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Haesendonckx S.,University of Geneva | Haesendonckx S.,Catholic University of Leuven | Tudisca V.,University of Buenos Aires | Voordeckers K.,Catholic University of Leuven | And 4 more authors.
Biochemical Journal | Year: 2012

PDK1 (phosphoinositide-dependent protein kinase 1) phosphorylates and activates PKA (cAMP-dependent protein kinase) in vitro. Docking of the HM (hydrophobic motif) in the C-terminal tail of the PKA catalytic subunits on to the PIF (PDK1-interacting fragment) pocket of PDK1 is a critical step in this activation process. However, PDK1 regulation of PKA in vivo remains controversial. Saccharomyces cerevisiae contains three PKA catalytic subunits, TPK1, TPK2 and TPK3. We demonstrate that Pkh [PKB (protein kinase B)-activating kinase homologue] protein kinases phosphorylate the activation loop of each Tpk in vivo with various efficiencies. Pkh inactivation reduces the interaction of each catalytic subunit with the regulatory subunit Bcy1 without affecting the specific kinase activity of PKA. Comparative analysis of the in vitro interaction and phosphorylation of Tpks by Pkh1 shows that Tpk1 and Tpk2 interact with Pkh1 through an HM-PIF pocket interaction. Unlike Tpk1, mutagenesis of the activation loop site in Tpk2 does not abolish in vitro phosphorylation, suggesting that Tpk2 contains other, as yet uncharacterized, Pkh1 target sites. Tpk3 is poorly phosphorylated on its activation loop site, and this is due to the weak interaction of Tpk3 with Pkh1 because of the atypical HM found in Tpk3. In conclusion, the results of the present study show that Pkh protein kinases contribute to the divergent regulation of the Tpk catalytic subunits. © The Authors Journal compilation © 2012 Biochemical Society.

Brown C.A.,Harvard University | Murray A.W.,Harvard University | Verstrepen K.J.,Harvard University | Verstrepen K.J.,VIB Laboratory for Systems Biology
Current Biology | Year: 2010

Background: Subtelomeres, regions proximal to telomeres, exhibit characteristics unique to eukaryotic genomes. Genes residing in these loci are subject to epigenetic regulation and elevated rates of both meiotic and mitotic recombination. However, most genome sequences do not contain assembled subtelomeric sequences, and, as a result, subtelomeres are often overlooked in comparative genomics. Results: We studied the evolution and functional divergence of subtelomeric gene families in the yeast lineage. Our computational results show that subtelomeric families are evolving and expanding much faster than families that do not contain subtelomeric genes. Focusing on three related subtelomeric MAL gene families involved in disaccharide metabolism that show typical patterns of rapid expansion and evolution, we show experimentally how frequent duplication events followed by functional divergence yield novel alleles that allow the metabolism of different carbohydrates. Conclusions: Taken together, our computational and experimental analyses show that the extraordinary instability of eukaryotic subtelomeres supports rapid adaptation to novel niches by promoting gene recombination and duplication followed by functional divergence of the alleles. © 2010 Elsevier Ltd. All rights reserved.

Stepanyan K.,Catholic University of Leuven | Wenseleers T.,University of Leuven Zoological Institute | Duenez-Guzman E.A.,University of Leuven Zoological Institute | Muratori F.,University of Leuven Zoological Institute | And 7 more authors.
Molecular Ecology | Year: 2015

Microbial populations often contain a fraction of slow-growing persister cells that withstand antibiotics and other stress factors. Current theoretical models predict that persistence levels should reflect a stable state in which the survival advantage of persisters under adverse conditions is balanced with the direct growth cost impaired under favourable growth conditions, caused by the nonreplication of persister cells. Based on this direct growth cost alone, however, it remains challenging to explain the observed low levels of persistence (<<1%) seen in the populations of many species. Here, we present data from the opportunistic human pathogen Pseudomonas aeruginosa that can explain this discrepancy by revealing various previously unknown costs of persistence. In particular, we show that in the absence of antibiotic stress, increased persistence is traded off against a lengthened lag phase as well as a reduced survival ability during stationary phase. We argue that these pleiotropic costs contribute to the very low proportions of persister cells observed among natural P. Aeruginosa isolates (3 × 10-8-3 × 10-4) and that they can explain why strains with higher proportions of persister cells lose out very quickly in competition assays under favourable growth conditions, despite a negligible difference in maximal growth rate. We discuss how incorporating these trade-offs could lead to models that can better explain the evolution of persistence in nature and facilitate the rational design of alternative therapeutic strategies for treating infectious diseases. © 2015 John Wiley & Sons Ltd.

Rezaei M.N.,Leuven Food Science and Nutrition Research Center oe | Verstrepen K.J.,VIB Laboratory for Systems Biology | Courtin C.M.,Leuven Food Science and Nutrition Research Center oe
Cereal Chemistry | Year: 2015

During dough fermentation, yeast (Saccharomyces cerevisiae) changes the physical properties of the dough matrix. In this study, we investigate if different yeast strains have an impact on dough rheology and on the gas holding capacity of fermenting dough. Furthermore, we analyze whether observed differences are linked to the metabolite profiles of the yeast strains. More specifically, the impact of 25 yeast strains on dough spread, dough fermentation properties, and dough metabolite profile was analyzed. Our results demonstrate large differences in the fermentation ability and metabolite profile of the 25 strains. Analysis of metabolites in fermented dough confirmed that acetic acid and succinic acid are likely responsible for the lowering of dough pH during fermentation and that the onset of CO2 release from dough is related to dough pH rather than to the volume of CO2 within the dough. Our results further suggest that the spread test is an inadequate tool to quantify rheological differences observed for strains with different fermentation profiles. © 2015 AACC International, Inc.

Voordeckers K.,Catholic University of Leuven | Voordeckers K.,VIB Laboratory for Systems Biology | Verstrepen K.J.,Catholic University of Leuven | Verstrepen K.J.,VIB Laboratory for Systems Biology
Current Opinion in Microbiology | Year: 2015

Understanding how changes in DNA drive the emergence of new phenotypes and fuel evolution remains a major challenge. One major hurdle is the lack of a fossil record of DNA that allows linking mutations to phenotypic changes. However, the emergence of high-throughput sequencing technologies now allows sequencing genomes of natural and experimentally evolved microbial populations to study how mutations arise and spread through a population, how new phenotypes arise and how this ultimately leads to adaptation. Here, we highlight key studies that have increased our mechanistic understanding of evolution. We specifically focus on the model eukaryote Saccharomyces cerevisiae because its relatively short replication time, much-studied biology and available molecular toolbox have made it a prime model for molecular evolution studies. © 2015 The Authors.

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