Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Proteomic LC-MS analysis of Arabidopsis cytosolic ribosomes: Identification of ribosomal protein paralogs and re-annotation of the ribosomal protein genes
Hummel, M. ; Dobrenel, T. ; Cordewener, J.H.G. ; Davanture, M. ; Meyer, C. ; Smeekens, J.C.M. ; Bailey-Serres, J. ; America, A.H.P. ; Hanson, J. - \ 2015
Journal of Proteomics 128 (2015). - ISSN 1874-3919 - p. 436 - 449.
Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classical sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MSE with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68%) of the 242 cytosolic r-proteins genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes.
Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics
Hummel, M. ; Cordewener, J.H.G.C. ; Groot, J.C.M. de; Smeekens, S. ; America, A.H.P. ; Hanson, J. - \ 2012
Proteomics 12 (2012)7. - ISSN 1615-9853 - p. 1024 - 1038.
messenger-rna translation - mass-spectrometric analysis - data-independent analysis - leaf adaxial identity - gene-expression - extraribosomal functions - 80s ribosome - eukaryotic ribosome - oxygen deprivation - subunit
Cytosolic ribosomes are among the largest multisubunit cellular complexes. Arabidopsis thaliana ribosomes consist of 79 different ribosomal proteins (r-proteins) that each are encoded by two to six (paralogous) genes. It is unknown whether the paralogs are incorporated into the ribosome and whether the relative incorporation of r-protein paralogs varies in response to environmental cues. Immunopurified ribosomes were isolated from A. thaliana rosette leaves fed with sucrose. Trypsin digested samples were analyzed by qTOF-LC-MS using both MSE and classical MS/MS. Peptide features obtained by using these two methods were identified using MASCOT and Proteinlynx Global Server searching the theoretical sequences of A. thaliana proteins. The A. thaliana genome encodes 237 r-proteins and 69% of these were identified with proteotypic peptides for most of the identified proteins. These r-proteins were identified with average protein sequence coverage of 32% observed by MSE. Interestingly, the analysis shows that the abundance of r-protein paralogs in the ribosome changes in response to sucrose feeding. This is particularly evident for paralogous RPS3aA, RPS5A, RPL8B, and RACK1 proteins. These results show that protein synthesis in the A. thaliana cytosol involves a heterogeneous ribosomal population. The implications of these findings in the regulation of translation are discussed.
Collecting vegetative material of forage grasses and legumes
Hanson, J. ; Wouw, M.J. van de - \ 2011
In: Collecting plant genetic diversity: Technical guidelines. 2011 update / Guarino, L, Ramanatha Rao, V, Goldberg, E., - p. 22 - 22.
Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways
Bentsink, L. ; Hanson, J. ; Hanhart, C.J. ; Blankestijn-de Vries, M.H.C. ; Coltrane, C. ; Keizer, P. ; El-Lithy, M.E.M. ; Alonso-Blanco, C. ; Andres, M.T. de; Reymond, M. ; Eeuwijk, F.A. van; Smeekens, S. ; Koornneef, M. - \ 2010
Proceedings of the National Academy of Sciences of the United States of America 107 (2010)9. - ISSN 0027-8424 - p. 4264 - 4269.
quantitative trait loci - inbred-line populations - allelic variation - qtl analysis - germination - thaliana - cvi - maturation - release - ler
Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways
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