@article{ThirumalaikumarGorkaSchulzetal.2020,
  author    = {Thirumalaikumar, Venkatesh P. and Gorka, Michal and Schulz, Karina and Masclaux-Daubresse, Celine and Sampathkumar, Arun and Skirycz, Aleksandra and Vierstra, Richard D. and Balazadeh, Salma},
  title     = {Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1},
  series = {Autophagy},
  volume    = {17},
  journal   = {Autophagy},
  number    = {9},
  publisher = {Taylor \& Francis},
  address   = {Abingdon},
  issn      = {1554-8635},
  doi       = {10.1080/15548627.2020.1820778},
  pages     = {2184 -- 2199},
  year      = {2020},
  abstract  = {In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS.},
  language  = {en}
}
@article{KuekenGennermannNikoloski2020,
  author    = {K{\"u}ken, Anika and Gennermann, Kristin and Nikoloski, Zoran},
  title     = {Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana},
  series = {The plant journal},
  volume    = {103},
  journal   = {The plant journal},
  number    = {6},
  publisher = {Wiley},
  address   = {Oxford},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.14890},
  pages     = {2168 -- 2177},
  year      = {2020},
  abstract  = {Availability of plant-specific enzyme kinetic data is scarce, limiting the predictive power of metabolic models and precluding identification of genetic factors of enzyme properties. Enzyme kinetic data are measuredin vitro, often under non-physiological conditions, and conclusions elicited from modeling warrant caution. Here we estimate maximalin vivocatalytic rates for 168 plant enzymes, including photosystems I and II, cytochrome-b6f complex, ATP-citrate synthase, sucrose-phosphate synthase as well as enzymes from amino acid synthesis with previously undocumented enzyme kinetic data in BRENDA. The estimations are obtained by integrating condition-specific quantitative proteomics data, maximal rates of selected enzymes, growth measurements fromArabidopsis thalianarosette with and fluxes through canonical pathways in a constraint-based model of leaf metabolism. In comparison to findings inEscherichia coli, we demonstrate weaker concordance between the plant-specificin vitroandin vivoenzyme catalytic rates due to a low degree of enzyme saturation. This is supported by the finding that concentrations of nicotinamide adenine dinucleotide (phosphate), adenosine triphosphate and uridine triphosphate, calculated based on our maximalin vivocatalytic rates, and available quantitative metabolomics data are below reportedKMvalues and, therefore, indicate undersaturation of respective enzymes. Our findings show that genome-wide profiling of enzyme kinetic properties is feasible in plants, paving the way for understanding resource allocation.},
  language  = {en}
}