TY  - JOUR
A1  - Schokraie, Elham
A1  - Warnken, Uwe
A1  - Hotz-Wagenblatt, Agnes
A1  - Grohme, Markus A.
A1  - Hengherr, Steffen
A1  - Förster, Frank
A1  - Schill, Ralph O.
A1  - Frohme, Marcus
A1  - Dandekar, Thomas
A1  - Schnölzer, Martina
T1  - Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state
JF  - PLoS One
N2  - Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
KW  - life-span regulation
KW  - genes
KW  - Yolk protein
KW  - water stress
KW  - expression
KW  - tolerance
KW  - richtersius coronifer
KW  - superoxide-dismutase
KW  - caenorhabditis elegans
KW  - arabidopsis thaliana
KW  - vitellogenin
Y1  - 2012
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134447
VL  - 7
IS  - 9
ER  - 
TY  - JOUR
A1  - Horn, Hannes
A1  - Keller, Alexander
A1  - Hildebrandt, Ulrich
A1  - Kämpfer, Peter
A1  - Riederer, Markus
A1  - Hentschel, Ute
T1  - Draft genome of the \(Arabidopsis\) \(thaliana\) phyllosphere bacterium, \(Williamsia\) sp. ARP1
JF  - Standards in Genomic Sciences
N2  - The Gram-positive actinomycete \(Williamsia\) sp. ARP1 was originally isolated from the \(Arabidopsis\) \(thaliana\) phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus \(Williamsia\) and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.
KW  - arabidopsis thaliana
KW  - whole genome sequencing
KW  - adaption
KW  - Williamsia sp. ARP1
KW  - phyllosphere
KW  - draft genome
KW  - next generation sequencing
KW  - assembly
KW  - annotation
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-146008
VL  - 11
IS  - 8
ER  - 
TY  - JOUR
A1  - Deeken, Rosalia
A1  - Gohlke, Jochen
A1  - Scholz, Claus-Juergen
A1  - Kneitz, Susanne
A1  - Weber, Dana
A1  - Fuchs, Joerg
A1  - Hedrich, Rainer
T1  - DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall Tumors
JF  - PLoS Genetics
N2  - Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA–encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown gall development is known to be accompanied by global changes in transcription, metabolite levels, and physiological processes. High levels of abscisic acid (ABA) in crown galls regulate expression of drought stress responsive genes and mediate drought stress acclimation, which is essential for wild-type-like tumor growth. An impact of epigenetic processes such as DNA methylation on crown gall development has been suggested; however, it has not yet been investigated comprehensively. In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. Bisulfite sequencing analysis revealed that the oncogenes Ipt, IaaH, and IaaM were unmethylated in crown galls. Nevertheless, the oncogenes were susceptible to siRNA–mediated methylation, which inhibited their expression and subsequently crown gall growth. Genome arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed a globally hypermethylated crown gall genome, while promoters were rather hypomethylated. Mutants with reduced non-CG methylation developed larger tumors than the wild-type controls, indicating that hypermethylation inhibits plant tumor growth. The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. Genes known to be transcriptionally inhibited by ABA and methylated in crown galls became promoter methylated upon treatment of A. thaliana with ABA. This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. In summary, our studies provide evidence that epigenetic processes regulate gene expression, physiological processes, and the development of crown gall tumors.
KW  - DNA methylation
KW  - DNA transcription
KW  - gene expression
KW  - oncogenes
KW  - plant genomics
KW  - sequence motif analysis
KW  - arabidopsis thaliana
KW  - agrobacterium tumefaciens
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-96318
ER  -