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Publikationen - Molekulare Signalverarbeitung

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Dekkers, B.J.W.; Pearce, S.; van Bolderen-Veldkamp, R.P.; Marshall, A.; Widera, P.; Gilbert, J.; Drost, H.-G.; Basseli, G.W.; Müller, K.; King, J.R.; Wood, A.T.A.; Grosse, I.; Quint, M.; Krasnogor, N.; Leubner-Metzger, G.; Holdsworth, M.J. & Bentsink, L. Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination Plant Physiol 163, 205-215, (2013) DOI: 10.1104/pp.113.223511

Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understandinggermination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa,endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes thatlead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seedswith both temporaland spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this highresolutiondata set for the construction ofmeaningful coexpression networks, which provide insight into the genetic control of germination.The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by largetranscriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptionalphase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start ofthe second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlightthe fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show thatexpression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase.Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.

Acosta, I. F.; Gasperini, D.; Chételat, A.; Stolz, S.; Santuari, L.; Farmer, E. E. Role of NINJA in root jasmonate signaling Proc Natl Acad Sci USA 110, 15473-15478, (2013) DOI: 10.1073/pnas.1307910110

Wound responses in plants have to be coordinated between organs so that locally reduced growth in a wounded tissue is balanced by appropriate growth elsewhere in the body. We used a JASMONATE ZIM DOMAIN 10 (JAZ10) reporter to screen for mutants affected in the organ-specific activation of jasmonate (JA) signaling in Arabidopsis thaliana seedlings. Wounding one cotyledon activated the reporter in both aerial and root tissues, and this was either disrupted or restricted to certain organs in mutant alleles of core components of the JA pathway including COI1, OPR3, and JAR1. In contrast, three other mutants showed constitutive activation of the reporter in the roots and hypocotyls of unwounded seedlings. All three lines harbored mutations in Novel Interactor of JAZ (NINJA), which encodes part of a repressor complex that negatively regulates JA signaling. These ninja mutants displayed shorter roots mimicking JA-mediated growth inhibition, and this was due to reduced cell elongation. Remarkably, this phenotype and the constitutive JAZ10 expression were still observed in backgrounds lacking the ability to synthesize JA or the key transcriptional activator MYC2. Therefore, JA-like responses can be recapitulated in specific tissues without changing a plant’s ability to make or perceive JA, and MYC2 either has no role or is not the only derepressed transcription factor in ninja mutants. Our results show that the role of NINJA in the root is to repress JA signaling and allow normal cell elongation. Furthermore, the regulation of the JA pathway differs between roots and aerial tissues at all levels, from JA biosynthesis to transcriptional activation.

Poeschl, Y.; Delker, C.; Trenner, J.; Ullrich, K.; Quint, M. & Grosse, I. Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species 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.

Huang, H.; Quint, M. & Gray, W.M. The <i>eta7/csn3-3</i> auxin response mutant of Arabidopsis defines a novel function for the CSN3 subunit of the COP9 signalosome  PLoS One 8, e66578, (2013) DOI: 10.1371/journal.pone.0066578

TIR1/AFBTIR1The COP9 signalosome (CSN) is an eight subunit protein complex conserved in all higher eukaryotes. In Arabidopsis thaliana, the CSN regulates auxin response by removing the ubiquitin-like protein NEDD8/RUB1 from the CUL1 subunit of the SCF ubiquitin-ligase (deneddylation). Previously described null mutations in any CSN subunit result in the pleiotropic cop/det/fus phenotype and cause seedling lethality, hampering the study of CSN functions in plant development. In a genetic screen to identify enhancers of the auxin response defects conferred by the tir1-1 mutation, we identified a viable csn mutant of subunit 3 (CSN3), designated eta7/csn3-3. In addition to enhancing tir1-1 mutant phenotypes, the csn3-3 mutation alone confers several phenotypes indicative of impaired auxin signaling including auxin resistant root growth and diminished auxin responsive gene expression. Unexpectedly however, csn3-3 plants are not defective in either the CSN-mediated deneddylation of CUL1 or in SCF-mediated degradation of Aux/IAA proteins. These findings suggest that csn3-3 is an atypical csn mutant that defines a novel CSN or CSN3-specific function. Consistent with this possibility, we observe dramatic differences in double mutant interactions between csn3-3 and other auxin signaling mutants compared to another weak csn mutant, csn1-10. Lastly, unlike other csn mutants, assembly of the CSN holocomplex is unaffected in csn3-3 plants. However, we detected a small CSN3-containing protein complex that is altered in csn3-3 plants. We hypothesize that in addition to its role in the CSN as a cullin deneddylase, CSN3 functions in a distinct protein complex that is required for proper auxin signaling.
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