TY - JOUR A1 - Batsios, Petros A1 - Ren, Xiang A1 - Baumann, Otto A1 - Larochelle, Denis A. A1 - Gräf, Ralph T1 - Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81 JF - Cells N2 - The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11–646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture. KW - Dictyostelium KW - lamin KW - nuclear lamina KW - nucleus KW - nucleolus KW - HeH-protein KW - LEM-domain protein Y1 - 2016 U6 - https://doi.org/10.3390/cells5010013 SN - 2073-4409 VL - 5 IS - 1 PB - MDPI CY - Basel ER - TY - THES A1 - Kamranfar, Iman T1 - Functional analysis of gene regulatory networks controlled by stress responsive transcription factors in Arabidopsis thaliana Y1 - 2015 ER - TY - THES A1 - Orf, Isabel T1 - Photorespiratory metabolism in the cyanobacterial model Synechocystis sp. strain PCC 6803 BT - a systems biology approach Y1 - 2016 ER - TY - JOUR A1 - Kappel, Christian A1 - Trost, Gerda A1 - Czesnick, Hjördis A1 - Ramming, Anna A1 - Kolbe, Benjamin A1 - Vi, Son Lang A1 - Bispo, Cláudia A1 - Becker, Jörg D. A1 - de Moor, Cornelia A1 - Lenhard, Michael T1 - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana JF - PLoS Genetics : a peer-reviewed, open-access journal N2 - The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. KW - messenger-rna polyadenylation KW - differential expression analysis KW - gene-expression KW - tail-length KW - cytoplasmic polyadenylation KW - poly(a)-binding protein KW - translational control KW - comprehensive analysis KW - specificity factor KW - mammalian-cells Y1 - 2015 U6 - https://doi.org/10.1371/journal.pgen.1005474 SN - 1553-7390 SN - 1553-7404 VL - 11 IS - 8 PB - Public Library of Science CY - San Francisco ER - TY - THES A1 - Reinecke, Antje Adriana T1 - Impact of protein structure on the mechanics and assembly of mytilus byssal threads Y1 - 2016 ER - TY - THES A1 - Sakschewski, Boris T1 - Impacts of major anthropogenic pressures on the terrestrial biosphere and its resilience to global change Y1 - 2015 ER - TY - JOUR A1 - Muiño, Jose M. A1 - de Bruijn, Suzanne A1 - Pajoro, Alice A1 - Geuten, Koen A1 - Vingron, Martin A1 - Angenent, Gerco C. A1 - Kaufmann, Kerstin T1 - Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor JF - Molecular biology and evolution : MBE N2 - lower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon. KW - MADS-domain transcription factor KW - plant development KW - cis-regulatory evolution Y1 - 2015 U6 - https://doi.org/10.1093/molbev/msv210 SN - 1537-1719 SN - 0737-4038 VL - 33 IS - 1 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Sicard, Adrien A1 - Kappel, Christian A1 - Josephs, Emily B. A1 - Wha Lee, Young A1 - Marona, Cindy A1 - Stinchcombe, John R. A1 - Wright, Stephen I. A1 - Lenhard, Michael T1 - Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella JF - Nature Communications N2 - In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms8960 SN - 2041-1723 VL - 6 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Valente, Luis M. A1 - Phillimore, Albert B. A1 - Etienne, Rampal S. T1 - Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands JF - Ecology letters N2 - Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms. KW - Community assembly KW - diversification KW - dynamic equilibrium KW - island biogeography KW - phylogeny Y1 - 2015 U6 - https://doi.org/10.1111/ele.12461 SN - 1461-0248 SN - 1461-023X VL - 18 SP - 844 EP - 852 PB - Wiley-Blackwell CY - Oxford ER - TY - THES A1 - Lämke, Jörn T1 - Determining the future in the past BT - analysis of the role of chromation in heat stress memory in Arabidopsis thaliana Y1 - 2015 ER -