May 23, 2014

Review: The Origin and Biosynthesis of the Benzenoid Moiety of Ubiquinone (Coenzyme Q) in Arabidopsis

The Plant Cell tpc.114.125807

Anna Blocka, Joshua R. Widhalmb, Abdelhak Fatihia, Rebecca E. Cahoona, Yashitola Wamboldta, Christian Elowskya, Sally A. Mackenziea, Edgar B. Cahoona, Clint Chappleb, Natalia Dudarevab and Gilles J. Basseta,*

* Corresponding author (

aCenter for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
bDepartment of Biochemistry, Purdue University, West Lafayette, Indiana 47907

Ubiquinone belongs to a family of prenylated quinone redox co-factors that are essential electron  and proton carriers in most organisms. While the biosynthesis of the prenyl side chain which anchors it to the mitochondrial membrane is fairly well understood, the biosynthesis of the benzenoid ring has long mystified plant scientists. In bacteria, the benzenoid ring is synthesized from 4-hydroxy benzoate, itself a derivative of chorismate. In fungi, the same moiety is made from para amino benzoic acid (pABA). Work headed by University of Nebraska scientist Gilles J. Basset reports this week a major advance in our understanding of the biosynthesis of the benzenoid ring of ubiquinone in plants. Using Arabidopsis thaliana, they showed that the benzenoid ring can come from either phenylalanine or tyrosine, two fully independent routes, while phenylalaine appears to provide the bulk of substrate leading to the final redox co-factor.

May 15, 2014

Review: Stitching together the Multiple Dimensions of Autophagy Using Metabolomics and Transcriptomics Reveals Impacts on Metabolism, Development, and Plant Responses to the Environment in Arabidopsis

The Plant Cell tpc.114.124677 

(click here to download the original article)

Céline Masclaux-Daubressea,b,*, Gilles Clémenta,b, Pauline Annea,b, Jean-Marc Routaboula,b, Anne Guiboileaua,b, Fabienne Soulaya,b, Ken Shirasuc and Kohki Yoshimotoa,b,c

* Corresponding author (
a Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France
b AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France
c RIKEN, Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan

    Autophagy is a cellular process whereby cytoplasmic materials and organelles are sequestered and  degraded for the purpose of recycling. This conserved process was originally discovered in yeast but also occurs in animals and plants. Chloroplast specific autophagy is known as chlorophagy. This week researchers from the RIKEN plant center in Yokohama as well as investigators from the INRA in Versaillles, France report on metabolomic and transcriptomic analysis of autophagy (atg) mutants. Extensive metabolomic analysis using GCMS of small molecules (amino acids, sugars, and organic acids), LCMS of larger metabolites (anthocynanins and phenylpropanoids), as well as enzyme assays for labile compounds (glutathione) revealed the accumulation of several amino acids, in particular glutamate and methionone, as well as amino acid intermediates (pipecolate and shikimate). These increases were noted in multiple mutant lines and were accompanied by decreases in hexose sugars. Various stress marker metabolites were also detected (raffinose, galacturonate, phytol, pipecolate, and stigmasterols). This established a link between amino acid metabolism and oxidative stress management. Transcriptomic analysis indicated a link between autophagy and cytokinin perception. This work extends our limited knowledge of autophagy in plants and highlights the metabolic pathways that are involved by identifying individual metabolites that accumulate when the genes involved in autophagy are disrupted.

May 2, 2014

Review: A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing

in Science 25 April 2014: Vol. 344 no. 6182 pp. 427-430 DOI: 10.1126/science.1250322 

(click here to download the original article)

 Ezequiel Petrillo1, Micaela A. Godoy Herz1, Armin Fuchs2, Dominik Reifer2, John Fuller3, Marcelo J. Yanovsky4, Craig Simpson3, John W. S. Brown3,5, Andrea Barta2, Maria Kalyna2, Alberto R. Kornblihtt1,*

* Corresponding author (
1Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
2Max F. Perutz Laboratories, Medical University of Vienna, A-1030 Vienna, Austria.
3Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.
4Fundación Instituto Leloir, IIBBA-CONICET, C1405BWE Buenos Aires, Argentina.
5Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland.

            The role of light again features prominently in this week’s report at the Plant Biology Review. We recently saw how light rapidly induces the transcription of the AP2/ERF transcription factor family in Arabidopsis, a process involving retrograde signaling from the chloroplast. Vogel et al. (2014) demonstrated the involvement of triose phosphates as the metabolite signal key to activating transcript on this short time scale when plants were moved from darkness to light conditions, a process leading to transcript level changes on the scale of minutes.Another report on chloroplast retrograde signaling mediated by light is reviewed here today, this time published in Science by the group of Alberto Kornblihtt from the Laboratorio de Fisiología y Biología Molecular at the University of Buenos Aires, Argentina.