Dierk Wanke

Dierk Wanke
LMU Munich / University of Tuebingen

Dr.

About

166
Publications
22,420
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3,375
Citations
Citations since 2016
23 Research Items
1796 Citations
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250

Publications

Publications (166)
Article
Polycomb repressive complexes (PRCs) play key roles e.g. in development by repressing a large number of genes involved in various functions. Much, however, remains to be discovered about PRC silencing mechanism as well as their targeting to specific genomic regions. Besides other mechanisms, GAGA-binding factors (GAFs) in animals can guide PRC memb...
Article
Full-text available
WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the ‘TTGACY’ W-box cons...
Article
Full-text available
Plant BZR1-BAM transcription factors contain a β-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be noncatalytic, but they determine the function of the two Arabidopsis thaliana BZR1-BAM isoforms (BAM7 and BAM8) during transcriptional initiation. Removal or swapping of the BAM...
Article
Full-text available
The caryopses of barley (Hordeum vulgare), as of all cereals, are complex sink organs optimized for starch accumulation and embryo development. While their early to late development has been studied in great detail, processes underlying the caryopses' diurnal adaptation to changes in light, temperature, and the fluctuations in phloem-supplied carbo...
Article
Full-text available
GAGA-motif binding proteins control transcriptional activation or repression of homeotic genes. Interestingly, there are no sequence similarities between animal and plant proteins. Plant BBR/BPC-proteins can be classified into two distinct groups: Previous studies have elaborated on group I members only and so little is known about group II protein...
Article
Full-text available
Sex determination is a central process for sexual reproduction and is often regulated by a sex determinant encoded on a sex chromosome. Rules that govern the evolution of sex chromosomes via specialization and degeneration following the evolution of a sex determinant have been well studied in diploid organisms. However, distinct predictions apply t...
Article
Cytokinin and auxin are key regulators of plant growth and development. During the last decade transport mechanisms have turned out to be the key for the control of local and long-distance hormone distributions. In contrast with auxin, cytokinin transport is poorly understood. Here, we show that Arabidopsis thaliana AZG2, a member of the AZG purine...
Preprint
Full-text available
The phytohormones cytokinin (CK) and auxin are key regulators of plant growth and development. During the last decade specialised transport mechanisms turned out to be the key for the control of local and long distance hormone distributions. In contrast to auxin, CK transport is poorly understood. Here we show that Arabidopsis thaliana AZG2, a memb...
Article
Plant GAGA-motif binding factors are encoded by the BARLEY B RECOMBINANT / BASIC PENTACYSTEINE (BBR/BPC) family, which fulfill indispensable functions in growth and development. BBR/BPC proteins control flower development, size of the stem cell niche and seed development through transcriptional regulation of homeotic transcription factor genes. The...
Data
920 genes differentially expressed in bpc1,2,3,4,6 mutant roots.
Data
Conserved amino acid residues in 59 BPC domains of different groups and subgroups. Different colors differentiate between the four major BBR/BPC groups. The invariant cysteines are indicated by black background. Other residues that are invariant within each subgroup are highlighted by gray background.
Data
Conserved protein sequence motifs outside the BPC domain. Overview over 14 conserved peptide motifs that are characteristic for group I to IV BBR/BPC proteins outside their invariant BPC domain.
Data
Visualization of additional GFP-BPC6 targets in the brassinosteroid signaling pathway. BPC6 binding sites upstream of multiple genes involved in the brassinosteroid response are visualized by using the Integrative Genome Browser. Raw GFP-BPC6 binding data were published before (Shanks et al., 2018). The top bedgraph displays GFP-BPC6 binding data;...
Data
Genes responsive after phytohormone treatment.
Data
Peak and promotor data of those 47 brassinosteroid signaling genes that are significantly targeted by BPC6 in vivo.
Data
Map of GAGA/TCTC motifs in the brassinosteroid signaling genes. Heat map distribution of the GAGA/TCTC in the brassinosteroid signaling genes with gene name and AGI. The map was centered to the highest binding peak. Red, TCTC; Blue, GAGA.
Data
Fluorescence of recombinant GFP-BPC6 in the qDPI-ELISA experiment with diverse DNA-probes.
Data
Regions associated with a gene locus that are significantly enriched in both GFP-BPC6 replicates compared to the GFP-controls.
Data
List of 48 BPC6 in vivo target genes of the brassinosteroid signaling pathway.
Data
Structural models for the BPC domains of BPC1 and BPC6. Derived model structures for the BPC domains of BPC1 (top; green) and BPC6 (bottom; red). Conserved amino acid residues are highlighted in gray color. Conserved Cysteines are indicated in yellow. The unique Histidin in BPC6 is indicated in blue color.
Data
List of 83 BPC-domain sequences used for the cladogram.
Data
List of 68 full-length BBR/BPC protein sequences used for the phylogram.
Article
Full-text available
Cytokinin plays diverse roles in plant growth and development, generally acting by modulating gene transcription in target tissues. The type‐B ARR transcription factors have emerged as primary targets of cytokinin signaling and are required for essentially all cytokinin‐mediated changes in gene expression. The diversity of cytokinin function is lik...
Article
Full-text available
GAGA-binding proteins in plants are encoded by the BARLEY B-RECOMBINANT / BASIC PENTACYSTEINE (BBR/ BPC) family, which can be spilt into several groups on the basis of sequence divergence. The proteins of the different groups share an evolutionary conserved BASIC PENTACYSTEINE (BPC) domain at their very C-terminus that is important for DNA binding....
Chapter
The specific binding of DNA-binding proteins to their cognate DNA motifs is a crucial step for gene expression control and chromatin organization in vivo. The development of methods for the identification of in vivo binding regions by, e.g. chromatin immunoprecipitation (ChIP) or DNA adenine methyltransferase identification (Dam-ID) added an additi...
Article
Full-text available
Polycomb-repressive complexes (PRCs) play key roles in development by repressing a large number of genes involved in various functions. Much, however, remains to be discovered about PRC-silencing mechanisms as well as their targeting to specific genomic regions. Besides other mechanisms, GAGA-binding factors in animals can guide PRC members in a se...
Article
Full-text available
One of the key mechanisms of transcriptional control are the specific connections between transcription factors (TF) and cis-regulatory elements in gene promoters. The elucidation of these specific protein-DNA interactions is crucial to gain insights into the complex regulatory mechanisms and networks underlying the adaptation of organisms to dynam...
Article
Full-text available
DNA-binding proteins (DBPs), such as transcription factors, constitute about 10% of the protein-coding genes in eukaryotic genomes and play pivotal roles in the regulation of chromatin structure and gene expression by binding to short stretches of DNA. Despite their number and importance, only for a minor portion of DBPs the binding sequence had be...
Article
Full-text available
Studying plant stress responses is an important issue in a world threatened by global warming. Unfortunately, comparative analyses are hampered by varying experimental setups. In contrast, the AtGenExpress abiotic stress experiment displays intercomparability. Importantly, six of the nine stresses (wounding, genotoxic, oxidative, UV-B light, osmoti...
Chapter
Full-text available
Recent fi…ndings showed that non-harmonic DNA-nanostructures are formed by Hoogsteen (HG) dinucleotides in vivo. In contrast to Waston-Crick (WC) base pairing, the purine base component is fl‡ipped from anti - to syn-conformation. This change consequently alters the width of the DNA-helix, the sizes of minor and major groove and biophysical propert...
Chapter
Full-text available
The analyses of molecular mechanisms that control eukaryote gene expression throughout growth and development is an important issue in understanding expression changes during environmental stress, pathogen response or cancer. Information flow within a cell is governed by DNA-binding proteins such as transcription factors and their binding to DNA-mo...
Article
Full-text available
In higher plants, a diverse array of developmental and growth-related processes is regulated by the plant hormone auxin. Recent publications have proposed that besides the well-characterized Auxin Response Factors (ARFs) that bind Auxin Response Elements (AuxREs), also members of the bZIP- and MYB-transcription factor (TF) families participate in t...
Article
The process of chloroplast biogenesis requires a multitude of pathways and processes to establish chloroplast function. In cotyledons of seedlings, chloroplasts develop either directly from proplastids (also named eoplasts) or, if germinated in the dark, via etioplasts, whereas in leaves chloroplasts derive from proplastids in the apical meristem a...
Article
During the last decade, microarrays became a routine tool for the analysis of transcripts in the model plant Arabidopsis thaliana and the crop plant species rice, poplar or barley. The overwhelming amount of data generated by gene expression studies is a valuable resource for every scientist. Here, we summarize the most important findings about the...
Chapter
Full-text available
At present, more than 400 volatiles are known to appear in bacterial headspace samples, but more are expected as more bacteria will be investigated and several identification technologies will be applied. A comprehensive list of bacteria and their respective effects on plants were presented. The volatiles emitted from Serratia plymuthica HRO-C48 an...
Article
Interactions with the (a)biotic environment play key roles in a plant's fitness and vitality. In addition to direct surface-to-surface contact, volatile chemicals can also affect the physiology of organism. Volatiles of Serratia plymuthica and Stenotrophomonas maltophilia significantly inhibited growth and induced H(2) O(2) production in Arabidopsi...
Conference Paper
Full-text available
Higher organisms are able to respond to continuously changing external conditions by transducing cellular signals into specific regulatory programs, which control gene expression states of thousands of different genes. One of the central problems in understanding gene regulation is to decipher how combinations of transcription factors control sets...
Article
Hydrophytes comprise aquatic macrophytes from various taxa that are able to sustain and to complete their lifecycle in a flooded environment. Their ancestors, however, underwent adaptive processes to withstand drought on land and became partially or completely independent of water for sexual reproduction. Interestingly, the step backwards into the...
Data
Secondary structure prediction of AtBPC6. Prediction of AtBPC6 protein secondary structure using SOPMA (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html). For orientation, schematic positions of the coiled-coil domain (checked-grey), nuclear localization signal (dark grey) and zinc-finger like DNA-binding domain (black) are sh...
Data
Homology model of alternating amino acids in the AtBPC6 Alanine zipper. The homology model of the coiled-coil structure of AtBPC6 was computed by using the backbone coordinates of the C-Jun Leucine zipper. For better visualization of the alternating amino acid residues inside the Alanine zipper region were color coded: blue -positive charged; red...
Data
Homology models of monomeric and homodimeric coiled-coil structures. The homology models of the monomeric and homodimeric coiled-coil regions of BPC6, C-Jun, C-Jun-Ala and BPC6-Leu were computed by using the backbone coordinates of the C-Jun Leucine-zipper. Conserved alanine and leucine residues (both at ’d’ position of the register) in BPC6 and C...
Data
Hydrogen bonds and salt bridges that were formed between the two monomers during the 19.5ns production run. The table gives the pairs of amino acids and their positions within the zipper domains. Only those amino acids of one monomer are listed that have formed either hydrogen bonds or salt bridges with the respective pairing residue of the other...
Data
Subcellular localization of GFP-fusion proteins of AtBPC6 fragments. Laser confocal microscopy analysis of GFP fusion proteins and free mGFP in transiently transformed Nicotiana benthamiana epidermis cells. All hybrid fusion proteins of AtBPC6 fragments containing the entire 31 amino-acid long NLS localize to the nucleus and the nucleolus. (TIF)
Data
Prediction of the coiled-coil region present in group II BPC proteins. Prediction of a coiled coil containing domain at the N-terminus of AtBPC6 has been performed with 5 programs independently (Coils; Paircoil; Paircoil2; Multicoil; 2ZIP). All programs predict an extended α-helical coiled-coil region, which does not resemble topological features...
Data
Alignment of the native AtBPC6 and the register shifted BPC versions with C-Jun. The register of the C-Jun alpha-helix is shown on top of each alignment. Conserved alanine or leucine residues are highlighted in red and yellow background. The native sequences are aligned to fit the conserved amino acids at ‘d’-position of the register. In BPC6-1 th...
Data
RMSD of the backbone atoms of the dimeric models during the production run (19.5ns). The 19.5ns production run was performed at constant pressure and constant temperature. Coordinates for analysis were saved every 1 ps. Root-mean-square deviations (RMSD) of the backbone atoms of the six indicated protein structures were computed from the MD trajec...
Data
Binding free energy components of the dimmers. The calculated binding free energies are listed. Values have been inferred from 5 ns of 19.5ns production run and are given in kcal mol−1. (XLS)
Data
Relative signal intensities of DAPI- and GFP-fluorescence in the nucleus and nucleolus. Relative signal intensities of DAPI- and GFP-fluorescence in nuclei are measured from laser confocal microscopy images of BPC6-GFP, BPC6-NLS-GFP and mGFP expressed in Nicotiana benthamiana epidermis cells (Figure 1D). Fluorescence intensities (y-axis) of BPC6-G...
Data
RMSD of the backbone atoms of the dimeric models during the time period that was used for the calculation of the binding free energies. Schematic overview of the 5 nanosecond periods from the RMSD of the backbone atoms that were taken for the calculation of ΔGBinding: BPC6 - 15.5ns to 19.5ns (black line); C-Jun - 11.0ns to 16.0ns (red line); BPC6-...
Data
Presence of BPC-like coiled-coil regions outside the BPC-family. BPC-like coiled-coil regions from green plants, brown algae, cyanobacteria, bacteria, fungi and animals are aligned. alanines with an evenly spacing of 7 amino acids are highlighted by black background color. Not perfectly matching alanines that still contribute to a possible zipper...
Data
Homology model of the register shifted BPC6-1. The homology model of the coiled-coil structure of AtBPC6 was computed by using the backbone coordinates of the C-Jun Leucine-zipper, but shifted by −1 register. The conserved alanine residues in BPC6 at ‘d’-position are not at ‘c’-position. Note that within the short period of 2.3ns the two helices d...
Article
Regulatory non-coding DNA is important to drive gene transcription and thereby influence mRNA and consequently protein abundance. Therefore, biologists and bioinformation scientists aim to extract meaningful information from these sequence regions, in particular upstream regulation regions called promoters, and conclude on regulatory sequence funct...
Data
Binding specificity models. The integrated PFM-dataset containing all PFM models of the test and trainings sets is provided in File S2. For the models from TRANSFAC Professional no matrix is given as they are proprietary. (0.71 MB TXT)
Data
All query TFs in input format. File S3 contains all 5723 TFs without experimentally derived PFMs but annotated DNA-binding domains. This dataset was used as input file for the prediction framework presented in this work. (4.21 MB TXT)
Data
Distribution of TFs with and without PFMs for six different species. The absolute numbers of TFs per species are taken from the work of Wilson et al. (www.transcriptionfactor.org) and reflect TFs predicted by HMMs. The number of known PFMs is taken from the integrated dataset compiled in this work (see File S3) and compared to the number of transfe...
Data
Sequence versus PFM similarities for all TF pairs. Depicted are sequence similarities of DNA-binding domains versus PFM similarities for different structural superclasses. To learn the PFM similarity score, all TF pairs with a normalized BLOSUM62-score of their DNA-binding domains over 0.3 are considered for training; these are referred to as local...
Data
Set of non-trivial example predictions. Depicted are several examples of non-trivial PFM transferrers from the test set, for which the prediction error is estimated. The best matches, i.e., the TFs for which a PFM similarity above a predefined threshold (default: 0.95) was predicted, are merged to a consensus PFM using STAMP. The predicted PFM simi...
Data
Examples of non-trivial PFM transfers between TFs from distinct classes. This figure shows sequence logos, PFM similarity scores and TF class affiliations where either one (first column) or all best matches (second column) belong to a different TF class than the query TF. We found that for 51 TFs (70%) of the query TFs all of the predicted best mat...
Data
Predicted TFs. File S1 contains all 645 TFs for which PFM transfers were performed by our prediction framework. For each TF various annotations are provided, i.e., UniProt ID, species information, protein sequence, DNA-binding domain annotation and the ID of the best matching PFM that was predicted by our method. All PFM models are listed in File S...
Article
Full-text available
Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small f...