Kees Pleij
Professor emeritus of Biochemistry
- Name
- Prof.dr. C.W.A. Pleij
- Telephone
- +31 71 527 4269
- c.pley@chem.leidenuniv.nl
Professor emeritus of Biochemistry
- Science
- Leiden Institute of Chemistry
- Koenig R., Lesemann D.-E. & Pleij C.W.A. (2012), Tobacco rattle virus genome alterations in the Hosta hybrid ‘Green Fountain’ and other plants: reassortments, recombinations and deletions, Archives of Virology 157(10): 2005-2008.
- Goultiaev A.P., Olsthoorn R.C.L., Pleij C.W.A. & Westhof E. (2012), RNA Structure: Pseudoknots. In: , Encyclopedia of Life Sciences. Encyclopedia of Life Sciences (eLS): Wiley.
- Yu C.-H., Noteborn M.H.M., Pleij C.W.A. & Olsthoorn R.C.L. (2011), Stem-loop structures can effectively substitute for an RNA pseudoknot in-1 ribosomal frameshifting, Nucleic Acids Research 39(20): 8952-8959.
- Olsthoorn R.C.L., Reumerman R., Hilbers C.W., Pleij C.W.A. & Heus H.A. (2010), Functional analysis of the SRV-1 RNA frameshifting pseudoknot, Nucleic Acids Research 38(21): 7665-7672.
- Smit M.H. de, Verlaan P.W.G., Duin J. van & Pleij C.W.A. (2009), In Vivo Dynamics of Intracistronic Transcriptional Polarity, Journal of Molecular Biology/JMB Online 385(3): 733-747.
- Chen S.C., Goultiaev A.P., Pleij C.W.A. & Olsthoorn R.C.L. (2009), A Secondary Structure Model for the 3'-Untranslated Region of Ilarvirus RNAs. In: Feng Z. & Long M. (Eds.), Viral Genomes: Diversity, Properties and Parameters: Nova Science Publishers, Inc.. 65-83.
- Chen S.C., Born E. van den, Pleij C.W.A., Snijder E.J., Olsthoorn R.R.C.L. & Worm S.H.E. van den (2007), A new structure model for the packaging signal in the genome of group IIa Coronaviruses, Journal of Virology 81(12): 6771-6774.
- Olsthoorn-Tieleman L.N., Palstra R.J., Wezel G.P. van, Bibb M.J. & Pleij C.W.A. (2007), Elongation factor Tu3 from the kirromycin-producer Streptomyces ramocissimus is resistant to three classes of EF-Tu-specific inhibitors, Journal of Bacteriology 189(9): 3581-3590.
- Nagel J.H.A., Flamm C., Hofacker I.L., Franke K., Smit M.H. de, Schuster P. & Pleij C.W.A. (2006), Structural parameters affecting the kinetics of RNA hairpin formation, Nucleic Acids Research 34(12): 3568-3576.
- Ongus J.R., Roode E.C., Pleij C.W.A., Vlak J.M. & Oers M.M. (2006), The 5' non-translated region of Varroa destructor virus 1 (genus Iflavirus): structure prediction and IRES activity in Lymantria dispar cells, Journal of General Virology 87(11): 3397-3407.
- Koening R., Barends S., Gultyaev A.P., Lesemann D.-E., Vetten H.J., Loss S. & Pleij C.W.A. (2005), Nemesia ring necrosis virus: a new tymovirus with a genomic RNA having a histidylatable tobamovirus-like 3' end, Journal of General Virology 86(6): 1827-1833.
- Koenig R., Pleij C.W.A., Leseman D.-E., Loss S. & Vetten H.J. (2005), Molecular characterization of isolates of anagyris vein yellowing virus, plantago mottle virus and scrophularia mottle virus – comparison of various approaches for tymovirus classification, Archives of Virology 150: 2325-2338.
- Gultyaev A.P., Pleij C.W.A. & Westhof E. (2005), RNA structure: Pseudoknots. In: , Encyclopedia of life sciences. Encyclopedia of Life Sciences (eLS). Chichester: John Wiley & Sons, Ltd.
- Giro A., Bergia A., Zuccheri G., Bink H.H.J., Pleij C.W.A. & Samori B. (2004), Single molecule studies of RNA secondary structure: AFM of viral RNA secondary structure, Microscopy Research and Technique 65(4-5): 235-245.
- Bink H.H.J., Roepan S.K. & Pleij C.W.A. (2004), Two histidines of the coat protein of turnip yellow mosaic virus at the capsid interior are crucial for viability, Proteins 55(2): 236-244.
- Livieratos I.C., Eliasco E., Muller G., Olsthoorn R.R.C.L., Salazar L.F., Pleij C.W.A. & Coutts R.H.A. (2004), Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved T-terminal structures among members of the genus Crinivirus, Journal of General Virology 85(7): 2065-2075.
- Olsthoorn R.C.L., Laurs M., Sohet F., Hilbers C.W., Heus H.A. & Pleij C.W.A. (2004), Novel application of sRNA: stimulation of ribosomal frameshifting, RNA 10(11): 1702-1703.
- Koenig R., Aust H., Schiemann J., Pleij C. W. A., Loss S. & Burgermeister W. (2004), Molecular characterisation of potexviruses isolated from three different genera in the family Cactaceae, Journal of Virology 149(5): 903-914.
- Barends S., Rudinger-Thirion J., Florentz C., Giegé R., Pleij C.W.A. & Kraal B. (2004), tRNA-like structure regulates translation of brome mosaic virus RNA, Journal of Virology 78(8): 4003-4010.
- Roon A.M.M. van, Bink H.H.J., Plaisier J.R., Pleij C.W.A., Abrahams J.P. & Pannu N.S. (2004), Crystal structure of an empty capsid of turnip yellow mosaic virus, Journal of Molecular Biology/JMB Online 341(5): 1205-1214.
- Meulewater F., Lipzig R. van, Gultyaev A.P., Pleij C.W.A., Damme D. van, Cornelissen M. & Eldik G. van (2004), Conservation of RNA structures enables TNV and BYDV 5' and 3' elements to cooperate synergistically in cap-independent translation, Nucleic Acids Research 32(5): 172-173.
- Barends S., Bink H.H.J., Worm S.H.E. van den, Pleij C.W.A. & Kraal B. (2003), Entrapping Ribosomes for viral translation: tRNA mimicry as a molecular Trojan horse, Cell 112(1): 123-129.
- Girard G.A.O., Roussis A., Gultyaev A.P., Pleij C.W.A. & Spaink H.P. (2003), Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean, Nucleic Acids Research 31(17): 5003-5015.
- Bink H.H.J., Schirawski J., Haenni A.-L. & Pleij C.W.A. (2003), The 5'-proximal hairpin of Turnip Yellow Mosaic Virus RNA: Its role in translation and encapsidation, Journal of Virology 77(13): 7452-7458.
- Charlier N., Leyssen P., Pleij C.W.A., Lemey P., Billoir F., Laethem K. van, Vandamme A.-M., Clercq E. de, Lamballerie X. de & Neyts J. (2002), Complete genome sequence of the Montana Myotis leukoencephalitis virus, phylogenetic analysis and comparative study of the 3' untranslated region of flaviviruses with no known vector, Journal of General Virology 83(8): 1875-1885.
- Gultyaev A.P., Batenburg F.H.D. van & Pleij C.W.A. (2002), Selective Pressures on RNA Hairpins In Vivo and In Vitro, Journal of Molecular Evolution 54: 1-8.
- Nagel J.H.A., Gultyaev A.P., Öistämö K.J., Gerdes K. & Pleij C.W.A. (2002), A pH-jump approach for investigating secondary structure refolding kinetics in RNA, Nucleic Acids Research 30(13): e63.
- Smit M.H. de, Gultyaev A.P., Hilge M., Bink H.H.J., Barends S., Kraal B. & Pleij C.W.A. (2002), Structural variation and functional importance of a D-loop-T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs, Nucleic Acids Research 30(19): 4232-4240.
- Barends S., Bjoerk K., Gultyaev A.P., Smit M.H. de, Pleij C.W.A. & Kraal B. (2002), Functional evidence for D- and T-loop interactions in tmRNA, FEBS Letters 514(1): 78-83.
- Bink H.H.J. & Pleij C.W.A. (2002), RNA-protein interaction in spherical viruses, Archives of Virology 174: 2261-2279.
- Bink H.H.J., Hellendoorn K., Meulen J van der & Pleij C.W.A. (2002), Protonartion of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA, Proceedings of the National Academy of Sciences 99(21): 13465-13470.
- Nagel J.H.A. & Pleij C.W.A. (2002), Self-induced structural switches in RNA, Biochimie 84(9): 913-923.
- Lipzig R. van, Gultyaev A.P., Pleij C.W.A., Montagu M. van, Cornelissen M. & Meulewaeter F. (2002), The 5' and 3' extremities of the satellite tobacco necrosis virus translational enhancer domain contribute differentially to stimulation of translation, RNA: A Publication of the RNA Society 8(2): 229-236.
- Batenburg F.H.D. van, Gultyaev A.P. & Pleij C.W.A. (2001), PseudoBase: structural information on RNA pseudoknots, Nucleic Acids Research 29(1): 194-195.
- Michiels P.J.A., Versleijen A.A.M., Verlaan P.W.G., Pleij C.W.A., Hilbers C.W. & Heus H.A. (2001), Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting, Journal of Molecular Biology/JMB Online 310(5): 1109-1123.
- Koenig R., Pleij C.W.A. & Büttner G. (2000), Structure and variability of the 3' end of RNA 3 of Beet soil-borne pomovirus - a virus with uncertain pathogenic effects, Archives of Virology 145: 1173-1181.
- Deiman A.L.M., Verlaan P.W.G. & Pleij C.W.A. (2000), In Vitro Transcription by the Turnip Yellow Mosaic Virus RNA Polymerase: a Comparison with the Alfalfa Mosaic Virus and Brome Mosaic Virus Replicases, Journal of Virology 74(1): 264-271.
- Batenburg F.H.D. van, Gultyaev A.P., Pleij C.W.A., Ng J. & Oliehoek J. (2000), PseudoBase: A database with RNA pseudoknots, Nucleic Acids Research 28(1): 201-204.
- Koenig R., Pleij C.W.A. & Huth W. (2000), Genome properties of a new furovirus which is widely spread in cereal crops in Europe. Sherwood J.L. & Rush C.M. (Eds.), Proceedings of the Fourth Symposium of the International Working Group on Plant Viruses with Fungal Vectors, Asilomar Conference Center, Monterey, California, October 5-8, 1999. Fourth Symposium of the International Working Group on Plant Viruses with Fungal Vectors 5 October 1999 - 8 October 1999 41-44.
- Bringloe D.H., Pleij C.W.A. & Coutts R.H.A. (1999), Mutation analysis of cis-elements in the 3'- and 5'-untranslated regions of satellite tobacco necrosis virus strain C RNA, Virology 264(1): 76-84.
- Nagel J.H.A., Gultyaev A.P., Gerdes K. & Pleij C.W.A. (1999), Metastable structures and refolding kinetics in hok mRNA of plasmid R1, RNA: A Publication of the RNA Society 5(11): 1408-1418.
- Koenig R., Pleij C.W.A. & Huth W. (1999), Molecular characterization of a new furovirus mainly infecting rye, Archives of Virology 144: 2125-2140.
- Gultyaev A.P., Batenburg F.H.D. van & Pleij C.W.A. (1999), An approximation of loop free energy values of RNA H-pseudoknots, RNA: A Publication of the RNA Society 5(5): 609-617.
- Deiman A.L.M., Koenen A.K., Verlaan P.W.G. & Pleij C.W.A. (1998), Minimal template requirements for initiation of minus strand synthesis in vitro by the RNA-dependent RNA polymerase of turnip yellow mosaic virus, Journal of Virology 72(5): 3965-3972.
- Koenig R., Pleij C.W.A., Beier C. & Commandeur U. (1998), Genome properties of beet virus Q, a new furo-like virus from sugarbeet, determined from unpurified virus, Journal of General Virology 79(8): 2027-2036.
- Bringloe D.H., Gultyaev A.P., Pelpel M., Pleij C.W.A. & Coutts R.H.A. (1998), The nucleotide sequence of satellite tobacco necrosis virus strain C and helper-assisted replication of wild-type and mutant clones of the virus, Journal of General Virology 79(6): 1539-1546.
- Poot R.A., Worm S.H.E. van den, Pleij C.W.A. & Duin J. van (1998), Base complementarity in helix 2 of the central pseudoknot in 16S ribosomal RNA is essential for ribosome functioning, Nucleic Acids Research 26(2): 549-553.
- Kolk M.H., Graaf M. van der, Fransen C.T.M., Wijmenga S.S., Pleij C.W.A., Heus H.A. & Hilbers C.W. (1998), Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding, The EMBO Journal 12(24): 7498-7504.
- Gultyaev A.P., Batenburg F.H.D. van & Pleij C.W.A. (1998), Dynamic competition between alternative structures in viroid RNAs stimulated by an RNA folding algorithm, Journal of Molecular Biology/JMB Online 276(1): 43-55.
- Gultyaev A.P., Batenburg F.H.D. van & Pleij C.W.A. (1998), RNA folding dynamics: Computer simulations by a genetic algorithm. In: Leontis N.B. & SantaLucia J. (Eds.), Molecular Modeling of Nucleic Acids. ACS Symposium Series no. 682. Washington, DC: American Chemical Society. 229-245.
- Poot R.A., Jeeninga R.E., Pleij C.W.A. & Duin J. van (1997), Acetylation of ribosomal protein S5 affected by defects in the central pseudoknot in 16S ribosomal RNA?, FEBS Letters 401(2-3): 175-179.
- Yang Q., McDermott P.J., Duzic E., Pleij C.W.A., Sherlock J.D. & Lanier S.M. (1997), The 3′-untranslated region of the α2C-adrenergic receptor mRNA impedes translation of the receptor message, The Journal of Biological Chemistry 272(24): 15466-15473.
- Deiman B.A., Kortlever R.M. & Pleij C.W.A. (1997), The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA polymerase, Journal of Virology 71(8): 5990-5996.
- Deiman B.A.L.M., Séron K., Jaspars E.M.J. & Pleij C.W.A. (1997), Efficient transcription obtained by a new procedure of the tRNA-like structure of turnip yellow mosaic virus by a template-dependent and specific viral RNA polymerase, Journal of Virological Methods 64(2): 181-195.
- Hellendoorn K., Verlaan P. W. & Pleij C.W.A. (1997), A functional role for the conserved protonatable hairpins in the 5' untranslated region of turnip yellow mosaic virus RNA, Journal of Virology 71(11): 8774-8779.
- Deiman B.A.L.M. & Pleij C.W.A. (1997), Pseudoknots: a vital feature in viral RNA, Seminars in Virology 8(3): 166-175.
- Hellendoorn K., Michiels P.J.A., Buitenhuis R. & Pleij C.W.A. (1996), Protonatable hairpins are conserved in the 5'-untranslated region of tymovirus RNAs, Nucleic Acids Research 24(24): 4910-4917.
- Poot R.A., Pleij C.W.A. & Duin J. van (1996), The central pseudoknot in 16S ribosomal RNA is needed for ribosome stability but is not essential for 30S initiation complex formation, Nucleic Acids Research 24(19): 3670-3676.
- Hellendoorn K., Mat A.W., Gultyaev A.P. & Pleij C.W.A. (1996), Secondary structure model of the coat protein gene of turnip yellow mosaic virus RNA: long, C-rich, single-stranded regions, Virology 224(1): 43-54.
- Gultyaev A.P., Batenburg F.H.D. van & Pleij C.W.A. (1995), The computer simulation of RNA folding pathways using a genetic algorithm, Journal of Molecular Biology/JMB Online 250(1): 37-51.
- Gultyaev A.P., Batenburg F.H.D. van & Pleij C.W.A. (1995), The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics, Nucleic Acids Research 23(18): 3718-3725.
- Batenburg F.H.D. van, Gultyaev A.P. & Pleij C.W.A. (1995), An APL-programmed genetic algorithm for the prediction of RNA secondary structure, Journal of Theoretical Biology 174(3): 269-280.
- Formenoy L.J., Cunningham P.R., Nurse K., Pleij C.W.A. & Ofengand J. (1994), Methylation of the conserved A1518-A1519 in Escherichia coli 16S ribosomal RNA by the ksgA methyltransferase is influenced by methylations around the similarly conserved U1512-G1523 base pair in the 3′ terminal hairpin, Biochimie 76(12): 1123-1128.
- Gultyaev A.P., Batenburg E. van & Pleij C.W.A. (1994), Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs, Journal of General Virology 75(10): 2851-2856.
- Garcia A., Duin J. van & Pleij C.W.A. (1993), Differential response to frameshift signals in eukaryotic and prokaryotic translational systems, Nucleic Acids Research 21(3): 401-406.
- Poot R.A., Brink M.F., Pleij C.W.A., Boer H.A. de & Duin J. van (1993), Separation of mutant and wild-type ribosomes based on differences in their anti Shine - Dalgarno sequence, Nucleic Acids Research 21(23): 5398-5402.
- Mans R.M.W., Steeg M.H. van, Verlaan P.W.G., Pleij C.W.A. & Bosch L. (1992), Mutational analysis of the pseudoknot in the tRNA-like structure of turnip yellow mosaic virus RNA, Journal of Molecular Biology/JMB Online 223(1): 221-232.
- Danthinne X., Seurinck J., Montagu M. van, Pleij C.W.A. & Emmelo J. van (1991), Structural similarities between the RNAs of two satellites of tobacco necrosis virus, Virology 185(2): 605-614.
- Jupin I., Richards K., Jonard G., Guilley H. & Pleij C.W.A. (1990), Mapping sequences required for productive replication of beet necrotic yellow vein virus RNA 3, Virology 178(1): 273-280.
- Abrahams J.P., Berg M. van den, Batenburg E. van & Pleij C. (1990), Prediction of RNA secondary structure, including pseudoknotting, by computer simulation, Nucleic Acids Research 18(10): 3035-3044.
- Mans R.M.W., Guerrier-Takada C., Altman S. & Pleij C.W.A. (1990), Interaction of RNase P fromEscherichia coliwith pseudoknotted structures in viral RNAs, Nucleic Acids Research 18(12): 3479-3487.
- Guerrier-Takada C., Belkum A. van, Pleij C.W.A. & Altman S. (1988), Novel reactions of RNAase P with a tRNA-like structure in turnip yellow mosaic virus RNA, Cell 53(2): 267-272.
- Belkum A. van, Bingkun J., Rietveld K., Pleij C.W.A. & Bosch L. (1987), Structural similarities among valine-accepting tRNA-like structures in tymoviral RNAs and elongator tRNAs, Biochemistry 26(4): 1144-1151.
- Dumas P., Moras D., Florentz C., Giegé R., Verlaan P., Belkum A. van & Pleij C. W.A. (1987), 3-D Graphics modelling of the tRNA-like 3′-end of turnip yellow mosaic virus RNA: structural and functional implications, Journal of Biomolecular Structure and Dynamics 4(5): 707-728.
- Pleij C.W.A., Rietveld K. & Bosch L. (1985), A new principle of RNA folding based on pseudoknotting, Nucleic Acids Research 13(5): 1717-1731.
- Eecen H.G., Dierendonck J.H. van, Pleij C.W.A., Mandel M. & Bosch L. (1985), Hydrodynamic properties of RNA: effect of multivalent cations on the sedimentation behavior of turnip yellow mosaic virus RNA, Biochemistry 24(14): 3610-3617.
- Rietveld K., Linschooten K., Pleij C.W.A. & Bosch L. (1984), The three-dimensional folding of the tRNA-like structure of tobacco mosaic virus RNA: a new building principle applied twice, The EMBO Journal 3(11): 2613-2619.
- Joshi S., Neeleman L., Pleij C.W.A., Haenni A.L., Chapeville F., Bosch L. & Vloten-Doting L. van (1984), Nonstructural alfalfa mosaic virus RNA-coded proteins present in tobacco leaf tissue, Virology 139(2): 231-242.
- Rietveld K., Pleij C.W. & Bosch L. (1983), Three-dimensional models of the tRNA-like 3′ termini of some plant viral RNAs, The EMBO Journal 2(7): 1079-1085.
- Joshi S., Pleij C.W.A., Haenni A.L. & Bosch L. (1983), Age dependence of cowpea protoplasts for uptake of spermidine and infectibility by alfalfa mosaic virus, Plant Molecular Biology 2(2): 89-94.
- Joshi S., Pleij C.W.A., Haenni A.L., Chapeville F. & Bosch L. (1983), Properties of the tobacco mosaic virus intermediate length RNA-2 and its translation, Virology 127(1): 100-111.
- Noort A., Dries C.L.A.M. van den, Pleij C.W.A., Jaspars E.M.J. & Bosch L. (1982), Properties of turnip yellow mosaic virus in cesium chloride solutions: the formation of high-density components, Virology 120(2): 412-421.
- Rietveld K., Poelgeest R. van, Pleij C.W.A., Boom J.H. van & Bosch L. (1982), The tRNA-Uke structure at the 3′ terminus of turnip yellow mosaic virus RNA: differences and similarities with canonical tRNA, Nucleic Acids Research 10(6): 1929-1946.
- Mellema J.-R., Benicourt C., Haenni A.-L., Noort A., Pleij C.W.A. & Bosch L. (1979), Translational studies with turnip yellow mosaic virus RNAs isolated from major and minor virus particles, Virology 96(1): 38-46.
- Pleij C.W A., Koot-Gronsveld E A.M. & Vloten-Doting L. van (1977), A sensitive and easy local lesion assay for turnip yellow mosaic virus, Journal of General Virology 35(3): 593-595.
- Pleij C.W.A., Eecen H.G., Bosch L. & Mandel M. (1977), The formation of fast-sedimenting turnip yellow mosaic virus RNA: structural rearrangement inside the capsid, Virology 76(2): 781-786.
- Pleij C.W.A., Mellema J.R., Noort A. & Bosch L. (1977), The occurrence of the coat protein messenger RNA in the minor components of turnip yellow mosaic virus, FEBS Letters 80(1): 19-22.
- Pleij C.W.A., Neeleman A., Vloten-Doting L. van & Bosch L. (1976), Translation of turnip yellow mosaic virus RNA in vitro: a closed and an open coat protein cistron, Proceedings of the National Academy of Sciences 73(12): 4437-4441.