biotechnological perspectives. Biotechnol Adv 23 (2005) 131-171
58. Galbraith D.W., and Birnbaum K. Global studies of cell type-specific gene expression in plants. Annu Rev Plant Biol 57 (2006) 451-475
59. Zhang C., Lambert G.M., Barthelson R.A., and Galbraith D.W. Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol 147 (2008) 30-40
60. Engel M.L., Chaboud A., Dumas C., and McCormick S. Sperm cells of Zea mays have a complex complement of mRNAs. Plant J 34 (2003) 697-707
61. Day R.C., Grossniklaus U., and Macknight R.C. Be more specific! Laser-assisted microdissection of plant cells. Trends Plant Sci 10 (2005) 397-406
62. Day R.C., McNoe L., and Macknight R.C. Evaluation of global RNA amplification and its use for high-throughput transcript analysis of laser-microdissected endosperm. Int J Plant Genomics (2007) 61028
63. Day R.C.M., Les A., and Macknight R.C. Transcript analysis of laser microdissected plant cells. Physiologia Plantarum 129 (2007) 267-282
64. Kerk N.M., Ceserani T., Tausta S.L., Sussex I.M., and Nelson T.M. Laser capture microdissection of cells from plant tissues. Plant Physiol 132 (2003) 27-35
65. Nakazono M., Qiu F., Borsuk L.A., and Schnable P.S. 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 tissues of maize. Plant Cell 15 (2003) 583-596
66. Nelson T., Tausta S.L., Gandotra N., and Liu T. Laser microdissection of plant tissue: what you see is what you get. Annu Rev Plant Biol 57 (2006) 181-201
67. Spencer M.W., Casson S.A., and Lindsey K. Transcriptional profiling of the Arabidopsis embryo. Plant Physiol 143 (2007) 924-940. The authors provide a rigorous comparison of cellular regions of developing Arabidopsis embryos, revealing gene sets with a variety of coordinate developmental profiles.
68. Kehr J. Single cell technology. Curr Opin Plant Biol 6 (2003) 617-621
69. Jiang K., Zhang S., Lee S., Tsai G., Kim K., Huang H., Chilcott C., Zhu T., and Feldman L.J. Transcription profile analyses identify genes and pathways central to root cap functions in maize. Plant Mol Biol 60 (2006) 343-363
70. Barbazuk W.B., Emrich S.J., Chen H.D., Li L., and Schnable P.S. SNP discovery via 454 transcriptome sequencing. Plant J 51 (2007) 910-918
71. Emrich S.J., Barbazuk W.B., Li L., and Schnable P.S. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17 (2007) 69-73
72. Ithal N., Recknor J., Nettleton D., Maier T., Baum T.J., and Mitchum M.G. Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Mol Plant Microbe Interact 20 (2007) 510-525
73. Le B.H., Wagmaister J.A., Kawashima T., Bui A.Q., Harada J.J., and Goldberg R.B. Using genomics to study legume seed development. Plant Physiol 144 (2007) 562-574
74. •], the authors employ LM to obtain SAM zones (rather than cell types) and produce a remarkable transcriptional view of the distribution of activities and potential regulatory factors associated with the maintenance of the SAM and the initiation of leaves.
75. Wu Y., Llewellyn D.J., White R., Ruggiero K., Al-Ghazi Y., and Dennis E.S. Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules. Planta 226 (2007) 1475-1490
76. ••]
77. Cai S., and Lashbrook C.C. Stamen abscission zone transcriptome profiling reveals new candidates for abscission control: enhanced retention of floral organs in transgenic plants overexpressing arabidopsis zinc finger protein2. Plant Physiol 146 (2008) 1305-1321
78. Kryvych S., Nikiforova V., Herzog M., Perazza D., and Fisahn J. Gene expression profiling of the different stages of Arabidopsis thaliana trichome development on the single cell level. Plant Physiol Biochem 46 (2008) 160-173
79. Corpas F.J., Fernandez-Ocana A., Carreras A., Valderrama R., Luque F., Esteban F.J., Rodriguez-Serrano M., Chaki M., Pedrajas J.R., Sandalio L.M., et al. The expression of different superoxide dismutase forms is cell-type dependent in olive (Olea europaea L.) leaves. Plant Cell Physiol 47 (2006) 984-994
80. Nakada M.K., Ochiai T., Ohtsu K., Nakazono M., Nishizawa N.K., Nitta K., Nishiyama R., Kameya T., and Kanno A. Isolation of MaDEF from Muscari armeniacum and analysis of its expression using laser microdissection. Plant Science 170 (2006) 143-150
81. Wu Y., Machado A.C., White R.G., Llewellyn D.J., and Dennis E.S. Expression profiling identifies genes expressed early during lint fibre initiation in cotton. Plant Cell Physiol 47 (2006) 107-127
82. Galbiati M., Simoni L., Pavesi G., Cominelli E., Francia P., Vavasseur A., Nelson T., Bevan M., and Tonelli C. Gene trap lines identify Arabidopsis genes expressed in stomatal guard cells. Plant J 53 (2008) 750-762
83. Roy S.J., Gilliham M., Berger B., Essah P.A., Cheffings C., Miller A.J., Widdowson L., Davenport R.J., Liu L.H., Skynner M.J., et al. Investigating glutamate receptor-like gene co-expression in Arabidopsis thaliana. Plant Cell Environ 31 (2008) 861-871
84. Santi S., and Schmidt W. Laser microdissection-assisted analysis of the functional fate of iron deficiency-induced root hairs in cucumber. J Exp Bot 59 (2008) 697-704
85. Dembinsky D., Woll K., Saleem M., Liu Y., Fu Y., Borsuk L.A., Lamkemeyer T., Fladerer C., Madlung J., Barbazuk B., et al. Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiol 145 (2007) 575-588
86. Angeles G., Berrio-Sierra J., Joseleau J.P., Lorimier P., Lefebvre A., and Ruel K. Preparative laser capture microdissection and single-pot cell wall material preparation: a novel method for tissue-specific analysis. Planta 224 (2006) 228-232
87. Li S.H., Schneider B., and Gershenzon J. Microchemical analysis of laser-microdissected stone cells of Norway spruce by cryogenic nuclear magnetic resonance spectroscopy. Planta 225 (2007) 771-779
88. Holscher D., and Schneider B. Laser microdissection and cryogenic nuclear magnetic resonance spectroscopy: an alliance for cell type-specific metabolite profiling. Planta 225 (2007) 763-770
89. Cai S., and Lashbrook C.C. Laser capture microdissection of plant cells from tape-transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling. Plant J 48 (2006) 628-637
90. Tang W., Coughlan S., Crane E., Beatty M., and Duvick J. 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 (2006) 1240-1250
91. Balestrini R., Gomez-Ariza J., Lanfranco L., and Bonfante P. 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 (2007) 1055-1062
92. Hobza R., and Vyskot B. Laser microdissection-based analysis of plant sex chromosomes. Methods Cell Biol 82 (2007) 433-453
93. Yu Y., Lashbrook C.C., and Hannapel D.J. Tissue integrity and RNA quality of laser microdissected phloem of potato. Planta 226 (2007) 797-803
94. van Driel K.G., Boekhout T., Wosten H.A., Verkleij A.J., and Muller W.H. Laser microdissection of fungal septa as visualised by scanning electron microscopy. Fungal Genet Biol 44 (2007) 466-473