TY  - JOUR
A1  - Mahlow, Sebastian
A1  - Hejazi, Mahdi
A1  - Kuhnert, Franziska
A1  - Garz, Andreas
A1  - Brust, Henrike
A1  - Baumann, Otto
A1  - Fettke, Jörg
T1  - Phosphorylation of transitory starch by -glucan, water dikinase during starch turnover affects the surface properties and morphology of starch granules
JF  - New phytologist : international journal of plant science
N2  - Glucan, water dikinase (GWD) is a key enzyme of starch metabolism but the physico-chemical properties of starches isolated from GWD-deficient plants and their implications for starch metabolism have so far not been described. Transgenic Arabidopsis thaliana plants with reduced or no GWD activity were used to investigate the properties of starch granules. In addition, using various in vitro assays, the action of recombinant GWD, -amylase, isoamylase and starch synthase 1 on the surface of native starch granules was analysed. The internal structure of granules isolated from GWD mutant plants is unaffected, as thermal stability, allomorph, chain length distribution and density of starch granules were similar to wild-type. However, short glucan chain residues located at the granule surface dominate in starches of transgenic plants and impede GWD activity. A similarly reduced rate of phosphorylation by GWD was also observed in potato tuber starch fractions that differ in the proportion of accessible glucan chain residues at the granule surface. A model is proposed to explain the characteristic morphology of starch granules observed in GWD transgenic plants. The model postulates that the occupancy rate of single glucan chains at the granule surface limits accessibility to starch-related enzymes.
KW  - Arabidopsis thaliana
KW  - glucan
KW  - water dikinase (GWD)
KW  - sex1-8
KW  - starch granule surface
KW  - starch phosphorylation
Y1  - 2014
U6  - https://doi.org/10.1111/nph.12801
SN  - 0028-646X
SN  - 1469-8137
VL  - 203
IS  - 2
SP  - 495
EP  - 507
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Omidbakhshfard, Mohammad Amin
A1  - Winck, Flavia Vischi
A1  - Arvidsson, Samuel Janne
A1  - Riano-Pachon, Diego M.
A1  - Müller-Röber, Bernd
T1  - A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana
JF  - Journal of integrative plant biology
N2  - The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.
KW  - Arabidopsis thaliana
KW  - chromatin
KW  - cis-regulatory elements
KW  - epigenomics
KW  - FAIRE-qPCR
KW  - FAIRE-seq
KW  - gene expression
KW  - gene regulatory network
KW  - transcription factor
Y1  - 2014
U6  - https://doi.org/10.1111/jipb.12151
SN  - 1672-9072
SN  - 1744-7909
VL  - 56
IS  - 6
SP  - 527
EP  - 538
PB  - Wiley-Blackwell
CY  - Hoboken
ER  -