Publications of iGRAD-Plant postdoctoral and doctoral researchers

2017

 

 

 

Hartmann M, Kim D, Bernsdorff F, Ajami-Rashidi Z, Scholten N, Schreiber S, Zeier T, Schuck S, Reichel-Deland V, Zeier J (2017) Biochemical Principles and Functional Aspects of Pipecolic Acid Biosynthesis in Plant Immunity. Plant Physiol. 174(1):124-153. undefineddoi: 10.1104/pp.17.00222

de Vries J, de Vries S, Slamovits C Rose LE, Archibald JM (2017) How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae? Plant Cell Physiol. 58(5):934-945. undefineddoi: 10.1093/pcp/pcx037

Rast-Somssich MI, Žádníková P, Schmid S, Kieffer M, Kepinski S, Simon R (2017) The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J Exp Bot erx131 undefineddoi: 10.1093/jxb/erx131

Heckmann D, Schlüter U, Weber APM (2017) Machine Learning Techniques for Predicting Crop Photosynthetic Capacity from Leaf Reflectance Spectra. Mol Plant. pii: S1674-2052(17)30130-2. undefineddoi: 10.1016/j.molp.2017.04.009

Fritzemeier CJ, Hartleb D, Szappanos B, Papp B, Lercher MJ (2017) Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal. PLoS Comput Biol. 13(4):e1005494. undefineddoi: 10.1371/journal.pcbi.1005494. 

Hielscher BCharton L, Mettler-Altmann T, Linka N (2017) Analysis of Peroxisomal β-Oxidation During Storage Oil Mobilization in Arabidopsis thaliana Seedlings. Methods Mol Biol. 1595:291-304. undefineddoi: 10.1007/978-1-4939-6937-1_27

Denton AKMaß JKülahoglu C, Lercher MJ, Bräutigam A, Weber AP (2017) Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. J Exp Bot. 68(2):147-160. undefineddoi: 10.1093/jxb/erw463.

Frantzeskakis FCourville KJPluecker L, Kellner R, Kruse J, Brachmann A, Feldbrügge M and Göhre V (2017) The plant-dependent life cycle of Thecaphora thlaspeos: a smut fungus adapted to Brassicacea. Mol Plant Microbe Interact. doi.org/10.1094/MPMI-08-16-0164-R

 

Brandenburg F, Schoffmann H, Kurz S, Kraemer U, Keren N, Weber APM, Eisenhut M (2017) The Synechocystis MANGANESE EXPORTER Mnx is essential for manganese homeostasis in cyanobacteria. Plant Physiology January 30, 2017 pp.01895.2016 DOI:10.1104/pp.16.01895

 

 

Hahn F, Mantegazza O, Greiner A, Hegemann P, Eisenhut M and Weber APM (2017) An Efficient Visual Screen for CRISPR/Cas9 Activity in Arabidopsis thaliana. Front. Plant Sci. 8:39. doi: 10.3389/fpls.2017.00039

 

 

2016

 

Bösch K, Frantzeskakis L, Vraneš M, Kämper J, Schipper K, Göhre V (2016) Genetic Manipulation of the Plant Pathogen Ustilago maydis to Study Fungal Biology and Plant Microbe Interactions. J Vis Exp. Sep 30;(115). undefineddoi: 10.3791/54522

Li Y, Heckmann D, Lercher MJ, Maurino VG (2016) Combining genetic and evolutionary engineering to establish C4 metabolism in C3 plants. J Exp Bot. Sep 22. pii: erw333. undefinedDOI: 10.1093/jxb/erw333

Hartleb D, Jarre F, Lercher MJ (2016) Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. PLoS Comput Biol Aug 2;12(8)e1005036 undefineddoi: 10.1371/journal.pcbi.1005036. eCollection 2016.

Correa-Galvis V, Redekop P, Guan K, Griess A, Truong TB, Wakao S, Niyogi KK, Jahns P (2016) Photosystem II Subunit PsbS Is Involved in the Induction of LHCSR Protein-dependent Energy Dissipation in Chlamydomonas reinhardtii. J Biol Chem. Aug 12;291(33):17478-87. undefineddoi: 10.1074/jbc.M116.737312.

Bisson MM, Kessenbrock M, Müller L, Hofmann A, Schmitz F, Cristescu SM, Groth G (2016) Peptides interfering with protein-protein interactions in the ethylene signaling pathway delay tomato fruit ripening. Sci Rep Aug 1;6:30634.undefined doi:1038/srep30634.

de Vries S, von Dahlen JK, Uhlmann C, Schnake A, Kloesges T, Rose LE (2016) Signatures of selection and host adapted gene expression of the Phytophthora infestans RNA-silencing suppressor PSR2. Mol Plant Pathol Aug 9 undefineddoi: 10.1111/mpp.12465. [Epub ahead of print] 

van Roermund CW, Schroers MG, Wiese J, Facchinelli F, Kurz S, Wilkinson S, Charton L, Wanders RJ, Waterham HR, Weber AP, Linka N (2016) The Peroxisomal NAD Carrier from Arabidopsis Imports NAD in Exchange with AMP. Plant Physiol. Jul;171(3):2127-39. undefineddoi: 10.1104/pp.16.00540.

Heckmann D (2016) C4 photosynthesis evolution: the conditional Mt. Fuji. Curr Opin Plant Biol. Jun;31:149-54. undefineddoi: 10.1016/j.pbi.2016.04.008.

Brilhaus D, Bräutigam A, Mettler-Altmann T, Winter K, Weber APM (2016) Reversible Burst of Transcriptional Changes during  Induction of Crassulacean Acid Metabolism in Talinum triangulare. Plant Physiol 170: 102–122, http://www.plantphysiol.org/content/170/1/102.full.pdf+html

Langner T, Göhre V (2016) Fungal chitinases: function, regulation, and potential roles in plant/pathogen interactions. Curr Genet. 62(2):243-54 undefineddoi: 10.1007/s00294-015-0530-x.

Schlüter U, Denton AK, Bräutigam A3 (2016) Understanding metabolite transport and metabolism in C4 plants through RNA-seq. Curr Opin Plant Biol 31:83-90. undefineddoi: 10.1016/j.pbi.2016.03.007

Bernsdorff F, Döhring AC, Gruner K, Schuck S, Bräutigam A, Zeier J (2016) Pipecolic Acid Orchestrates Plant Systemic Acquired Resistance and Defense Priming via Salicylic Acid-Dependent and -Independent Pathways. Plant Cell 28(1):102-29 undefineddoi: 10.1105/tpc.15.00496

Stahl E, Bellwon P, Huber S, Schlaeppi K, Bernsdorff F, Vallat-Michel A, Mauch F, Zeier J (2016) Regulatory and Functional Aspects of Indolic Metabolism in Plant Systemic Acquired Resistance. Mol Plant 9(5):662-81 undefineddoi: 10.1016/j.molp.2016.01.005.

Correa-Galvis V, Poschmann G, Melzer M, Stühler K, Jahns P (2016) PsbS interactions involved in the activation of energy dissipation in Arabidopsis. Nat Plants. Feb 1;2:15225.undefined doi: 10.1038/nplants.2015.225.

2015

de Vries S, Kloesges T, Rose LE (2015) Evolutionarily Dynamic, but Robust, Targeting of Resistance Genes by the miR482/2118 Gene Family in the Solanaceae , Genome Biol Evol 7 (12): 3307-3321. undefineddoi: 10.1093/gbe/evv225

Heckmann D (2015) Modelling metabolic evolution on phenotypic fitness landscapes: a case study on C4 photosynthesis. Biochem Soc Trans. Dec;43(6):1172-6. undefineddoi: 10.1042/BST20150148.

Boyer F, Simon R. (2015) Asymmetric cell divisions constructing Arabidopsis stem cell niches: the emerging role of protein phosphatases. Plant Biol (Stuttg). Sep;17(5):935-45. undefineddoi: 10.1111/plb.12352. 

Richards S, Wink RH, Simon R (2015) Mathematical modelling of WOX5-and CLE40-mediated columella stem cell homeostasis in Arabidopsis. J Exp Bot. Aug;66(17):5375-84. undefineddoi: 10.1093/jxb/erv257

Thorsten Langner, Merve Öztürk, Sarah Hartmann, Stefan Cord-Landwehr, Bruno Moerschbacher, Jonathan D. Walton, Vera Göhre (2015) "Chitinases are essential for cell separation in Ustilago maydis". Eukaryotic Cell 14(9):846-57 undefineddoi: 10.1093/gbe/evv225.

Rauch C, Vries Jd, Rommel S, Rose LE, Woehle C, Christa G, Laetz EM, Wägele H, Tielens AG, Nickelsen J, Schumann T, Jahns P, Gould SB. (2015) Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs. Genome Biol Evol. Aug 29;7(9):2602-7. undefineddoi: 10.1093/gbe/evv173.

Göhre V (2015) Immune responses: Photosythetic defense Nature Plants 1:15079 ​doi:10.1038/nplants.2015.79, http://www.nature.com/articles/nplants201579

Wu G, Hufnagel DE, Denton AK, Shiu SH (2015) Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains. BMC Genomics. 16:149. undefineddoi: 10.1186/s12864-015-1335-5.https://www.ncbi.nlm.nih.gov/pubmed/25880851

2014

 

Armbruster U, Carrillo LR, Venema K, Pavlovic L, Schmidtmann E, Kornfeld A, Jahns P, Berry JA, Kramer DM, Jonikas MC (2014) Ion antiport accelerates photosynthetic acclimation in fluctuating light environments. Nat Commun. Nov 13;5:5439. undefineddoi: 10.1038/ncomms6439.

Kleinmanns JA, Schubert D (2014) Polycomb and Trithorax group protein-mediated control of stress responses in plants. Biol Chem. Nov 1;395(11):1291-300. undefineddoi: 10.1515/hsz-2014-0197.    

Pick TR, Weber APM (2014) Unknown components of the plastidial permeome. Front. Plant Sci. 4(410) doi: 10.3389/fpls.2014.00410.

Aldous SA, Weise SE, Sharkey TD, Waldera-Lupa DM, Stühler K, Malmann J, Groth G, Gowik U, Westhoff P, Arsova B (2014): Evolution of the phosphoenolpyruvate carboxylase protein kinase family in C3 and C4 Flaveria species. Plant Physiol DOI:10.1104/ pp.114.240283.

Bräutigam A, Schliesky S, Külahoglu C, Osborne C, Weber APM (2014) Towards an integrative model of C4 photosynthetic subtypes – insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. J Exp Bot, doi: 10.1093/jxb/eru100.

Brouwer P, Bräutigam A, Külahoglu C, Tazelaar A, Kurz S, Nierop K, van der Werf A, Weber APM, Schluepmann H (2014) Azolla domestication towards a biobased economy? Transcriptome database and methods for dissemination, cross fertilization, and storage of Azolla fllliculoides. New Phytol 202(3): 1069-1082.

Esser C, Kuhn A, Groth G, Lercher MJ, Maurino VG (2014) Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases. Mol Biol Evol 31(5):1089-101.

Külahoglu C and Bräutigam A (2014) Quantitative transcriptome analysis using RNA-seq. Methods Mol Biol. 1158:71-91. doi: 10.1007/978-1-4939-0700-7_5.

Külahoglu C, Denton AK, Sommer M, Maß J, Schliesky S, Wrobel TJ, Berckmans B, Gongora-Castillo E, Buell CR, Simon R, De Veylder L, Bräutigam A, Weber APM (2014) Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species. Plant Cell, in press.

Levey T, Westhoff P, Meierhoff K (2014) Expression of a nuclear-encoded psbH gene complements the plastidic RNA processing defect in the PSII mutant hcf107 in Arabidopsis thaliana. Plant Journal doi: 10.1111/tpj.12632.

Mallmann J*, Heckmann D*, Bräutigam A, Lercher MJ, Weber APM, Westhoff P, Gowik U (2014) The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria. eLife 10.7554/eLife.02478#sthash.CCB3QOPb.dpuf.

2013

Bordych C, Eisenhut M, Pick TR, Külahoglu C, Weber APM (2013): Co-expression analysis as tool for the discovery of transport proteins in photorespiration. Plant Biol 15 (4): 686-93.

Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Külahoglu C, Bian C, Chen J, Fan G, Kaufmann K, Hall JC, Becker A, Bräutigam A, Weber APM, Shi C, Zheng Z, Li W, Lv M, Wang J, Zou H, Quan Z, Hibberd JM, Zhang G, Zhu XG, Xu X, Schranz E (2013) The genome of Tarenaya hassleriana provides insights into reproductive trait and genome evolution of crucifers. Plant Cell (8): 2813-30.

Denton AK, Simon R, Weber APM (2013) C4 photosynthesis: from evolutionary analyses to strategies for synthetic reconstruction of the trait. Curr Opin Plant Biol 16 (3): 315-21.

Heckmann D, Schulze S, Denton A, Gowick U, Westhoff P, Weber APM, Lercher M (2013) Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a Mount Fuji fitness landscape. Cell 153, 1579-1588.

Kessel-Vigelius SK, Wiese J, Schroers MG, Wrobel TJ, Hahn F, Linka N (2013) An engineered plant peroxisome and its application in biotechnology. Plant Sci 210:232-40.

Návarová H, Bernsdorff F, Döring A-C, Zeier J (2013) Pipecolic acid, an endogenous mediator of defense amplification and priming, is a critical regulator of inducible plant immunity. Plant Cell 24: 5123-41.

Paulus JK, Niehus C, Groth G (2013) Evolution of C4 Phosphoenolpyruvate Carboxylase - enhanced feedback inhibitor tolerance is determined by a single residue. Mol Plant 6 (6): 1996 -9.

Paulus JK, Schlieper D, Groth G (2013) Greater efficiency of photosynthetic carbon fixation due to single amino-acid substitution. Nature Commun 4:1518.

Pick TR, Bräutigam A, Schulz MA, Obata T, Fernie AR, and Weber APM (2013): Mesophyll envelope protein 1, the photorespiratory glycolate glycerate transporter, defines a new class of metabolite transporters. Proc Natl Acad Sci USA 110 (8): 3185-90.

Ruts T, Matsubara S, Walter A (2013) Synchronous high-resolution phenotyping of leaf and root growth in Nicotiana tabacum over 24h periods with GROWMAP-plant. Plant Methods 9: 2.

Schlieper D, Foerster K, Paulus JK, Groth G (2013) Resolving the activation site of positive regulators in plant phosphoenolpyruvate carboxylase, Mol Plant 7 (2): 437 – 40.

Schulze S, Mallmann J, Burscheidt J, Koczor M, Streubel M, Bauwe H, Gowik U, Westhoff P (2013) Evolution of C4 photosynthesis in the genus Flaveria - establishment of a photorespiratory CO2 pump. Plant Cell 25, 2522-2535.

Stahl Y, Grabowski S, Bleckmann A, Kühnemuth R, Weidtkamp-Peters S, Gustavo Pinto K, Kirschner GK, Schmid JB, Wink RH, Hülsewede A, Felekyan S, Seidel CAM, Simon R (2013) Moderation of Arabidopsis Root Stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 Receptor Kinase Complexes. Current Biology 23 (5): 362-71.

Theodoulou FL, Bernhardt K, Linka N, Baker A (2013) Peroxisome membrane proteins: multiple trafficking routes and multiple functions? Biochem Journal 451 (3): 345-52.

2012

Bernhardt K, Vigelius SK, Wiese J, Linka N, Weber APM (2012) Agrobacterium-mediated Arabidopsis thaliana transformation: An overview of T-DNA binary vectors, floral dip and screening for homozygous lines. Endocytobiosis Cell Res 22: 19-28.

Breuers FKH, Bräutigam A, Geimer S, Welzel UY, Stefano G, Renna L, Brandizzi F, Weber APM (2012) Dynamic remodeling of the plastid envelope membranes – a tool for chloroplast envelope in vivo localizations. Frontiers in Plant Sci 3: 7.

Colmsee C, Mascher M, Czauderna T, Hartmann A, Schlüter U, Zellerhoff N, Schmitz J, Bräutigam A, Pick TR, Alter P, Gahrtz M, Witt S, Fernie AR, Börnke F, Fahnenstich H, Bucher M, Dresselhaus T, Weber AP, Schreiber F, Scholz U, Sonnewald U (2012) OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biol. 12(1):245.

Eisenhut M, Pick TR, Bordych C, Weber APM (2012) Towards closing the remaining gaps in photorespiration - the essential but unexplored role of transport proteins. Plant Biol 15 (4): 676-85.

Gruenheit N, Deusch O, Esser C, Becker M, Voelckel C, Lockhart P (2012) Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics 13: 92.

Göhre V, Jones AME, Sklenář J, Robatzek S, Weber APM (2012) Molecular crosstalk between PAMP-triggered immunity and photosynthesis. MPMI 25: 1083-92.

Göhre V, Vollmeister E, Bölker M, Feldbrügge M (2012) Microtubule-dependent membrane dynamics in Ustilago maydis: Trafficking and function of Rab5a-positive endosomes. Commun Integr Biol 5: 485-90.

Juszczak I, Rudnik R, Pietzeniuk B, Baier M (2012) Natural genetic variation in the expression regulation of the chloroplast antioxidant system among Arabidopsis thaliana accessions. Physiol Plant 146: 53-70.

Linka N, Esser C (2012) Transport proteins regulate the flux of metabolites and cofactors across the membrane of plant peroxisomes. Frontiers in Plant Sci 3: 3.

Nyathi Y, Zhang X, Baldwin JM, Bernhardt K, Johnson B, Baldwin SA, Theodoulou FL and Baker A (2012) Pseudo half-molecules of the ABC transporter, COMATOSE, bind Pex19 and target to peroxisomes independently but are both required for activity. FEBS Letters 586 (16): 2280-6.

Rosar C, Kanonenberg K, Nanda AM, Mielewczik M, Bräutigam A, Novák O, Strnad M, Walter A, Weber APM (2012) The leaf reticulate mutant dov1 is impaired in the first step of purine metabolism. Mol Plant 5: 1227-1241.

Ruts T, Matsubara S, Wiese-Klinkenberg A, Walter A (2012) Diel patterns of leaf and root growth: endogenous rhythmicity or environmental response? J Exp Botany 63 (9): 3339 – 51.

Ruts T, Matsubara S, Wiese-Klinkenberg A, Walter A (2012) Aberrant temporal growth pattern and morphology of root and shoot caused by a defective circadian clock in Arabidopsis thaliana. Plant Journal 72 (1): 154-61.

Wiludda C, Schulze S, Gowik U, Engelmann S, Koczor M, Streubel M, Bauwe H, Westhoff P (2012) Regulation of the Photorespiratory GLDPA Gene in C4 Flaveria: An Intricate Interplay of Transcriptional and Posttranscriptional Processes. Plant Cell 24: 137-151.

2011

Berckmans B, Vassileva V, Schmid SP, Maes S, Parizot B, Naramoto S, Magyar Z, Kamei CL, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon R, Beeckman T, De Veylder L (2011) Auxin-Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins. Plant Cell 23: 3671-3683.

Bräutigam A, Kajala K, Wullenweber J, Sommer M, Gagneul D, Weber KL, Carr KM, Gowik U, Maß J, Lercher MJ, Westhoff P, Hibberd JM, Weber AP. (2011) An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. Plant Physiology 155 (1): 142-156.

Breuers FKH, Bräutigam A, Weber APM (2011) The plastid outer envelope – a highly dynamic interface between plastid and cytoplasm. Frontiers in Plant Sci 2: 97.

Pick TR, Bräutigam A, Schlüter U, Denton AK, Colmsee C, Scholz U, Fahnenstich H, Pieruschka R, Rascher U, Sonnewald U, Weber APM (2011) Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell 23: 1-13.

2009

Stahl Y, Wink R, Ingram G, Simon R (2009) A signalling module controlling the stem cell niche in Arabidopsis root meristems. Current Biology 19, 909-914.

 

* The authors contributed equally to this work.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

iGRAD-Plant Coordinator

Dr. Petra Fackendahl

Institute of Plant Biochemistry
Universitätsstr. 1
Building: 26.13.
Floor/Room: U1.78
40225 Düsseldorf
Phone +49 211 81-10588
Responsible for the content: E-MailDr. Petra Fackendahl