TY - JOUR A1 - Yu, Tien-Shin A1 - Kofler, Heike A1 - Häusler, Rainer E. A1 - Hille, Diana A1 - Flügge, Ulf-Ingo A1 - Zeeman, Samuel C. A1 - Smith, Alison M. A1 - Kossmann, Jens A1 - Lloyd, James R. A1 - Ritte, Gerhard A1 - Steup, Martin A1 - Lue, Wei-Ling A1 - Chen, Jychian A1 - Weber, Andreas P. M. T1 - The Arabidopsis sex1 mutant is defective in the R1 protein, a general regulator of starch degradation in plants, and not in the chloroplast hexose transporter Y1 - 2001 SN - 1040-4651 ER - TY - JOUR A1 - Weber, Andreas P. M. A1 - Oesterhelt, Christine A1 - Gross, Wolfgang A1 - Bräutigam, Andrea A1 - Imboden, Lori A1 - Krassovskaya, Inga A1 - Linka, Nicole A1 - Truchina, Julia A1 - Schneidereit, Jörg A1 - Voll, Lars A1 - Zimmermann, Marc A1 - Jamai, Aziz A1 - Riekhof, Wayne A1 - Yu, Bin A1 - Garavito, Michael R. A1 - Benning, Christoph T1 - EST-analysis of the thermo-acidophilic red microalga Galdieria sulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts N2 - When we think of extremophiles, organisms adapted to extreme environments, prokaryotes come to mind first. However, the unicellular red micro-alga Galdieria sulphuraria (Cyanidiales) is a eukaryote that can represent up to 90% of the biomass in extreme habitats such as hot sulfur springs with pH values of 0-4 and temperatures of up to 56 degreesC. This red alga thrives autotrophically as well as heterotrophically on more than 50 different carbon sources, including a number of rare sugars and sugar alcohols. This biochemical versatility suggests a large repertoire of metabolic enzymes, rivaled by few organisms and a potentially rich source of thermo-stable enzymes for biotechnology. The temperatures under which this organism carries out photosynthesis are at the high end of the range for this process, making G. sulphuraria a valuable model for physical studies on the photosynthetic apparatus. In addition, the gene sequences of this living fossil reveal much about the evolution of modern eukaryotes. Finally, the alga tolerates high concentrations of toxic metal ions such as cadmium, mercury, aluminum, and nickel, suggesting potential application in bioremediation. To begin to explore the unique biology of G. sulphuraria, 5270 expressed sequence tags from two different cDNA libraries have been sequenced and annotated. Particular emphasis has been placed on the reconstruction of metabolic pathways present in this organism. For example, we provide evidence for (i) a complete pathway for lipid A biosynthesis; (ii) export of triose-phosphates from rhodoplasts; (iii) and absence of eukaryotic hexokinases. Sequence data and additional information are available at http://genomics.msu.edu/galdieria Y1 - 2004 ER - TY - JOUR A1 - Cheng, Shifeng A1 - van den Bergh, Erik A1 - Zeng, Peng A1 - Zhong, Xiao A1 - Xu, Jiajia A1 - Liu, Xin A1 - Hofberger, Johannes A1 - de Bruijn, Suzanne A1 - Bhide, Amey S. A1 - Kuelahoglu, Canan A1 - Bian, Chao A1 - Chen, Jing A1 - Fan, Guangyi A1 - Kaufmann, Kerstin A1 - Hall, Jocelyn C. A1 - Becker, Annette A1 - Bräutigam, Andrea A1 - Weber, Andreas P. M. A1 - Shi, Chengcheng A1 - Zheng, Zhijun A1 - Li, Wujiao A1 - Lv, Mingju A1 - Tao, Yimin A1 - Wang, Junyi A1 - Zou, Hongfeng A1 - Quan, Zhiwu A1 - Hibberd, Julian M. A1 - Zhang, Gengyun A1 - Zhu, Xin-Guang A1 - Xu, Xun A1 - Schranz, M. Eric T1 - The Tarenaya hassleriana Genome Provides insight Into Reproductive Trait and Genome Evolution of Crucifers JF - The plant cell N2 - The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-alpha) that is independent of the Brassicaceae-specific duplication (At-alpha) and nested Brassica (Br-a) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes. Y1 - 2013 U6 - https://doi.org/10.1105/tpc.113.113480 SN - 1040-4651 VL - 25 IS - 8 SP - 2813 EP - 2830 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Barbier, Guillaume A1 - Oesterhelt, Christine A1 - Larson, Matthew D. A1 - Halgren, Robert G. A1 - Wilkerson, Curtis A1 - Garavito, Michael R. A1 - Benning, Christoph A1 - Weber, Andreas P. M. T1 - Comparative genomics of two closely related unicellular thermo-acidophilic red algae, Galdieria sulphuraria and Cyanidioschyzon merolae, reveals the molecular basis of the metabolic flexibility of Galdieria sulphuraria and sigant differences in carbohydrate metabolism of both algae N2 - Unicellular algae serve as models for the study and discovery of metabolic pathways, for the functional dissection of cell biological processes such as organellar division and cell motility, and for the identification of novel genes and gene functions. The recent completion of several algal genome sequences and expressed sequence tag collections and the establishment of nuclear and organellar transformation methods has opened the way for functional genomics approaches using algal model systems. The thermo-acidophilic unicellular red alga Galdieria sulphuraria represents a particularly interesting species for a genomics approach owing to its extraordinary metabolic versatility such as heterotrophic and mixotrophic growth on more than 50 different carbon sources and its adaptation to hot acidic environments. However, the ab initio prediction of genes required for unknown metabolic pathways from genome sequences is not trivial. A compelling strategy for gene identification is the comparison of similarly sized genomes of related organisms with different physiologies. Using this approach, candidate genes were identified that are critical to the metabolic versatility of Galdieria. Expressed sequence tags and high-throughput genomic sequence reads covering >70% of the G. sulphuraria genome were compared to the genome of the unicellular, obligate photoautotrophic red alga Cyanidioschyzon merolae. More than 30% of the Galdieria sequences did not relate to any of the Cyandioschyzon genes. A closer inspection of these sequences revealed a large number of membrane transporters and enzymes of carbohydrate metabolism that are unique to Galdieria. Based on these data, it is proposed that genes involved in the uptake of reduced carbon compounds and enzymes involved in their metabolism are crucial to the metabolic flexibility of G. sulphuraria Y1 - 2005 ER -