TY  - JOUR
A1  - Riaño-Pachón, Diego Mauricio
A1  - Kleessen, Sabrina
A1  - Neigenfind, Jost
A1  - Durek, Pawel
A1  - Weber, Elke
A1  - Engelsberger, Wolfgang R.
A1  - Walther, Dirk
A1  - Selbig, Joachim
A1  - Schulze, Waltraud X.
A1  - Kersten, Birgit
T1  - Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana
JF  - BMC Genomics
N2  - Background: Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites.

Results: From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented.

These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected.

Conclusions: We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future.
KW  - Gene Ontology
KW  - Phosphorylation Site
KW  - phosphorylated amino acid
KW  - slim term
KW  - single nucleotide polymorphism mapping
Y1  - 2010
U6  - https://doi.org/10.1186/1471-2164-11-411
SN  - 1471-2164
VL  - 11
PB  - Biomed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Creutzig, Felix
A1  - Becker, Sophia
A1  - Berrill, Peter
A1  - Bongs, Constanze
A1  - Bussler, Alexandra
A1  - Cave, Ben
A1  - Constantino, Sara M.
A1  - Grant, Marcus
A1  - Heeren, Niko
A1  - Heinen, Eva
A1  - Hintz, Marie Josefine
A1  - Ingen-Housz, Timothee
A1  - Johnson, Eric
A1  - Kolleck, Nina
A1  - Liotta, Charlotte
A1  - Lorek, Sylvia
A1  - Mattioli, Giulio
A1  - Niamir, Leila
A1  - McPhearson, Timon
A1  - Milojevic-Dupont, Nikola
A1  - Nachtigall, Florian
A1  - Nagel, Kai
A1  - Närger, Henriette
A1  - Pathak, Minal
A1  - Perrin de Brichambaut, Paola
A1  - Reckien, Diana
A1  - Reisch, Lucia A.
A1  - Revi, Aromar
A1  - Schuppert, Fabian
A1  - Sudmant, Andrew
A1  - Wagner, Felix
A1  - Walkenhorst, Janina
A1  - Weber, Elke
A1  - Wilmes, Michael
A1  - Wilson, Charlie
A1  - Zekar, Aicha
T1  - Towards a public policy of cities and human settlements in the 21st century
JF  - npj urban sustainability
N2  - Cities and other human settlements are major contributors to climate change and are highly vulnerable to its impacts. They are also uniquely positioned to reduce greenhouse gas emissions and lead adaptation efforts. These compound challenges and opportunities require a comprehensive perspective on the public policy of human settlements. Drawing on core literature that has driven debate around cities and climate over recent decades, we put forward a set of boundary objects that can be applied to connect the knowledge of epistemic communities and support an integrated urbanism. We then use these boundary objects to develop the Goals-Intervention-Stakeholder-Enablers (GISE) framework for a public policy of human settlements that is both place-specific and provides insights and tools useful for climate action in cities and other human settlements worldwide. Using examples from Berlin, we apply this framework to show that climate mitigation and adaptation, public health, and well-being goals are closely linked and mutually supportive when a comprehensive approach to urban public policy is applied.
Y1  - 2024
U6  - https://doi.org/10.1038/s42949-024-00168-7
SN  - 2661-8001
VL  - 4
IS  - 1
SP  - 1
EP  - 14
PB  - Springer Nature
CY  - London
ER  -