@article{KnoxBrownRindfleischGuentheretal.2020,
  author    = {Knox-Brown, Patrick and Rindfleisch, Tobias and G{\"u}nther, Anne and Balow, Kim and Bremer, Anne and Walther, Dirk and Miettinen, Markus S. and Hincha, Dirk K. and Thalhammer, Anja},
  title     = {Similar Yet Different},
  series = {International Journal of Molecular Sciences},
  volume    = {21},
  journal   = {International Journal of Molecular Sciences},
  number    = {8},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms21082794},
  pages     = {25},
  year      = {2020},
  abstract  = {The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.},
  language  = {en}
}
@article{NavarroRetamalBremerIngolfssonetal.2018,
  author    = {Navarro-Retamal, Carlos and Bremer, Anne and Ingolfsson, Helgi I. and Alzate-Morales, Jans and Caballero, Julio and Thalhammer, Anja and Gonzalez, Wendy and Hincha, Dirk K.},
  title     = {Folding and Lipid Composition Determine Membrane Interaction of the Disordered Protein COR15A},
  series = {Biophysical journal},
  volume    = {115},
  journal   = {Biophysical journal},
  number    = {6},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2018.08.014},
  pages     = {968 -- 980},
  year      = {2018},
  abstract  = {Plants from temperate climates, such as the model plant Arabidopsis thaliana, are challenged with seasonal low temperatures that lead to increased freezing tolerance in fall in a process termed cold acclimation. Among other adaptations, this involves the accumulation of cold-regulated (COR) proteins, such as the intrinsically disordered chloroplast-localized protein COR15A. Together with its close homolog COR15B, it stabilizes chloroplast membranes during freezing. COR15A folds into amphipathic alpha-helices in the presence of high concentrations of low-molecular-mass crowders or upon dehydration. Under these conditions, the (partially) folded protein binds peripherally to membranes. In our study, we have used coarse-grained molecular dynamics simulations to elucidate the details of COR15A-membrane binding and its effects on membrane structure and dynamics. Simulation results indicate that at least partial folding of COR15A and the presence of highly unsaturated galactolipids in the membranes are necessary for efficient membrane binding. The bound protein is stabilized on the membrane by interactions of charged and polar amino acids with galactolipid headgroups and by interactions of hydrophobic amino acids with the upper part of the fatty acyl chains. Experimentally, the presence of liposomes made from a mixture of lipids mimicking chloroplast membranes induces additional folding in COR15A under conditions of partial dehydration, in agreement with the simulation results.},
  language  = {en}
}
@article{BremerKentHaussetal.2017,
  author    = {Bremer, Anne and Kent, Ben and Hauss, Thomas and Thalhammer, Anja and Yepuri, Nageshwar R. and Darwish, Tamim A. and Garvey, Christopher J. and Bryant, Gary and Hincha, Dirk K.},
  title     = {Intrinsically Disordered Stress Protein COR15A Resides at the Membrane Surface during Dehydration},
  series = {Biophysical journal},
  volume    = {113},
  journal   = {Biophysical journal},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2017.06.027},
  pages     = {572 -- 579},
  year      = {2017},
  abstract  = {Plants from temperate climate zones are able to increase their freezing tolerance during exposure to low, above zero temperatures in a process termed cold acclimation. During this process, several cold-regulated (COR) proteins are accumulated in the cells. One of them is COR15A, a small, intrinsically disordered protein that contributes to leaf freezing tolerance by stabilizing cellular membranes. The isolated protein folds into amphipathic a-helices in response to increased crowding conditions, such as high concentrations of glycerol. Although there is evidence for direct COR15A-membrane interactions, the orientation and depth of protein insertion were unknown. In addition, although folding due to high osmolyte concentrations had been established, the folding response of the protein under conditions of gradual dehydration had not been investigated. Here we show, using Fourier transform infrared spectroscopy, that COR15A starts to fold into a-helices already under mild dehydration conditions (97\% relative humidity (RH), corresponding to freezing at -3 degrees C) and that folding gradually increases with decreasing RH. Neutron diffraction experiments at 97 and 75\% RH established that the presence of COR15A had no significant influence on the structure of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes. However, using deuterated POPC we. could clearly establish that COR15A interacts with the membranes and penetrates below the headgroup region into the upper part of the fatty acyl chain region. This localization is in agreement with our hypothesis that COR15A-membrane interaction is at least, in part, driven by a hydrophobic interaction between the lipids and the hydrophobic face of the amphipathic protein alpha-helix.},
  language  = {en}
}
@article{ShouBremerRindfleischetal.2019,
  author    = {Shou, Keyun and Bremer, Anne and Rindfleisch, Tobias and Knox-Brown, Patrick and Hirai, Mitsuhiro and Rekas, Agata and Garvey, Christopher J. and Hincha, Dirk K. and Stadler, Andreas M. and Thalhammer, Anja},
  title     = {Conformational selection of the intrinsically disordered plant stress protein COR15A in response to solution osmolarity - an X-ray and light scattering study},
  series = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  volume    = {21},
  journal   = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  number    = {34},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  doi       = {10.1039/c9cp01768b},
  pages     = {18727 -- 18740},
  year      = {2019},
  abstract  = {The plant stress protein COR15A stabilizes chloroplast membranes during freezing. COR15A is an intrinsically disordered protein (IDP) in aqueous solution, but acquires an alpha-helical structure during dehydration or the increase of solution osmolarity. We have used small- and wide-angle X-ray scattering (SAXS/WAXS) combined with static and dynamic light scattering (SLS/DLS) to investigate the structural and hydrodynamic properties of COR15A in response to increasing solution osmolarity. Coarse-grained ensemble modelling allowed a structure-based interpretation of the SAXS data. Our results demonstrate that COR15A behaves as a biomacromolecule with polymer-like properties which strongly depend on solution osmolarity. Biomacromolecular self-assembly occurring at high solvent osmolarity is initiated by the occurrence of two specific structural subpopulations of the COR15A monomer. The osmolarity dependent structural selection mechanism is an elegant way for conformational regulation and assembly of COR15A. It highlights the importance of the polymer-like properties of IDPs for their associated biological function.},
  language  = {en}
}
@article{SprengerErbanSeddigetal.2017,
  author    = {Sprenger, Heike and Erban, Alexander and Seddig, Sylvia and Rudack, Katharina and Thalhammer, Anja and Le, Mai Q. and Walther, Dirk and Zuther, Ellen and Koehl, Karin I. and Kopka, Joachim and Hincha, Dirk K.},
  title     = {Metabolite and transcript markers for the prediction of potato drought tolerance},
  series = {Plant Biotechnology Journal},
  volume    = {16},
  journal   = {Plant Biotechnology Journal},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1467-7644},
  doi       = {10.1111/pbi.12840},
  pages     = {939 -- 950},
  year      = {2017},
  abstract  = {Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6\% and 9\%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3\%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.},
  language  = {en}
}
@article{RohdeHinchaHeyer2004,
  author    = {Rohde, P. and Hincha, Dirk K. and Heyer, Arnd G.},
  title     = {Heterosis in the freezing tolerance of crosses between two Arabidopsis thaliana accessions (Columbia-0 and C24) that show differences in non-acclimated and acclimated freezing tolerance},
  issn      = {0960-7412},
  year      = {2004},
  language  = {en}
}
@misc{KnoxBrownRindfleischGuentheretal.2020,
  author    = {Knox-Brown, Patrick and Rindfleisch, Tobias and G{\"u}nther, Anne and Balow, Kim and Bremer, Anne and Walther, Dirk and Miettinen, Markus S. and Hincha, Dirk K. and Thalhammer, Anja},
  title     = {Similar Yet Different},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {901},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-46941},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-469419},
  pages     = {27},
  year      = {2020},
  abstract  = {The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.},
  language  = {en}
}
@article{BremerWolffThalhammeretal.2017,
  author    = {Bremer, Anne and Wolff, Martin and Thalhammer, Anja and Hincha, Dirk K.},
  title     = {Folding of intrinsically disordered plant LEA proteins is driven by glycerol-induced crowding and the presence of membranes},
  series = {The FEBS journal},
  volume    = {284},
  journal   = {The FEBS journal},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1742-464X},
  doi       = {10.1111/febs.14023},
  pages     = {919 -- 936},
  year      = {2017},
  abstract  = {Late embryogenesis abundant (LEA) proteins are related to cellular dehydration tolerance. Most LEA proteins are predicted to have no stable secondary structure in solution, i.e., to be intrinsically disordered proteins (IDPs), but they may acquire alpha-helical structure upon drying. In the model plant Arabidopsis thaliana, the LEA proteins COR15A and COR15B are highly induced upon cold treatment and are necessary for the plants to attain full freezing tolerance. Freezing leads to increased intracellular crowding due to dehydration by extracellular ice crystals. In vitro, crowding by high glycerol concentrations induced partial folding of COR15 proteins. Here, we have extended these investigations to two related proteins, LEA11 and LEA25. LEA25 is much longer than LEA11 and COR15A, but shares a conserved central sequence domain with the other two proteins. We have created two truncated versions of LEA25 (2H and 4H) to elucidate the structural and functional significance of this domain. Light scattering and CD spectroscopy showed that all five proteins were largely unstructured and monomeric in dilute solution. They folded in the presence of increasing concentrations of trifluoroethanol and glycerol. Additional folding was observed in the presence of glycerol and membranes. Fourier transform infra red spectroscopy revealed an interaction of the LEA proteins with membranes in the dry state leading to a depression in the gel to liquid-crystalline phase transition temperature. Liposome stability assays revealed a cryoprotective function of the proteins. The C- and N-terminal extensions of LEA25 were important in cryoprotection, as the central domain itself (2H, 4H) only provided a low level of protection.},
  language  = {en}
}
@article{ThalhammerHundertmarkPopovaetal.2010,
  author    = {Thalhammer, Anja and Hundertmark, Michaela and Popova, Antoaneta V. and Seckler, Robert and Hincha, Dirk K.},
  title     = {Interaction of two intrinsically disordered plant stress proteins (COR15A and COR15B) with lipid membranes in the dry state},
  issn      = {0005-2736},
  doi       = {10.1016/j.bbamem.2010.05.015},
  year      = {2010},
  abstract  = {COR15A and COR15B form a tandem repeat of highly homologous genes in Arabidopsis thaliana. Both genes are highly cold induced and the encoded proteins belong to the Pfam LEA_4 group (group 3) of the late embryogenesis abundant (LEA) proteins. Both proteins were predicted to be intrinsically disordered in solution. Only COR15A has previously been characterized and it was shown to be localized in the soluble stroma fraction of chloroplasts. Ectopic expression of COR15A in Arabidopsis resulted in increased freezing tolerance of both chloroplasts after freezing and thawing of intact leaves and of isolated protoplasts frozen and thawed in vitro. In the present study we have generated recombinant mature COR15A and COR15B for a comparative study of their structure and possible function as membrane protectants. CD spectroscopy showed that both proteins are predominantly unstructured in solution and mainly a-helical after drying. Both proteins showed similar effects on the thermotropic phase behavior of dry liposomes. A decrease in the gel to liquid-crystalline phase transition temperature depended on both the unsaturation of the fatty acyl chains and lipid headgroup structure. FTIR spectroscopy indicated no strong interactions between the proteins and the lipid phosphate and carbonyl groups, but significant interactions with the galactose headgroup of the chloroplast lipid monogalactosyldiacylglycerol. These findings were rationalized by modeling the secondary structure of COR15A and COR15B. Helical wheel projection indicated the presence of amphipathic a-helices in both proteins. The helices lacked a clear separation of positive and negative charges on the hydrophilic face, but contained several hydroxylated amino acids.},
  language  = {en}
}
@article{HundertmarkDimovaLengefeldetal.2011,
  author    = {Hundertmark, Michaela and Dimova, Rumiana and Lengefeld, Jan and Seckler, Robert and Hincha, Dirk K.},
  title     = {The intrinsically disordered late embryogenesis abundant protein LEA18 from Arabidopsis thaliana modulates membrane stability through binding and folding.},
  issn      = {0006-3002},
  year      = {2011},
  abstract  = {Intrinsically disordered proteins (IDPs) constitute a substantial part of cellular proteomes. Late embryogenesis abundant (LEA) proteins are mostly predicted to be IDPs associated with dehydration tolerance in many plant, animal and bacterial species. Their functions, however, are largely unexplored and also their structure and interactions with potential target molecules have only recently been experimentally investigated in a small number of proteins. Here, we report on the structure and interactions with membranes of the Pfam LEA_1 protein LEA18 from the higher plant Arabidopsis thaliana. This functionally uncharacterized positively charged protein specifically aggregated and destabilized negatively charged liposomes. Isothermal titration calorimetry showed binding of the protein to both charged and uncharged membranes. LEA18 alone was largely unstructured in solution. While uncharged membranes had no influence on the secondary structure of LEA18, the protein partially folded into ;-sheet structure in the presence of negatively charged liposomes. These data suggest that LEA18 does not function as a membrane stabilizing protein, as suggested for other LEA proteins. Instead, a possible function of LEA18 could be the composition-dependent modulation of membrane stability, e.g., during signaling or vesicle-mediated transport. Research Highlights},
  language  = {en}
}
@article{PopovaHundertmarkSeckleretal.2011,
  author    = {Popova, Antoaneta V. and Hundertmark, Michaela and Seckler, Robert and Hincha, Dirk K.},
  title     = {Structural transitions in the intrinsically disordered plant dehydration stress protein LEA7 upon drying are modulated by the presence of membranes},
  series = {Biochimica et biophysica acta : Biomembranes},
  volume    = {1808},
  journal   = {Biochimica et biophysica acta : Biomembranes},
  number    = {7},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0005-2736},
  doi       = {10.1016/j.bbamem.2011.03.009},
  pages     = {1879 -- 1887},
  year      = {2011},
  abstract  = {Dehydration stress-related late embryogenesis abundant (LEA) proteins have been found in plants, invertebrates and bacteria. Most LEA proteins are unstructured in solution, but some fold into amphipathic a-helices during drying. The Pfam LEA_4 (Group 3) protein LEA7 from the higher plant Arabidopsis thaliana was predicted to be 87\% alpha-helical, while CD spectroscopy showed it to be largely unstructured in solution and only 35\% alpha-helical in the dry state. However, the dry protein contained 15\% beta-sheets. FTIR spectroscopy revealed the (beta-sheets to be largely due to aggregation. beta-Sheet content was reduced and alpha-helix content increased when LEA7 was dried in the presence of liposomes with secondary structure apparently influenced by lipid composition. Secondary structure was also affected by the presence of membranes in the fully hydrated state. A temperature-induced increase in the flexibility of the dry protein was also only observed in the presence of membranes. Functional interactions of LEA7 with membranes in the dry state were indicated by its influence on the thermotropic phase transitions of the lipids and interactions with the lipid headgroup phosphates.},
  language  = {en}
}
@article{HundertmarkPopovaRauschetal.2012,
  author    = {Hundertmark, Michaela and Popova, Antoaneta V. and Rausch, Saskia and Seckler, Robert and Hincha, Dirk K.},
  title     = {Influence of drying on the secondary structure of intrinsically disordered and globular proteins},
  series = {Biochemical and biophysical research communications},
  volume    = {417},
  journal   = {Biochemical and biophysical research communications},
  number    = {1},
  publisher = {Elsevier},
  address   = {San Diego},
  issn      = {0006-291X},
  doi       = {10.1016/j.bbrc.2011.11.067},
  pages     = {122 -- 128},
  year      = {2012},
  abstract  = {Circular dichroism (CD) spectroscopy of five Arabidopsis late embryogenesis abundant (LEA) proteins constituting the plant specific families LEA_5 and LEA_6 showed that they are intrinsically disordered in solution and partially fold during drying. Structural predictions were comparable to these results for hydrated LEA_6, but not for LEA_5 proteins. FTIR spectroscopy showed that verbascose, but not sucrose, strongly affected the structure of the dry proteins. The four investigated globular proteins were only mildly affected by drying in the absence, but strongly in the presence of sugars. These data highlight the larger structural flexibility of disordered compared to globular proteins and the impact of sugars on the structure of both disordered and globular proteins during drying.},
  language  = {en}
}
@article{HundertmarkDimovaLengefeldetal.2011,
  author    = {Hundertmark, Michaela and Dimova, Rumiana and Lengefeld, Jan and Seckler, Robert and Hincha, Dirk K.},
  title     = {The intrinsically disordered late embryogenesis abundant protein LEA18 from Arabidopsis thaliana modulates membrane stability through binding and folding},
  series = {Biochimica et biophysica acta : Biomembranes},
  volume    = {1808},
  journal   = {Biochimica et biophysica acta : Biomembranes},
  number    = {1},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0005-2736},
  doi       = {10.1016/j.bbamem.2010.09.010},
  pages     = {446 -- 453},
  year      = {2011},
  abstract  = {Intrinsically disordered proteins (IDPs) constitute a substantial part of cellular proteomes. late embryogenesis abundant (LEA) proteins are mostly predicted to be IDPs associated with dehydration tolerance in many plant, animal and bacterial species. Their functions, however, are largely unexplored and also their structure and interactions with potential target molecules have only recently been experimentally investigated in a small number of proteins. Here, we report on the structure and interactions with membranes of the Pfam LEA_1 protein LEA18 from the higher plant Arabidopsis thaliana. This functionally uncharacterized positively charged protein specifically aggregated and destabilized negatively charged liposomes. Isothermal titration calorimetry showed binding of the protein to both charged and uncharged membranes. LEA18 alone was largely unstructured in solution. While uncharged membranes had no influence on the secondary structure of LEA18, the protein partially folded into beta-sheet structure in the presence of negatively charged liposomes. These data suggest that LEA18 does not function as a membrane stabilizing protein, as suggested for other LEA proteins. Instead, a possible function of LEA18 could be the composition-dependent modulation of membrane stability, e.g., during signaling or vesicle-mediated transport.},
  language  = {en}
}
@misc{SprengerErbanSeddigetal.2018,
  author    = {Sprenger, Heike and Erban, Alexander and Seddig, Sylvia and Rudack, Katharina and Thalhammer, Anja and Le, Mai Q. and Walther, Dirk and Zuther, Ellen and K{\"o}hl, Karin I. and Kopka, Joachim and Hincha, Dirk K.},
  title     = {Metabolite and transcript markers for the prediction of potato drought tolerance},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {673},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42463},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-424630},
  pages     = {12},
  year      = {2018},
  abstract  = {Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker-assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT-PCR and GC-MS profiling, respectively. Transcript marker candidates were selected from a published RNA-Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6\% and 9\%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3\%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.},
  language  = {en}
}
@article{NavarroRetamalBremerAlzateMoralesetal.2016,
  author    = {Navarro-Retamal, Carlos and Bremer, Anne and Alzate-Morales, Jans H. and Caballero, Julio and Hincha, Dirk K. and Gonzalez, Wendy and Thalhammer, Anja},
  title     = {Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana},
  series = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  volume    = {18},
  journal   = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  doi       = {10.1039/c6cp02272c},
  pages     = {25806 -- 25816},
  year      = {2016},
  abstract  = {The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain alpha-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40\%) or prevented (100\%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.},
  language  = {en}
}
@misc{NavarroRetamalBremerAlzateMoralesetal.2016,
  author    = {Navarro-Retamal, Carlos and Bremer, Anne and Alzate-Morales, Jans H. and Caballero, Julio and Hincha, Dirk K. and Gonz{\´a}lez, Wendy and Thalhammer, Anja},
  title     = {Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-394503},
  pages     = {25806 -- 25816},
  year      = {2016},
  abstract  = {The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain α-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40\%) or prevented (100\%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.},
  language  = {en}
}
@article{SprengerRudackSchudomaetal.2015,
  author    = {Sprenger, Heike and Rudack, Katharina and Schudoma, Christian and Neumann, Arne and Seddig, Sylvia and Peters, Rolf and Zuther, Ellen and Kopka, Joachim and Hincha, Dirk K. and Walther, Dirk and Koehl, Karin},
  title     = {Assessment of drought tolerance and its potential yield penalty in potato},
  series = {Functional plant biology : an international journal of plant function},
  volume    = {42},
  journal   = {Functional plant biology : an international journal of plant function},
  number    = {7},
  publisher = {CSIRO},
  address   = {Clayton},
  issn      = {1445-4408},
  doi       = {10.1071/FP15013},
  pages     = {655 -- 667},
  year      = {2015},
  abstract  = {Climate models predict an increased likelihood of seasonal droughts for many areas of the world. Breeding for drought tolerance could be accelerated by marker-assisted selection. As a basis for marker identification, we studied the genetic variance, predictability of field performance and potential costs of tolerance in potato (Solanum tuberosum L.). Potato produces high calories per unit of water invested, but is drought-sensitive. In 14 independent pot or field trials, 34 potato cultivars were grown under optimal and reduced water supply to determine starch yield. In an artificial dataset, we tested several stress indices for their power to distinguish tolerant and sensitive genotypes independent of their yield potential. We identified the deviation of relative starch yield from the experimental median (DRYM) as the most efficient index. DRYM corresponded qualitatively to the partial least square model-based metric of drought stress tolerance in a stress effect model. The DRYM identified significant tolerance variation in the European potato cultivar population to allow tolerance breeding and marker identification. Tolerance results from pot trials correlated with those from field trials but predicted field performance worse than field growth parameters. Drought tolerance correlated negatively with yield under optimal conditions in the field. The distribution of yield data versus DRYM indicated that tolerance can be combined with average yield potentials, thus circumventing potential yield penalties in tolerance breeding.},
  language  = {en}
}
@article{HilkerSchwachtjeBaieretal.2016,
  author    = {Hilker, Monika and Schwachtje, Jens and Baier, Margarete and Balazadeh, Salma and B{\"a}urle, Isabel and Geiselhardt, Sven and Hincha, Dirk K. and Kunze, Reinhard and Mueller-Roeber, Bernd and Rillig, Matthias G. and Rolff, Jens and Schm{\"u}lling, Thomas and Steppuhn, Anke and van Dongen, Joost and Whitcomb, Sarah J. and Wurst, Susanne and Zuther, Ellen and Kopka, Joachim},
  title     = {Priming and memory of stress responses in organisms lacking a nervous system},
  series = {Biological reviews},
  volume    = {91},
  journal   = {Biological reviews},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {1464-7931},
  doi       = {10.1111/brv.12215},
  pages     = {1118 -- 1133},
  year      = {2016},
  language  = {en}
}