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Publications - Molecular Signal Processing

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Publications

Delker, C.; Pöschl, Y.; Raschke, A.; Ullrich, K.; Ettingshausen, S.; Hauptmann, V.; Grosse, I.; Quint, M. Natural Variation of Transcriptional Auxin Response Networks in Arabidopsis thaliana Plant Cell 22, 2184-2200, (2010) DOI: 10.1105/tpc.110.073957

Natural variation has been observed for various traits in Arabidopsis thaliana. Here, we investigated natural variation in the context of physiological and transcriptional responses to the phytohormone auxin, a key regulator of plant development. A survey of the general extent of natural variation to auxin stimuli revealed significant physiological variation among 20 genetically diverse natural accessions. Moreover, we observed dramatic variation on the global transcriptome level after induction of auxin responses in seven accessions. Although we detect isolated cases of major-effect polymorphisms, sequencing of signaling genes revealed sequence conservation, making selective pressures that favor functionally different protein variants among accessions unlikely. However, coexpression analyses of a priori defined auxin signaling networks identified variations in the transcriptional equilibrium of signaling components. In agreement with this, cluster analyses of genome-wide expression profiles followed by analyses of a posteriori defined gene networks revealed accession-specific auxin responses. We hypothesize that quantitative distortions in the ratios of interacting signaling components contribute to the detected transcriptional variation, resulting in physiological variation of auxin responses among accessions.
Publications

Schumann, N.; Navarro-Quezada, A.; Ullrich, K.; Kuhl, C.; Quint, M. Molecular Evolution and Selection Patterns of Plant F-box Proteins with C-terminal Kelch Repeats Plant Physiol 155, 835-850, (2011) DOI: 10.1104/pp.110.166579

The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization.
Publications

Kopycki, J.; Wieduwild, E.; Kohlschmidt, J.; Brandt, W.; Stepanova, A.N.; Alonso, J.M.; Pedras, M.S.; Abel, S.; Grubb, C.D. Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition Biochem J 450, 37-46, (2013) DOI: 10.1042/BJ20121403

Plant genomes encode numerous small molecule glycosyltransferases which modulate the solubility, activity, immunogenicity and/or reactivity of hormones, xenobiotics and natural products. The products of these enzymes can accumulate to very high concentrations, yet somehow avoid inhibiting their own biosynthesis. Glucosyltransferase UGT74B1 (UDP-glycosyltransferase 74B1) catalyses the penultimate step in the core biosynthetic pathway of glucosinolates, a group of natural products with important functions in plant defence against pests and pathogens. We found that mutation of the highly conserved Ser284 to leucine [wei9-1 (weak ethylene insensitive)] caused only very mild morphological and metabolic phenotypes, in dramatic contrast with knockout mutants, indicating that steady state glucosinolate levels are actively regulated even in unchallenged plants. Analysis of the effects of the mutation via a structural modelling approach indicated that the affected serine interacts directly with UDP-glucose, but also predicted alterations in acceptor substrate affinity and the kcat value, sparking an interest in the kinetic behaviour of the wild-type enzyme. Initial velocity and inhibition studies revealed that UGT74B1 is not inhibited by its glycoside product. Together with the effects of the missense mutation, these findings are most consistent with a partial rapid equilibrium ordered mechanism. This model explains the lack of product inhibition observed both in vitro and in vivo, illustrating a general mechanism whereby enzymes can continue to function even at very high product/precursor ratios.
Publications

Poeschl, Y.; Delker, C.; Trenner, J.; Ullrich, K.; Quint, M. & Grosse, I. Optimized probe masking for comparative transcriptomics of closely related species.<!--[if gte mso 9]><![endif]--><!--[if gte mso 9]><xml> Normal 0 21 false false false DE X-NONE X-NONE</xml><![endif]--><!--[if gte mso 9]><![endif]--><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Normale Tabelle"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-fareast-language:EN-US;}</style> <![endif]--> PLOS ONE 8, e78497, (2013) DOI: 10.1371/journal.pone.0078497

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays arerestricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence,transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or morespecies often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to amicroarray of a closely related species. When analyzing these cross-species microarray expression data, differences in thetranscriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes dueto mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts ofnon-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach forcomparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcriptsof orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarraydesigned for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomicDNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resultingexpression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringencyand accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. Asan added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides asuperior base for biological interpretation of the measured expression responses.
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