
Wolfgang NellenUniversity of Brawijaya · Department of Biology
Wolfgang Nellen
Prof. Dr. rer.nat.
About
194
Publications
23,263
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
5,424
Citations
Introduction
Mechanisms of gene regulation by siRNAi and miRNA, argonaute proteins, dsRBD proteins; silencing of retroelements, chromatin organization, biological & biochemical function of the DNA/tRNA methyltransferase Dnmt2; scanning force microscopy of DNA structure and nucleic acid – protein interactions. The model organism: Dictyostelium discoideum.
Indonesian-German Network for training & research collaborations (http://www.ign-ttrc.org/)
Public understanding of science (http://www.sciencebridge.net/)
Publications
Publications (194)
We have developed simple CRISPR-Cas experiments that can serve to introduce pupils, students and non-scientists alike to the fascinating power of targeted gene editing. The experimental course is divided in two parts. In part 1, we target plasmid borne lacZ to convert blue E. coli to white E. coli. In part 2, we analyse the CRISPR-Cas9 mediated dou...
Geht das Vertrauen in die Wissenschaft durch skrupellose, korrupte Raubtierverlage, Fake-Konferenzen und Fake-Publikationen verloren? Betrügen Wissenschaftler systematisch und verpulvern Steuergelder, um ihre Reputation und ihre Eitelkeit aufzuplustern? Die Antwort ist nein – aber es gibt Einschränkungen, und die Probleme, warum es diese Einschränk...
Was ist ein Protein Tag? Ein Tag, an dem man besonders viele und besonders schöne Proteine isolieren kann! Das war zwar eine Antwort in einer Klausur, stimmt aber nicht so ganz.
Education in molecular biology is considered difficult because it is complex and requires a lot of basic knowledge. Focused on basic science facts, it is usually taught with little connection to everyday life. A second problem is that the topic is rather abstract and results are only indirectly observed: we know that DNA is a double helix - but nob...
de Fast jede Zeitung und Zeitschrift, viele Fernsehsender und Internetseiten berichten über wissenschaftliche Themen. Doch was davon ist vertrauenswürdig – und was eine Sensationsmeldung, um Auflage zu schaffen? Dieser Artikel nennt Kriterien für guten Wissenschaftsjournalismus und zeigt auf, warum so viele Berichte auch in sogenannten Qualitätsmed...
The maturation pathways of microRNAs (miRNAs) have been delineated for plants and several animals, belonging to the evolutionary supergroups of Archaeplastida and Opisthokonta, respectively. Recently, we reported the discovery of the microprocessor complex in Dictyostelium discoideum of the Amoebozoa supergroup. The complex is composed of the Dicer...
Author Summary
miRNAs are essential regulators in eukaryotic cells and serve to control translation and stability of mRNAs. Processing of primary miRNA transcripts is carried out in two steps by evolutionary conserved machineries consisting mainly of double-strand specific RNases of the Dicer family and accessory double-strand RNA binding proteins...
srtA [RNAi] but not abpA [RNAi] knockdown strains show elevated miRNA levels/verification of srtA knockdown.
A: Ddi-miR-7097 expression was analyzed by Northern Blot in the AX2 wt and in srtA [RNAi 1] and srtA [RNAi 2] knockdown strains. 12 μg total RNA were loaded per lane. Mature ddi-miR-7079 was detected by the 32P labelled oligonucleotide DM217...
RbdB has a C-terminal NLS.
A: Schematic representation of RbdB and truncated protein versions. Identified NLS and NoLS sequences are indicated in RbdB and in RbdB (Δ504–612). All signal sequences are absent in RbdB (Δ504–733). B: Amino acid sequence of the predicted signal sequences that were identified by the cNLS Mapper and by NoD, respectively....
Visualization of miRNA expression in the wild type and in the angA- and rbdB- strains.
Normalized RNA-seq data were visualized using the IGB browser [63]. Screen shots were taken. On the X-axis genomic coordinates are shown. Read Counts are shown on the y-axis. As a comparison, miRNAs ddi-miR-1176 and ddi-miR-1177 were shown, too [9].
(PDF)
Specification of knockout plasmids.
The position of the knockout arms is given relative to the start codon of the respective gene. In addition, the number of deleted base pairs is annotated.
(DOCX)
Control of IP experiments.
Different control co-immunoprecipitations were performed. Samples (IN = input, Pre = preclear, SN = supernatant, E = elution) were analyzed by Western Blots. A: RbdB (Δ 504–612) GFP and HcpA 3xHA were expressed in the AX2 wild type background and co-immunoprecipitation by GFP tagged RbdB (Δ 504–612) was performed. HcpA 3x...
Validation of rbdA and rbdB gene deletions.
Schematic representation of the rbdA (A, top) and rbdB (B, top) wild type alleles, the knockout constructs and the null alleles after successful homologous recombination and insertion of the BsR cassette flanked by Lox-P sites (flox). We transformed each knockout construct twice in the AX2 wild type strai...
DrnB and RbdB localize independent of each other.
We monitored localization of DrnB GFP in the rbdB- strain and localization of RbdB mRFP in the drnB- strain, respectively by fluorescence microscopy. Both tagged proteins are mostly found in nucleoli associated foci though RbdB mRFP may also be more diffusely distributed in the nucleoli of some cell...
validation of identified miRNAs (canonical miRNAs).
A: Predicted hairpin structures of new miRNA candidates (canonical ones) and of ddi-mir-7097 [8] by M-fold [66]. Red: miRNA-5p, green: miRNA-3p. We only indicated the second miRNA, if it could be identified by our RNAseq approach. This was for example true for the previously identified miRNA ddi-m...
Expression of RbdB GFP from high copy and low copy integrating plasmids.
A: rbdB or rbdB gfp mRNA levels were determined by qRT-PCR in the indicated strains. Expression levels in the AX2 were compared with rbdB- strains that were transformed with pDbsr2a RbdB GFP [LC] or with pDneo2a RbdB GFP [HC]. Values are means from two independent RNA preparat...
Oligonucleotides used in this study.
(DOCX)
Absolute and relative read counts of identified miRNAs.
Absolute read counts are given for the denoted genomic positions. Relative read counts were calculated as follows: absolute read counts were divided by the total number of aligned reads and then normalized to the AX2.
(XLSX)
Identified miRNAs.
Genome positions of the identified miRNAs are shown. The coordinates may deviate by a few nucleotides. Plus and minus indicate the respective strand.
(DOCX)
Kommentar zu: “Arctic Apples” von Christiane Högermann in BIUZ 2/2016, S. 87f.
A group of homologous nucleic acid modification enzymes called Dnmt2, Trdmt1, Pmt1, DnmA, and Ehmet in different model organisms catalyze the transfer of a methyl group from the cofactor S-adenosyl-methionine (SAM) to the carbon-5 of cytosine residues. Originally considered as DNA MTases, these enzymes were shown to be tRNA methyltransferases about...
A fungus associated with the leaf spot of German iris (Iris germanica) was identified as Cladosporium iridis based on the morphological characteristics of the condiophores and conidia. A conidial suspension of the fungus was artificially inoculated onto a healthy unwounded plant, proving its pathogenicity. This is the first record of this disease f...
Additional information to the DIRS-1 based knock-down system
Dnmt2 enzymes are cytosine-5 methyltransferases that methylate C38 of several tRNAs. We report here that the activities of
two Dnmt2 homologs, Pmt1 from Schizosaccharomyces pombe and DnmA from Dictyostelium discoideum, are strongly stimulated by prior queuosine (Q) modification of the substrate tRNA. In vivo tRNA methylation levels were stimulated...
In the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability. The non-long terminal repeat retrotransposon TRE5-A amplifies continuously in D. discoideum cells even though it produces considerable amounts of minus-strand (antisense) RNA in the presence of an active RN...
Characteristics of dirs-1 mediated knock-downs:
We have previously shown that the most abundant Dictyostelium discoideum retroelement DIRS-1 is suppressed by RNAi mechanisms. Here we provide evidence that both inverted terminal repeats have strong promoter activity and that bidirectional expression apparently generates a substrate for Dicer. A cas...
Artificial inoculation is an important method for understanding the plant-virus interaction. Currently available techniques for virus artificial infection are whitefly based inoculation, grafting, mechanical, agroinoculation and particle bombardment. In fact, almost all the available inoculation methods do not result in ideal efficiency nor practic...
In den 1740er-Jahren erhielt Carl von Linné eine Pfl anzenprobe, die dem Echten Leinkraut (Linaria vulgaris) sehr ähnlich sah, jedoch völlig andere Blü-ten aufwies (> Titelbild). Der schwedische Forscher war darüber entsetzt, stellte dieses pfl anzliche Ex-emplar doch seine Theorie in Frage, nach der sich Pfl anzenarten anhand ihrer Blüten kategori...
The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms.
We investigated the role of two of th...
Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of
one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had
only a weak activity toward its matching Geob...
The aim of our research is predicting the alpha-patchouli alcohol isomer Pogostemon Herba as inhibitors cyclooxygenase (COX-1 and COX-2) isoenzymes. The data for the alpha-patchouli alcohol isomer (CD521903, CD442384, and/or CD6432585) Pogostemon Herba were explored from the pubchem database. Molecular interaction studies with COX-1 and COX-2 from...
Whiteflies have attracted intensive attention from many agriculturists due to their direct feeding and plant virus transmission. The economic losses depend on certain species population existing on the field during chilli-pepper cultivation. More over, biotype characteristic will determine the effectivity of applied pest management. Based on this ,...
Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable
elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tig...
Kleine Netzwerke zur Vermittlung ausländischer Wissenschaftler an deutsche Universitäten können die Anstrengungen des Deutschen Akademischen Austauschdienstes (DAAD) effektiv ergänzen, persönliche Ansprechpartner liefern und den deutschen Laboren sowie den ausländischen Studenten Enttäuschungen ersparen.
Project plan The linker histone H1 seems to localize in the periphery of the nucleus, presumably associated with inactivated genes (Dubin, 2010), indicates. Close to that region, epichromatin a structure localized at the exterior chromatin of interphase nuclei and mitotic chromosomes was described by Olins et al. in 2011. This structure seems to ha...
The involvement of aldo-keto reductases (AKRs) in cancer and tumorgenesis is widely reported but especially their roles in the pathological process are not generally established. This protein superfamily of AKR includes aldehyde reductases, aldose reductases, dihydrodiol dehydrogenases and hydroxysteroid dehydrogenases [J. M. Jez et. al, 1997]. All...
Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies...
The introduction of transgenes in Dictyostelium discoideum typically results in the integration of the transformation vector into the genome at one or a few insertion sites as tandem arrays of approximately 100 copies. Exceptions are extrachromosomal vectors, which do not integrate into chromosomes, and vectors containing resistance markers such as...
The pupose of this study was to identify genetic polymorphisms of bovine growth hormone gene exon 4, and intron 4 in local cattle breeds in West Sumatera Province of Indonesia. DNA was isolated from 60 blood samples and polymerase chain reaction (PCR) product of GH5 fragment (366 bp) were directly sequenced. Multiple alignments, including 60 bGH DN...
Editor's suggested further reading in BioEssays Epigenetics meets mathematics: Towards a quantitative understanding of chromatin biology Abstract.
The fission yeast Schizosaccharomyces pombe carries a cytosine 5-methyltransferase homolog of the Dnmt2 family (termed pombe methyltransferase 1, Pmt1), but contains no detectable DNA methylation. Here, we found that Pmt1, like other Dnmt2 homologs, has
in vitro methylation activity on cytosine 38 of tRNAAsp and, to a lesser extent, of tRNAGlu, des...
Structural studies showed that Dnmt3a has two interfaces for protein-protein interaction in the heterotetrameric Dnmt3a/3L
C-terminal domain complex: the RD interface (mediating the Dnmt3a-3a contact) and the FF interface (mediating the Dnmt3a-3L
contact). Here, we demonstrate that Dnmt3a-C forms dimers via the FF interface as well, which further o...
Structural studies showed that Dnmt3a has two interfaces for protein-protein interaction in the heterotetrameric Dnmt3a/3L
C-terminal domain complex: the RD interface (mediating the Dnmt3a-3a contact) and the FF interface (mediating the Dnmt3a-3L
contact). Here, we demonstrate that Dnmt3a-C forms dimers via the FF interface as well, which further o...
DET1 (De-etiolated 1) is a chromatin binding protein involved in developmental regulation in both plants and animals. DET1
is largely restricted to multicellular eukaryotes, and here we report the characterization of a DET1 homolog from the social
amoeba Dictyostelium discoideum. As in other species, Dictyostelium DET1 is nuclear localized. In cont...
The centromeric histone H3 variant (CenH3) serves to target the kinetochore to the centromeres and thus ensures correct chromosome
segregation during mitosis and meiosis. The Dictyostelium H3-like variant H3v1 was identified as the CenH3 ortholog. Dictyostelium CenH3 has an extended N-terminal domain with no similarity to any other known proteins a...
Der gemeinnützige Verein Science Bridge aus dem Umfeld der Universität Kassel hat zusammen mit der Firma Febikon begonnen, einfache Geräte- und Versuchskits zu entwickeln, die in der Schule schnell, problemlos und preisgünstig eingesetzt werden können.
We describe here a series of vectors for ectopic expression of tagged proteins in Dictyostelium discoideum. These vectors allow the addition of N- or C-terminal tags (GFP, mRFP, 3xFLAG, 3xHA, 6xMYC or TAP) with an optimised polylinker sequence and no additional amino acid residues at the N- or C-terminus of the protein. The expression cassettes wer...
This article focuses on the evolutionary conserved and most widely distributed DNA methyltransferase in eukaryotes - Dnmt2. Recent findings give rise to the assumption that Dnmt2 may harbour dual specificity and acts on DNA and RNA.
This article focuses on the evolutionary conserved and most widely distributed DNA methyltransferase in eukaryotes - Dnmt2. Recent findings give rise to the assumption that Dnmt2 may harbour dual specificity and acts on DNA and tRNA.
Epigenetic modifications of histones regulate gene expression and lead to the establishment and maintenance of cellular phenotypes during development. Histone acetylation depends on a balance between the activities of histone acetyltransferases and histone deacetylases (HDACs) and influences transcriptional regulation. In this study, we analyse the...
The CSL (CBF1/RBP-Jkappa/Suppressor of Hairless/LAG-1) family is comprised of transcription factors essential for metazoan development, mostly due to their involvement in the Notch receptor signaling pathway. Recently, we identified two novel classes of CSL genes in the genomes of several fungal species, organisms lacking the Notch pathway. In this...
The UNISTAFF program from ISOS, University Kassel Germany has brought together sixty scholars from various universities in Indonesia. These scholars come from different scientific backgrounds. Upon their return they are expected to become agents-of-change and create a multiplier effect to contribute improvement of quality in higher education in the...
The C-terminal domains of Dnmt3a and Dnmt3L form elongated heterotetramers (3L-3a-3a-3L). Analytical ultracentrifugation confirmed the Dnmt3a-C/3L-C complex exists as a 2:2 heterotetramer in solution. The 3a-3a interface is the DNA-binding site, while both interfaces are essential for AdoMet binding and catalytic activity. Hairpin bisulfite analysi...
Although their amino acid sequences and structure closely resemble DNA methyltransferases, Dnmt2 proteins were recently shown by Goll and colleagues to function as RNA methyltransferases transferring a methyl group to the C5 position of C38 in tRNA(Asp). We observe that human DNMT2 methylates tRNA isolated from Dnmt2 knock-out Drosophila melanogast...
Aurora kinases are highly conserved proteins with important roles in mitosis. Metazoans contain two kinases, Aurora A and
B, which contribute distinct functions at the spindle poles and the equatorial region respectively. It is not currently known
whether the specialized functions of the two kinases arose after their duplication in animal cells or...
Nanocrystalline diamond/amorphous carbon (NCD/a-C) composite films have been prepared by microwave plasma chemical vapor deposition (MWCVD) from methane/nitrogen mixtures and investigated with respect of their bioproperties. By means of atomic force microscopy (AFM) it was shown that RNA molecules can be attached to the NCD/a-C surface, which has b...
Im Juli tagt zum ersten Mal seit 80 Jahren der Internationale Kongress für Genetik in Deutschland. Weit über tausend Genetiker aus aller Welt werden vom 12. bis 17. Juli 2008 in Berlin erwartet, um in mehreren hundert Fachvorträgen die aktuelle Forschung in allen Teilgebieten der Genetik zu diskutieren. Parallel hat die Gesellschaft für Genetik (Gf...
The M.EcoRV DNA methyltransferase recognizes GATATC sites. It is related to EcoDam, which methylates GATC sites. The DNA binding domain of M.EcoRV is similar to that of EcoDam suggesting a similar mechanism of DNA recognition. We show that amino acid residue Lys 11 of M.EcoRV is involved in recognition of Gua 1 and Arg 128 contacts the Gua in base...
Die rasante Entwicklung von Genetik und Molekularbiologie hat eine unerwartet komplexe Organisation des Genoms aufgedeckt. Es zeigt sich, dass die Funktionen des Genoms nicht mehr ausschließlich durch proteincodierende Gene beschrieben werden können. Der Genbegriff umfasst heute auch Nukleotidsequenzen, die für eine Vielfalt verschiedener RNAs mit...
The M.EcoRV DNA methyltransferase recognizes GATATC sites. It is related to EcoDam, which methylates GATC sites. The DNA binding domain of M.EcoRV is similar to that of EcoDam suggesting a similar mechanism of DNA recognition. We show that amino acid residue Lys11 of M.EcoRV is involved in recognition of Gua1 and Arg128 contacts the Gua in base pai...
Gene silencing by RNA interference (RNAi) and by antisense RNA are powerful tools to interfere with the expression of eukryotic
genes. Since the first description of RNAi in 1998, antisense-mediated gene silencing has been considered to have essentially
the same mechanism as gene silencing by RNAi. However, while substantial effort has been made to...