Ruud M.W. Mans's research while affiliated with Leiden University and other places

Publications (6)

Chapter
Our view on RNA has changed radically over the last decade. In addition to its function as carrier of genetic information, RNA was shown to have several catalytic properties, culminating recently in the stunning fact that probably 23S ribosomal RNA alone participates in peptide bond formation (Noller et al. 1992).
Article
Site-directed mutations were introduced in the connecting loops and one of the two stem regions of the RNA pseudoknot in the tRNA-like structure of turnip yellow mosaic virus RNA. The kinetic parameters of valylation for each mutated RNA were determined in a cell-free extract from wheat germ. Structure mapping was performed on most mutants with enz...
Article
The present model of the L-shaped tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA encompasses 82 nucleotides. A previous kinetic study on 3' terminal TYMV RNA fragments that contain the tRNA-like structure and a 5' nonviral GGGAGA sequence, suggested that viral sequences upstream of the tRNA-like domain, i.e., upstream of nucleotide 82...
Article
Full-text available
In a previous study it was shown that RNase P from E. coli cleaves the tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA in vitro (Guerrier-Takada et al. (1988) Cell, 53, 267–272). Cleavage takes place at the 3' side of the loop that crosses the deep groove of the pseudoknot structure present in the aminoacyl acceptor domain. In the pres...
Article
Full-text available
NMR studies were carried out on various equimolar mixtures consisting of a combination of oligomers: d(ACGGCT) (I), d(pACGGCT) (la), d(TGCAGT) (II), d(AGCCGTACTGCA) (III), d(TGCAGTACGGCT) (IV). It is shown that I + II + III (Ml) and la + II + III (M2) form stable duplexes with nicks in the centre of the respective double helices. A close analysis o...

Citations

... The structure of this pseudoknot is unusual. In principle, it corresponds to one of the three stem stacking topologies proposed for the so-called H-type (hairpin) pseudoknots (Westhof and Jaeger, 1992;Mans and Pleij, 1993). In contrast to the widespread classical H-type pseudoknot topology (Fig 1. inset), the inverted stacking configuration of the proposed pseudoknot we find is very rare and has been observed only in the structural context of long-range tertiary interactions in various ribozymes (Jaeger et al., 1991;Michel et al., 1989;Bergman et al., 2004;Soukup, 2006). ...
... L1, the connecting string that crosses the major groove of the pseudoknot helix (Fig. 3A), which is only one nt long, is also unusually short. This should not preclude pseudoknot formation, however, since the TYMV acceptor stem pseudoknot (shown in Fig. 3B) is retained when L1 is shortened from four to one nucleotide (Mans et al., 1992). ...
... An interesting class of functional RNA elements found in viruses are the transfer RNA (tRNA)-like structures (TLSs) found at the 3′ terminus of certain positive-sense single-stranded plant-infecting RNA viruses Yot et al. 1970;Rietveld et al. 1983;Mans et al. 1991;Dreher 2010). These RNAs were identified by their ability to induce in cis aminoacylation of the 3′ end of the viral RNAs by host cell aminoacyl tRNA synthetases (AARSs) Yot et al. 1970;Hall et al. 1972;Öberg and Philipson 1972). ...
... In this study, we have focused particularly on the roles of the multiple archaeal/eukaryal RPPs in the fidelity of processing of non-consensus pre-tRNAs. Bacterial RNase P processes precursors to 4.5S RNA and tmRNA, select viral RNAs, C4 antisense RNA from bacteriophage P1 and P7, and some mRNAs, not all of which have a tRNA-like motif (44)(45)(46)(47)(48)(49). Recently, human and yeast RNase P have been implicated in processing certain short-lived non-coding (nc) RNAs and mRNAs, and shown to even cleave single-stranded (ss) RNAs (50)(51)(52)(53)(54)(55)(56); intriguingly, common recognition determinants (tRNA-like or otherwise) in these substrates are not apparent. ...
... Despite some overlapping functions and the shared ability to be aminoacylated and to interact with eEF1A, the TYMV, BMV, and TMV TLSs differ dramatically in sequence, length, and predicted secondary structure. The minimal length of the TYMV TLS for aminoacylation has been reported as 82 nucleotides (nt) (Mans et al. 1990), the BMV TLS has been reported to require 134 nt for aminoacylation (although more efficient aminoacylation requires 169 nt) (Fechter et al. 2001a), and the TMV TLS needs 106 nt (Rietveld et al. 1984). While the 39 and 59 ends base pair in the acceptor stem in canonical tRNAs (Fig. 1B), this is not the case in any TLS. ...
... When the crystal structure of a 12 bp nicked DNA duplex was solved by Alexander Rich and colleagues, only very limited distortions were observed at the nick site 78 . An NMR study of nicked DNA duplexes enabled a similar conclusion to be reached 79 . Base stacking interactions were proposed to be sufficient to overcome the loss of DNA strand connectivity. ...