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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    The evolutionary journey of Argonaute proteins
    Swarts, D.C. ; Makarova, K. ; Wang, Y. ; Nakanishi, K. ; Ketting, R.F. ; Koonin, E.V. ; Patel, D.J. ; Oost, J. van der - \ 2014
    Nature Structural and Molecular Biology 21 (2014)9. - ISSN 1545-9985 - p. 743 - 753.
    eukaryote trypanosoma-brucei - germline gene-expression - seed-target recognition - piwi-interacting rnas - dicer-like proteins - crystal-structure - paz domain - structural basis - slicer activity - guide rna
    Argonaute proteins are conserved throughout all domains of life. Recently characterized prokaryotic Argonaute proteins (pAgos) participate in host defense by DNA interference, whereas eukaryotic Argonaute proteins (eAgos) control a wide range of processes by RNA interference. Here we review molecular mechanisms of guide and target binding by Argonaute proteins, and describe how the conformational changes induced by target binding lead to target cleavage. On the basis of structural comparisons and phylogenetic analyses of pAgos and eAgos, we reconstruct the evolutionary journey of the Argonaute proteins through the three domains of life and discuss how different structural features of pAgos and eAgos relate to their distinct physiological roles.
    DNA-guided DNA interference by a prokaryotic Argonaute
    Swarts, D.C. ; Jore, M.M. ; Westra, E.R. ; Zhu, Y. ; Janssen, J.H. ; Snijders, A.P. ; Wang, Y. ; Patel, D.J. ; Berenguer, J. ; Brouns, S.J.J. ; Oost, J. van der - \ 2014
    Nature 507 (2014)7491. - ISSN 0028-0836 - p. 258 - 261.
    thermophile thermus-thermophilus - silencing complex - structural basis - rna - archaebacteria - recognition - eubacteria - cleavage - sequence - protein
    RNA interference is widely distributed in eukaryotes and has a variety of functions, including antiviral defence and gene regulation. All RNA interference pathways use small single-stranded RNA (ssRNA) molecules that guide proteins of the Argonaute (Ago) family to complementary ssRNA targets: RNA-guided RNA interference. The role of prokaryotic Ago variants has remained elusive, although bioinformatics analysis has suggested their involvement in host defence. Here we demonstrate that Ago of the bacterium Thermus thermophilus (TtAgo) acts as a barrier for the uptake and propagation of foreign DNA. In vivo, TtAgo is loaded with 5'-phosphorylated DNA guides, 13-25 nucleotides in length, that are mostly plasmid derived and have a strong bias for a 5'-end deoxycytidine. These small interfering DNAs guide TtAgo to cleave complementary DNA strands. Hence, despite structural homology to its eukaryotic counterparts, TtAgo functions in host defence by DNA-guided DNA interference
    Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage
    Sheng, G. ; Zhao, H. ; Wang, J. ; Rao, Y. ; Tian, W. ; Swarts, D.C. ; Oost, J. van der; Patel, D.J. ; Wang, Y. - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)2. - ISSN 0027-8424 - p. 652 - 657.
    crystal-structure - rna recognition - silencing complex - substrate-specificity - slicer activity - piwi protein - paz domain - human risc - endonuclease - interference
    We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5'-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 Å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg2+ cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand
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