Aims and Topics - Proteins and Genes - Methodologies - Teaching/Education - Collaborative Services - Publications - Scripts/Programs (Motif Mapper) - Contact
Aims and Topics
My research focuses on the discovery of protein-protein and protein-DNA network interactions of transcription factors and other proteins. Transcription factors are gene products that interact with DNA and influence gene transcription alone, synergistically or antagonistically with other factors. Although transcription itself is only one of all possible control mechanisms active during homeostatic and non-homeostatic regulation, transcription is a measurable and fairly accurate indication of protein activity. Thus, by taking advantage of these phenomena in plants, we are approaching the challenge of exploring the lifespan of transcription factors using a variety of approaches. One method is the employment and refinement of in vivo protein-protein interaction studies using the technique of bi-molecular fluorescence complementation (BiFC; a.k.a split-YFP, s-YFP) in living plant cells. Secondly, we search for the DNA binding sites of transcription factors by using and developing many bioinformatic tools (programs, scripts, pipelines, workflows) in-house and encouraging collaborative projects with the aim of capturing biological information which can be applied in the laboratory.
Proteins and Genes
We are especially interested in two classes of transcription factors (TFs). One class is the The basic region/leucine zipper (bZIP) transcription factors and another is the response-regulator TFs belonging to the two-component system.
The bZIP transcription factors have a basic region that binds DNA and a leucine zipper for homo- and heterodimerization. We focus on one particular class of bZIP proteins, the plant bZIP subclass C. These proteins are involved in diverse signaling cascades, some of which involve plant pathogen interactions (see publications (PubMed IDs); PMID: 16957775, PMID: 17671505, PMID: 14597573).
The other class is the two-component system (TCS) in plants and its respective proteins are conserved from bacteria to plants, but not found in humans. Signal input is perceived by a histidine kinase and this induces autophosphorylation of a conserved histidine (H) residue. The phosphoryl group (P) is relayed to a conserved Asp residue (D) that is localized in the C-terminal domain, called the receiver-like domain, of the histidine kinase. Plants have evolved an intermediate protein, called phosphotransfer proteins. The histidine-containing phosphotransfer proteins function as intermediates between the histidine kinase and the response regulator adding combinatorial complexity to the two-component system in plants.
The method is correctly called Bi-molecular Flourescence Complementation, or BiFC for short. The method bases itself around the principle of reconstituting the amino-acid chromophore of a YFP protein by fusing two halves of a split protein to other proteins that interact; since the YFP protein has been split into two halves (using molecular cloning techniques), this system constitutes a two molecule or binary system of (i.e. bi-molecular). Once the two halves are brought and held within close proximity of each other, the chromophore is reconstituted (i.e. Fluorescence Complementation). The interaction has been shown to be dependent on the other proteins the two halves are fused to. Provided that these two other proteins interact, is it possible (excluding steric hindrance) that the two halves come within close enough proximity to re-constitute the chromophore and we detect fluorescence. This method has spawned a new passion in the study of protein-protein interactions. One of the major advantages of this method is that one can study the interaction without fixation of the tissue that is in living cells. The method has also been expanded to use other derivatives of YFP: CFP, BFP, GFP (partially) and other molecules, RFP, LUC, DHFR, NAN. These split-molecule systems are alternatives to Fluorescence Resonance Energy Transfer (FRET) and Bio-luminescence Energy Transfer (BRET) which "capture" fluorescence light from one fluorescing molecule to excite another. As with all systems, each has its advantages and its disadvantages and must be weighed when considering what scientific question is being asked.
The progressive accumulation of data in any research field now requires the storage and computation retrieval power of computers. Moreover, it is not only data retrieval that requires micro-processors, but also highly complex or timely calculations on massive amounts of data require them, which is an aspect of Informatics. Bioinformatics has the same overall goals as informatics, with the major difference that it works with biological information.
I have programmed a set of scripts for the detection and distribution analysis of cis-elements; the script package is called Motif Mapper. I had originally developed it at the package at the Max-Planck Institute of Plant Breeding Research in Cologne, Germany and am now making updates here at the Center for Plant Molecular Biology at the University of Tübingen. The latest release versions and version history can be found here: Motif Mapper (ZMBP updates). I have also created a script to calculate the enrichment or depletion of motifs from a subset of sequences against a randomized background; this script has the benefit of unlimited list lengths (a general limitation of most online services).
Motif Mapper (inc. ZMBP Updates)
Identity List Comparison Scripts (compare lists against each other for basic set analysis, graph analysis, or tree analysis)
Seminar Classes being offered:
I am currently working at the Central Facilities FACS and Transformation and provide advanced courses, practical courses, etc. from there.
I am the Core Manager and Principle Operator for the ZMBP Flow Cytometry and FACS Unit. The MoFlo Legacy is up and running! Please visit the web site or contact me for more detailed information: ZMBP Central Facilities FACS.
I am also the Core Manager of the ZMBP Plant Transformation Unit. We are responsible for providing the ZMBP with expertise and service for difficult stable or transient plant transformation techniques. I have developed techniques for transfecting 96 samples at a time using 96-deep-well plates and can provide training via the Facility or scientific collaboration.
These are publications based on basic research questions I am engaged in.
Faciltiy based publications are placed in their respective pages.
ARR22 overexpression can suppress plant Two-Component Regulatory Systems. Wallmeroth N, Jeschke D, Slane D, Nägele J, Veerabagu M, Mira-Rodado V, Berendzen KW. PLoS One. 2019 Feb 11;14(2):e0212056. doi: 10.1371/journal.pone.0212056. eCollection 2019.
2in1 Vectors Improve In Planta BiFC and FRET Analyses. Mehlhorn DG, Wallmeroth N, Berendzen KW, Grefen C. Methods Mol Biol. 2018;1691:139-158. doi: 10.1007/978-1-4939-7389-7_11.
Chimeric Autofluorescent Proteins as Photophysical Model System for Multicolor Bimolecular Fluorescence Complementation (mcBiFC). Peter S, Zur Oven-Krockhaus S, Veerabagu M, Mira-Rodado V, Berendzen KW, Meixner AJ, Harter K, Schleifenbaum FE. J Phys Chem B. 2017 Feb 27. doi: 10.1021/acs.jpcb.6b11623
The metabolic sensor AKIN10 modulates the Arabidopsis circadian clock in a light-dependent manner. Shin J, Sánchez-Villarreal A, Davis AM, Du SX, Berendzen KW, Koncz C, Ding Z, Li C, Davis SJ. Plant Cell Environ. 2017 Jan 5. doi: 10.1111/pce.12903.
Arabidopsis response regulator 22 inhibits cytokinin-regulated gene transcription in vivo. Wallmeroth N, Anastasia AK, Harter K, Berendzen KW, Mira-Rodado V. Protoplasma. 2017 Jan;254(1):597-601. doi: 10.1007/s00709-016-0944-4. Epub 2016 Jan 15.
Techniques for the Analysis of Protein-Protein Interactions in Vivo. Xing S, Wallmeroth N, Berendzen KW, Grefen C. Plant Physiol. 2016 Jun;171(2):727-58. doi: 10.1104/pp.16.00470. Review.
See Facility work FACS.
Plant Core Environmental Stress Response Genes Are Systemically Coordinated during Abiotic Stresses. Hahn A, Kilian J, Mohrholz A, Ladwig F, Peschke F, Dautel R, Harter K, Berendzen KW, Wanke D. Int J Mol Sci. 2013 Apr 8;14(4):7617-41.
Reevaluation of the Reliability and Usefulness of the Somatic Homologous Recombination Reporter Lines. Ülker B, Hommelsheim CM, Berson T, Thomas S, Chandrasekar B, Olcay AC, Berendzen KW, Frantzeskakis L. Plant Cell. 2012 Nov 9.
Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription. Berendzen KW, Weiste C, Wanke D, Kilian J, Harter K, Dröge-Laser W. BMC Plant Biol. 2012 Aug 1;12:125.
Screening for in planta protein-protein interactions combining bimolecular fluorescence complementation with flow cytometry. Berendzen KW, Böhmer M, Wallmeroth N, Peter S, Vesić M, Zhou Y, Tiesler FK, Schleifenbaum F, Harter K. Plant Methods. 2012 Jul 12;8(1):25.
Molecular interactions of ROOTLESS CONCERNING CROWN AND SEMINAL ROOTS, a LOB domain protein regulating shoot-borne root initiation in maize (Zea mays L.). Majer C, Xu C, Berendzen KW, Hochholdinger F. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2012 Jun 5;367(1595):1542-51
Volatiles of two growth-inhibiting rhizobacteria commonly engage AtWRKY18 function. Wenke K, Wanke D, Kilian J, Berendzen K, Harter K, Piechulla B. Plant J. 2012 May;70(3):445-59. doi: 10.1111/j.1365-313X.2011.04891.x. Epub 2012 Feb 14.
Prerequisites, performance and profits of transcriptional profiling the abiotic stress response. Kilian J, Peschke F, Berendzen KW, Harter K, Wanke D. Biochimica et biophysica acta. 2012 Feb;1819(2):166-75. Epub 2011 Oct 6. Review
Alanine zipper-like coiled-coil domains are necessary for homotypic dimerization of plant GAGA-factors in the nucleus and nucleolus. Wanke D, Hohenstatt ML, Dynowski M, Bloss U, Hecker A, Elgass K, Hummel S, Hahn A, Caesar K, Schleifenbaum F, Harter K, Berendzen KW. PLoS One. 2011 Feb 10;6(2):e16070.
Rootless with undetectable meristem 1 encodes a monocot-specific AUX/IAA protein that controls embryonic seminal and post-embryonic lateral root initiation in maize. von Behrens I, Komatsu M, Zhang Y, Berendzen KW, Niu X, Sakai H, Taramino G, Hochholdinger F. Plant J. 2011 Apr;66(2):341-53. doi: 10.1111/j.1365-313X.2011.04495.x. Epub 2011 Mar 1.
Promoter specificity and interactions between early and late Arabidopsis heat shock factors. Li M, Berendzen KW, Schöffl F. Plant Mol Biol. 2010 Jul;73(4-5):559-67. Epub 2010 May 11.
Detection of in vivo interactions between Arabidopsis class A-HSFs, using a novel BiFC fragment, and identification of novel class B-HSF interacting proteins. Li M, Doll J, Weckermann K, Oecking C, Berendzen KW, Schöffl F. Eur J Cell Biol. 2010 Feb-Mar;89(2-3):126-32. Epub 2009 Nov 27.
ModuleMaster: a new tool to decipher transcriptional regulatory networks. Wrzodek C, Schröder A, Dräger A, Wanke D, Berendzen KW, Kronfeld M, Harter K, Zell A. Biosystems. 2010 Jan;99(1):79-81. Epub 2009 Oct 9.
Fluorescence Intensity Decay Shape Analysis Microscopy (FIDSAM) for Quantitative and Sensitive Live-Cell Imaging: A Novel Technique for Fluorescence Microscopy of Endogenously Expressed Fusion-Proteins. Schleifenbaum F, Elgass K, Sackrow M, Caesar K, Berendzen K, Meixner AJ, Harter K. Mol Plant. 2009 Dec 28. [Epub ahead of print]
Analysis of plant regulatory DNA sequences by transient protoplast assays and computer aided sequence evaluation. Berendzen KW, Harter K, Wanke D. Methods Mol Biol. 2009;479:311-35.
Analysis of plant regulatory DNA sequences by transient protoplast assays and computer aided sequence evaluation. Berendzen KW, Harter K, Wanke D. Methods Mol Biol. 2009;479:311-35. Plant Signal Transduction, Methods and Protocols, Series: Methods in Molecular Biology, Vol. 479 Chapter 20, Pfannschmidt, Thomas (Ed.), 2008.
Modeling gene regulation and spatial organization of sequence based motifs. (2008). Jochen Supper, Claas aufm Kampe, Dierk Wanke, Kenneth W Berendzen, Klaus Harter, Richard Bonneau, and Andreas Zell. IEEE International Conference on Bioinformatics and Bioengineering, BIBE. accepted.
The Arabidopsis thaliana response regulator ARR22 is a putative AHP phospho-histidine phosphatase expressed in the chalaza of developing seeds. (2008). Horák J, Grefen C, Berendzen KW, Hahn A, Stierhof YD, Stadelhofer B, Stahl M, Koncz C, Harter K. BMC Plant Biol. 2008 Jul 15;8:77.
Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots. Elke Mangelsen, Joachim Kilian, Kenneth W. Berendzen, Üner H. Kolukisaoglu, Klaus Harter, Christer Jansson, Dierk Wanke. BMC Genomics 2008, 9:194
The Analysis of Gene Expression and Cis-Regulatory Elements in Large Microarray Expession Datasets. D. Wanke, J. Kilian, J. Supper, K. W. Berendzen, A. Zell, and K. Harter, pp.294 - 314 (March 2007). QP-PQ: Quantum Probability and White Noise Analysis - Vol. 21 "Qunatum Bio-Informatics: From Quantum Information to Bio-Informatics". World Scientific (2008; ISSN: 1793-5121).
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. Berendzen KW, Stüber K, Harter K, Wanke D. BMC Bioinformatics. 2006 Nov 30;7:522.
A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta. Berendzen K, Searle I, Ravenscroft D, Koncz C, Batschauer A, Coupland G, Somssich IE, Ulker B. Plant Methods. 2005 Aug 23;1(1):4.
The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Santi L, Wang Y, Stile MR, Berendzen K, Wanke D, Roig C, Pozzi C, Müller K, Müller J, Rohde W, Salamini F. The Plant journal : for cell and molecular biology. 2003 Jun;34(6):813-26.
Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes. Ríos G, Lossow A, Hertel B, Breuer F, Schaefer S, Broich M, Kleinow T, Jásik J, Winter J, Ferrando A, Farrás R, Panicot M, Henriques R, Mariaux JB, Oberschall A, Molnár G, Berendzen K, Shukla V, Lafos M, Koncz Z, Rédei GP, Schell J, Koncz C.The Plant journal: for cell and molecular biology. 2002 Oct;32(2):243-53.
University of Tübingen
ZMBP Central Facilities
Kenneth W Berendzen
Auf der Morgenstelle 32, 5X17
tel.fax(ZMBP) +49-07071-29 32 87
email: kenneth.berendzen (a) zmbp uni-tuebingen de