Abstract Higher plant microspores, when subjected to various stress treatments in vitro, are able to reprogram their regular gametophytic development towards the sporophytic pathway to form haploid embryos and plants. Suppression subtractive hybridization (SSH) and metabolic profiling were used to characterize this developmental switch. Following differential reverse Northern hybridizations 90 distinct up-regulated sequences were identified in stressed, embryogenic microspores (accessible at www.univie.ac.at/ntsm). Sequence analyses allowed the classification of these genes into functional clusters such as metabolism, chromosome remodeling, signaling, transcription and translation, while the putative functions of half of the sequences remained unknown. A comparison of meta- bolic profiles of non-stressed and stressed microspores using gas chromatography/mass spectrometry (GC/MS) identified 70 compounds, partly displaying significant changes in metabolite levels, e.g., highly elevated levels of isocitrate and isomaltose in stressed micro- spores compared to non-stressed microspores. The formation of embryogenic microspores is discussed on the basis of the identified transcriptional and metabolic profiles. Keywords Tobacco Æ Microspores Æ Embryogenesis Æ Metabolic profiling Æ Suppression subtractive hybridization Æ Transcripts Abbreviations ROS Reactive oxygen species SSH Suppression subtractive hybridization GC/MS Gas chromatography/mass spectrometry TCA Tricarbonic acid/Acetyl-CoA Introduction Isolated and in vitro cultured microspores of flowering plants can be induced to undergo a developmental switch by certain physical and chemical stress treat- ments. More precisely, microspores convert from their gametophytic development towards a sporophytic pathway, involving a stage of totipotency resulting in the formation of haploid embryos and plants (Touraev et al. 1997). Sucrose and nitrogen starvation applied to J. Hosp Æ A. Tashpulatov Æ H. Katholnigg Æ E. Heberle-Bors Æ A. Touraev (&) Max F. Perutz Laboratories, University Departments at the Campus Vienna Biocenter, Department of Plant Molecular Biology, Vienna University, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria e-mail: Alisher.Touraev@univie.ac.at U. Roessner Australian Centre for Plant Functional Genomics, School of Botany, University of Melbourne, Melbourne, Victoria 3010, Australia E. Barsova Æ S. Lukyanov Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia R. Steinborn Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Veterina ¨ rplatz 1, A-1210 Vienna, Austria Present Address: B. Melikant Intercell AG, Campus Vienna Biocenter 2, A-1030 Vienna, Austria Plant Mol Biol (2007) 63:137–149 DOI 10.1007/s11103-006-9078-y 123 Transcriptional and metabolic profiles of stress-induced, embryogenic tobacco microspores Julia Hosp Æ Alisher Tashpulatov Æ Ute Roessner Æ Ekaterina Barsova Æ Heidrun Katholnigg Æ Ralf Steinborn Æ Bala ´ zs Melikant Æ Sergey Lukyanov Æ Erwin Heberle-Bors Æ Alisher Touraev Received: 29 May 2006 / Accepted: 16 August 2006 / Published online: 3 October 2006 Ó Springer Science+Business Media B.V. 2006