Institute for Genome Research and Systems Biology

Bielefeld, Germany

Institute for Genome Research and Systems Biology

Bielefeld, Germany
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Lohr B.,Bielefeld University | Streitner C.,Bielefeld University | Steffen A.,Bielefeld University | Lange T.,TU Braunschweig | And 2 more authors.
Molecular Biology Reports | Year: 2014

The RNA-binding protein Arabidopsis thaliana glycine-rich RNA-binding protein 7 (AtGRP7) regulates the steady-state abundance of numerous target transcripts in A. thaliana. Here we show that the GA1 and GA2 transcripts encoding the first enzymes of the gibberellin biosynthetic pathway are expressed at reduced levels in transgenic plants ectopically over-expressing AtGRP7 (AtGRP7-ox plants). Furthermore, the levels of the bioactive phytohormone GA4 as well as of several intermediates of the GA biosynthetic pathway are reduced in AtGRP7-ox plants. The transgenic plants show a reduced length of the vegetative stem. The application of exogenous GA largely reverses the phenotype by increasing the number of vegetative internodes. AtGRP7-ox plants flower with fewer leaves than wt plants, suggesting that the floral promotive effect of AtGRP7 bypasses the effect of a reduced GA level in AtGRP7-ox plants. Upon GA treatment, AtGRP7-ox plants flower only slightly earlier than wild type plants. Thus, exogenous GA has only a small additional effect in reducing the number of leaves at the onset of flowering in AtGRP7-ox plants. © 2013 Springer Science+Business Media Dordrecht.

Staiger D.,Bielefeld University | Staiger D.,Institute for Genome Research and Systems Biology | Green R.,Hebrew University of Jerusalem
Trends in Plant Science | Year: 2011

The circadian clock is an endogenous, approximately 24-h timer that enables plants to anticipate daily changes in their environment and regulates a considerable fraction of the transcriptome. At the core of the circadian system is the oscillator, made up of interconnected feedback loops, involving transcriptional regulation of clock genes and post-translational modification of clock proteins. Recently, it has become clear that post-transcriptional events are also critical for shaping rhythmic mRNA and protein profiles. This review covers regulation at the RNA level of both the core clock and output genes in Arabidopsis (Arabidopsis thaliana), with comparisons with other model organisms. We discuss the role of splicing, mRNA decay and translational regulation as well as recent insights into rhythms of noncoding regulatory RNAs. © 2011.

Streitner C.,Bielefeld University | Simpson C.G.,James Hutton Institute | Shaw P.,James Hutton Institute | Danisman S.,Bielefeld University | And 3 more authors.
Plant Signaling and Behavior | Year: 2013

Alternative splicing (AS) gives rise to multiple mRNA isoforms from the same gene, providing possibilities to reg-ulate gene expression beyond the level of transcription. In a recent paper in Nucleic Acids Research we used a high resolution RT-PCR based panel to study changes in AS patterns in plants with altered levels of an hnRNP-like RNA-binding protein in Arabidopsis thaliana. Furthermore, we detected significant changes in AS pat-terns between different Arabidopsis eco-types. Here we investigated how small changes in ambient temperature affect AS. We found significant changes in AS for 12 of 28 investigated events (43%) upon transfer of Arabidopsis plants from 20°C to 16°C and for 6 of the 28 inves-tigated events (21%) upon transfer from 20°C to 24°C. © 2013 Landes Bioscience.

Staiger D.,Bielefeld University | Staiger D.,Institute for Genome Research and Systems Biology | Brown J.W.S.,James Hutton Institute
Plant Cell | Year: 2013

High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely. © 2013 American Society of Plant Biologists. All rights reserved.

Kutyniok M.,Bielefeld University | Kutyniok M.,Institute for Genome Research and Systems Biology | Muller C.,Bielefeld University | Muller C.,Institute for Genome Research and Systems Biology
Journal of Experimental Botany | Year: 2012

Plants are frequently under attack by multiple herbivores and can be infested at their shoots as well as their roots. As a consequence, plant metabolites are readily induced, mediated by phytohormones such as salicylic acid and jasmonic acid. Thereby, cross-talk between signal transduction pathways may occur if different herbivores attack the plant simultaneously. In turn, modifications in the plant metabolic pattern can affect herbivores infesting local and systemic tissue. Here, an integrative approach combining metabolomics and performance experiments was used to study the induction of plant metabolites in Arabidopsis thaliana by the specialist aphid Brevicoryne brassicae feeding on shoots and the generalist nematode Heterodera schachtii infesting root tissue. In contrast to most other studies, low infestation rates typical for the decisive early stages of infestation were used. Moreover, the consequences of induction responses on plant-mediated indirect interactions between these herbivores were investigated. In aphid-treated plants, several metabolites including glucosinolates, important defence compounds of Brassicaceae, were reduced in the shoot, but only minute changes took part in the systemic root tissue. Primary metabolites as well as phytohormones were not altered 3 days post infestation. In contrast, nematodes did not evoke significant metabolic alterations locally or systemically. In accordance, nematode presence did not affect aphid population growth, whereas aphids mediated a considerably reduced nematode infestation. These results demonstrate that plants respond in a very fine-tuned way to different challenges. Although they show only minute systemic responses to low herbivore stress, these changes can have pronounced effects on plant-mediated interactions between herbivores. © 2012 The Author.

Streitner C.,Bielefeld University | Koster T.,Bielefeld University | Simpson C.G.,James Hutton Institute | Shaw P.,James Hutton Institute | And 4 more authors.
Nucleic Acids Research | Year: 2012

Alternative splicing (AS) of pre-mRNAs is an important regulatory mechanism shaping the transcriptome. In plants, only few RNA-binding proteins are known to affect AS. Here, we show that the glycine-rich RNA-binding protein AtGRP7 influences AS in Arabidopsis thaliana. Using a high-resolution RT-PCR-based AS panel, we found significant changes in the ratios of AS isoforms for 59 of 288 analyzed AS events upon ectopic AtGRP7 expression. In particular, AtGRP7 affected the choice of alternative 5′ splice sites preferentially. About half of the events are also influenced by the paralog AtGRP8, indicating that AtGRP7 and AtGRP8 share a network of downstream targets. For 10 events, the AS patterns were altered in opposite directions in plants with elevated AtGRP7 level or lacking AtGRP7. Importantly, RNA immunoprecipitation from plant extracts showed that several transcripts are bound by AtGRP7 in vivo and indeed represent direct targets. Furthermore, the effect of AtGRP7 on these AS events was abrogated by mutation of a single arginine that is required for its RNA-binding activity. This indicates that AtGRP7 impacts AS of these transcripts via direct interaction. As several of the AS events are also controlled by other splicing regulators, our data begin to provide insights into an AS network in Arabidopsis. © 2012 The Author(s).

Lummer M.,Bielefeld University | Lummer M.,Institute for Genome Research and Systems Biology | Humpert F.,Bielefeld University | Wiedenlubbert M.,Bielefeld University | And 4 more authors.
Molecular Plant | Year: 2013

Fluorescent reporter proteins that allow repeated switching between a fluorescent and a non-fluorescent state in response to specific wavelengths of light are novel tools for monitoring of protein trafficking and super-resolution fluorescence microscopy in living organisms. Here, we describe variants of the reversibly photoswitchable fluorescent proteins rsFastLime, bsDronpa, and Padron that have been codon-optimized for the use in transgenic Arabidopsis plants. The synthetic proteins, designated rsFastLIME-s, bsDRONPA-s, and PADRON C-s, showed photophysical properties and switching behavior comparable to those reported for the original proteins. By combining the 'positively switchable' PADRON C-s with the 'negatively switchable' rsFastLIME-s or bsDRONPA-s, two different fluorescent reporter proteins could be imaged at the same wavelength upon transient expression in Nicotiana benthamiana cells. Thus, co-localization analysis can be performed using only a single detection channel. Furthermore, the proteins were used to tag the RNA-binding protein AtGRP7 (Arabidopsis thaliana glycine-rich RNA-binding protein 7) in transgenic Arabidopsis plants. Because the new reversibly photoswitchable fluorescent proteins show an increase in signal strength during each photoactivation cycle, we were able to generate a large number of scans of the same region and reconstruct 3-D images of AtGRP7 expression in the root tip. Upon photoactivation of the AtGRP7:rsFastLIME-s fusion protein in a defined region of a transgenic Arabidopsis root, spreading of the fluorescence signal into adjacent regions was observed, indicating that movement from cell to cell can be monitored. Our results demonstrate that rsFastLIME-s, bsDRONPA-s, and PADRON C-s are versatile fluorescent markers in plants. Furthermore, the proteins also show strong fluorescence in mammalian cells including COS-7 and HeLa cells. © 2013 © The Author 2013. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS.

Kutyniok M.,Bielefeld University | Kutyniok M.,Institute for Genome Research and Systems Biology | Muller C.,Bielefeld University | Muller C.,Institute for Genome Research and Systems Biology
Oecologia | Year: 2013

The plant metabolite composition is modulated by various abiotic and biotic factors including nutrient availability and herbivory. In turn, induced changes in plant quality can affect herbivore performance and mediate indirect interactions between spatially separated herbivores sharing a host. Studies on plant-mediated herbivore interactions have been carried out at single fertilization regimes only, but we hypothesized that nutrient availability modifies these interactions. Therefore, we studied the interactions between two vascular tissue herbivores, the aboveground feeding aphid Brevicoryne brassicae and the belowground infesting nematode Heterodera schachtii, on Arabidopsis thaliana grown under two nitrate fertilization conditions (varying by 33 %). Furthermore, we investigated plant growth and primary metabolic responses to fertilization and herbivore treatments, which could potentially mediate these interactions, as the herbivores may act as metabolic sinks. Whereas nematodes had no effects on aphids, aphid presence influenced nematodes in opposite directions, depending on fertilization: at low nitrate supply, aphids had a promoting effect on nematodes, whereas at high nitrate fertilization they lowered the nematode infestation compared to control plants. Plants produced significantly more biomass under high nitrate supply but C and N contents were not altered. Primary metabolite profiles differed only marginally between roots of both fertilization treatments in plants with and without aphids, indicating that nematodes may respond to these or other metabolic modifications, which are caused by minute environmental changes, in a sensitive way. Our results highlight the need to consider the importance of plant nutrient availability on the outcome of interactions between co-occurring herbivores in future studies. © 2013 Springer-Verlag Berlin Heidelberg.

Ramos R.T.J.,Federal University of Pará | Carneiro A.R.,Federal University of Pará | de Castro Soares S.,Federal University of Minas Gerais | Barbosa S.,Federal University of Pará | And 6 more authors.
Journal of Microbiological Methods | Year: 2013

With the advent of high-throughput DNA sequencing platforms, there has been a reduction in the cost and time of sequencing. With these advantages, new challenges have emerged, such as the handling of large amounts of data, quality assessment, and the assembly of short reads. Currently, benchtop high-throughput sequencers enable the genomes of prokaryotic organisms to be sequenced within two hours with a reduction in coverage compared with the SOLiD, Illumina and 454 FLX Titanium platforms, making it necessary to evaluate the efficiency of less expensive benchtop instruments for prokaryotic genomics. In the present work, we evaluate and propose a methodology for the use of the Ion Torrent PGM platform for decoding the gram-positive bacterium Corynebacterium pseudotuberculosis, for which 15 complete genome sequences have already been deposited based on fragment and mate-paired libraries with a 3-kb insert size. Despite the low coverage, a single sequencing run using a mate-paired library generated 39 scaffolds after de novo assembly without data curation. This result is superior to that obtained by sequencing using libraries generated from fragments marketed by the equipment's manufacturer, as well as that observed for mate-pairs sequenced by SOLiD. The generated sequence added an extra 91. kb to the genome available at NCBI. © 2013.

Ramos R.T.J.,Federal University of Pará | Carneiro A.R.,Federal University of Pará | Soares S.D.C.,Federal University of Minas Gerais | Santos A.R.D.,Federal University of Minas Gerais | And 7 more authors.
Microbial Biotechnology | Year: 2013

New sequencing platforms have enabled rapid decoding of complete prokaryotic genomes at relatively low cost. The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. One particular problem is the lack of genomes that enable reference-based assembly, such as the one used in the present study, Corynebacterium pseudotuberculosis biovar equi, which causes high economic losses in the US equine industry. The quality treatment strategy incorporated into the assembly pipeline enabled a 16-fold greater use of the sequencing data obtained compared with traditional quality filter approaches. Data preprocessing prior to the de novo assembly enabled the use of known methodologies in the next-generation sequencing data assembly. Moreover, manual curation was proved to be essential for ensuring a quality assembly, which was validated by comparative genomics with other species of the genus Corynebacterium. The present study presents a modus operandi that enables a greater and better use of data obtained from semiconductor sequencing for obtaining the complete genome from a prokaryotic microorganism, C. pseudotuberculosis, which is not a traditional biological model such as Escherichia coli. © 2012 The Authors. Published by Society for Applied Microbiology and Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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