Netherlands Bioinformatics Conference 2014

Netherlands Bioinformatics Conference 2014

Vera van Noort

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Prof. dr. Vera van Noort

van Noort Group
Computational Systems Biology
Centre of Microbial and Plant Genetics
Faculty of Bioscience Engineering
Kasteelpark Arenberg 22 - box 2460
3001 Leuven

Vera van Noort is a professor in Computational Systems Biology within the Faculty of Bioscience Engineering at the KU Leuven (Belgium). Vera van Noort earned her MSc in Biology with specialization in Bioinformatics from Utrecht University in 2002. Her thesis work was done under the supervision of prof. dr. Paulien Hogeweg and in the group of prof. dr. Soren Brunak and focused around biological sequence analysis. Afther the MSc, Vera van Noort joined prof. dr. Martijn Huynen at the CMBI, Nijmegen to work on comparative genomics of eukaryotes. She obtained her PhD cum laude in 2007 and received an NWO Rubicon fellowship to join the group of Peer Bork at the EMBL, Germany. At EMBL she worked together with experimental groups, and developed novel methodologies to analyse large-scale biological data. The close collaboration of computational with experimental scientist multiplicated the scientific achievements of both and resultingly Vera van Noort was (co-)author on one Cell and three Science publications. After two years as a postdoctoral fellow, Vera van Noort was appointed as Staff Scientist in 2009 within the Bork group and in 2010 work package leader in an FP7 project. In October 2013, Vera van Noort started her own group within the Centre of Microbial and Plant Genetics at the KU Leuven. The focus of her Computational Systems Biology group is to generate biological sense from the growing amount of biological data becoming available and turn biological information into biological knowledge.


Title: Post-Translational Modification Networks

Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. We systematically investigated the interplay of protein phosphorylation with other post-transcriptional regulatory mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae. Systematic perturbations by deletion of its only two protein kinases and its unique protein phosphatase identified not only the protein-specific effect on the phosphorylation network, but also a modulation of proteome abundance and lysine acetylation patterns, mostly in the absence of transcriptional changes. Reciprocally, deletion of the two putative N-acetyltransferases affects protein phosphorylation, confirming cross-talk between the two PTMs. The measured M. pneumoniae phosphoproteome and lysine acetylome revealed that both PTMs are very common, that (as in Eukaryotes) they often co-occur within the same protein and that they are frequently observed at interaction interfaces and in multifunctional proteins. The results imply previously unreported hidden layers of post-transcriptional regulation intertwining phosphorylation with lysine acetylation and other mechanisms that define the functional state of a cell. Aiming at a more global view of the interplay between PTM types, we collected modifications for 13 frequent PTM types in 8 eukaryotes, compared their speed of evolution and developed a method for measuring PTM co-evolution within proteins based on the co-occurrence of sites across eukaryotes. We found that PTM types are vastly interconnected, forming a global network that comprise in human alone >50,000 residues in about 6000 proteins.

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