Functional Genomics

Using a systems biology approach, we are modeling biochemical pathways and regulatory processes that affect plant function and development. Among the central biochemical pathways in plants, isoprenoid synthesis produces key molecules for cellular function and metabolites of pharmacological interest. Genetic or biochemical disruption of pathway flux triggers changes in gene expression and metabolite end products. We are linking databases to explore the interdependence of biochemical pathway information and regulatory networks. A similar approach is applied to cell cycle regulation, which is the basis for developmental and differentiation processes.

The complete analysis of the chloroplast proteome is at the frontiers of understanding the organelle as a functional system. Exploiting advanced technologies and computing algorithms, we are discovering many novel proteins. Their genetic characterization will provide important new information on chloroplast pathways. The combined knowledge from systems approaches will allow us to model and predict plant functions.

• Symplasmic phloem unloading and radial post-phloem transport via vascular rays in tuberous roots of Manihot esculenta
  Mehdi, Rabih; Lamm, Christian E.; Bodampalli Anjanappa, Ravi; Muedsam, Christina; Saeed, Muhammad; et al.
  Journal Of Experimental Botany,  https://doi.org/10.1093/jxb/erz297, OCT 15 2019
• Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
  Kuon, JE; Qi, WH; Schlapfer, P; Hirsch-Hoffmann, M; von Bieberstein, PR; Patrignani, A; Poveda, L; Grob, S; Keller, M; Shimizu-Inatsugi, R; Grossniklaus, U; Vanderschuren, H; Gruissem, W
  BMC BIOLOGY, 17 (1):10.1186/s12915-019-0697-6 SEP 18 2019
• Enhancement of vitamin B-6 levels in rice expressing Arabidopsis vitamin B-6 biosynthesis de novo genes
  Mangel, N; Fudge, JB; Li, KT; Wu, TY; Tohge, T; Fernie, AR; Szurek, B; Fitzpatrick, TB; Gruissem, W; Vanderschuren, H
  PLANT JOURNAL, 10.1111/tpj.14379 
• Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings
  Uhrig, RG; Schlapfer, P; Roschitzki, B; Hirsch-Hoffmann, M; Gruissem, W
  PLANT JOURNAL, 99 (1):176-194; 10.1111/tpj.14315 JUL 2019
• A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field
  Mehta, D; Hirsch-Hoffmann, M; Were, M; Patrignani, A; Zaidi, SSEA; Were, H; Gruissem, W; Vanderschuren, H
  NUCLEIC ACIDS RESEARCH, 47 (2):10.1093/nar/gky914 JAN 25 2019
• Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses
  Mehta, D; Sturchler, A; Anjanappa, RB; Zaidi, SSEA; Hirsch-Hoffmann, M; Gruissem, W; Vanderschuren, H
  GENOME BIOLOGY, 20 10.1186/s13059-019-1678-3 APR 25 2019
• Targeting intracellular transport combined with efficient uptake and storage significantly increases grain iron and zinc levels in rice
  Wu, Ting-Ying; Gruissem, Wilhelm; Bhullar, Navreet K.
  PLANT BIOTECHNOLOGY JOURNAL, 17 (1):9-20; 10.1111/pbi.12943 JAN 2019
• A tribute to Lars Hennig (1970-2018) Obituary
  Mozgova, I; Alexandre, C; Steinbach, Y; Derkacheva, M; Schafer, E; Gruissem, W
  JOURNAL OF EXPERIMENTAL BOTANY, 69 (21):4989-4991; https://doi.org/10.1093/jxb/ery337 OCT 12 2018
• Accelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch
  Simon E. Bull, David Seung, Christelle Chanez, Devang Mehta, Joel‑Elias Kuon, Elisabeth Truernit, Anton Hochmuth, Irene Zurkirchen, Samuel C. Zeeman, Wilhelm Gruissem and Hervé Vanderschuren
  Science Advances, 4 (9): 10.1126/sciadv.aat6086, Washington, DC: AAAS, SEP 2018.  
• Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots
  Lentz, EM; Kuon, JE; Alder, A; Mangel, N; Zainuddin, IM; McCallum, EJ; Anjanappa, RB; Gruissem, W; Vanderschuren, H
  PLANT METHODS, 14 10.1186/s13007-018-0340-5 AUG 27 2018
• Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
  Seaton, DD; Graf, A; Baerenfaller, K; Stitt, M; Millar, AJ; Gruissem, W
  MOLECULAR SYSTEMS BIOLOGY, 14 (3):10.15252/msb.20177962 MAR 2018
• Cassava post-harvest physiological deterioration: From triggers to symptoms
  Zainuddin, Ima M.; Fathoni, Ahmad; Sudarmonowati, Enny; Beeching, John R.; Gruissem, Wilhelm; Vanderschuren, Herve
  POSTHARVEST BIOLOGY AND TECHNOLOGY, 142 115-123; https://doi.org/10.1016/j.postharvbio.2017.09.004 AUG 2018
• Facilitated citrate-dependent iron translocation increases rice endosperm iron and zinc concentrations
  Wu, Ting-Ying; Gruissem, Wilhelm; Bhullar, Navreet K.
  PLANT SCIENCE, 270 13-22; https://doi.org/10.1016/j.plantsci.2018.02.002 MAY 2018
• Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
  Seaton, Daniel D.; Graf, Alexander; Baerenfaller, Katja; Stitt, Mark; Millar, Andrew J.; Gruissem, Wilhelm
  MOLECULAR SYSTEMS BIOLOGY, 14 (3): https://doi.org/10.15252/msb.20177962 MAR 2018
• …

• Pathway functional genomics
• Cell cycle and chromatin
• Biotechnology of crop improvement

• Functional genomics technologies
• Reverse engineering