Volker Knoop

Summary

Affiliation: University of Bonn
Country: Germany

Publications

  1. ncbi request reprint Transport of magnesium and other divalent cations: evolution of the 2-TM-GxN proteins in the MIT superfamily
    Volker Knoop
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik IZMB, Universitat Bonn, Germany
    Mol Genet Genomics 274:205-16. 2005
  2. pmc A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii
    Felix Grewe
    Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    Nucleic Acids Res 37:5093-104. 2009
  3. ncbi request reprint The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective
    Volker Knoop
    IZMB Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, Bonn, Germany
    Curr Genet 46:123-39. 2004
  4. doi request reprint When you can't trust the DNA: RNA editing changes transcript sequences
    Volker Knoop
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik IZMB, Bonn, Germany
    Cell Mol Life Sci 68:567-86. 2011
  5. doi request reprint DYW-type PPR proteins in a heterolobosean protist: plant RNA editing factors involved in an ancient horizontal gene transfer?
    Volker Knoop
    IZMB Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Bonn, Germany
    FEBS Lett 584:4287-91. 2010
  6. doi request reprint Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria
    Mareike Rüdinger
    IZMB Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    J Mol Evol 74:37-51. 2012
  7. doi request reprint Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature
    Henning Lenz
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    Curr Genet 56:189-201. 2010
  8. doi request reprint Tracing plant Mitochondrial DNA evolution: rearrangements of the ancient mitochondrial gene cluster trnA-trnT-nad7 in liverwort phylogeny
    Ute Wahrmund
    IZMB Institut für Zelluläre und Molekulare Botanik, Abt Molekulare Evolution, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    J Mol Evol 66:621-9. 2008
  9. doi request reprint Magnesium deficiency phenotypes upon multiple knockout of Arabidopsis thaliana MRS2 clade B genes can be ameliorated by concomitantly reduced calcium supply
    Henning Lenz
    Abteilung Molekulare Evolution, IZMB Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, D 53115 Bonn, Germany
    Plant Cell Physiol 54:1118-31. 2013
  10. doi request reprint Membrane protein interactions between different Arabidopsis thaliana MRS2-type magnesium transporters are highly permissive
    Johanna Schmitz
    IZMB Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Kirschallee 1, D 53115 Bonn, Germany
    Biochim Biophys Acta 1828:2032-40. 2013

Collaborators

Detail Information

Publications29

  1. ncbi request reprint Transport of magnesium and other divalent cations: evolution of the 2-TM-GxN proteins in the MIT superfamily
    Volker Knoop
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik IZMB, Universitat Bonn, Germany
    Mol Genet Genomics 274:205-16. 2005
    ..This presumably forms an integral part of the pore surface, and changes in its structure may result in altered transport capacities for different divalent cations...
  2. pmc A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii
    Felix Grewe
    Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    Nucleic Acids Res 37:5093-104. 2009
    ..As a unique molecular novelty, the Isoetes cox1 gene requires trans-splicing via a discontinuous group I intron demonstrating disrupted, but functional, RNAs for yet another class of natural ribozymes...
  3. ncbi request reprint The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective
    Volker Knoop
    IZMB Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, Bonn, Germany
    Curr Genet 46:123-39. 2004
    ..This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective...
  4. doi request reprint When you can't trust the DNA: RNA editing changes transcript sequences
    Volker Knoop
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik IZMB, Bonn, Germany
    Cell Mol Life Sci 68:567-86. 2011
    ..The present review aims for an overview on the current states of research in the different systems of RNA editing by following a historic timeline along the respective original discoveries...
  5. doi request reprint DYW-type PPR proteins in a heterolobosean protist: plant RNA editing factors involved in an ancient horizontal gene transfer?
    Volker Knoop
    IZMB Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Bonn, Germany
    FEBS Lett 584:4287-91. 2010
    ..We here report the first case of DYW-type PLS proteins outside of the plant kingdom in the protist Naegleria gruberi and hypothesize on horizontal gene transfer in very early land plant evolution...
  6. doi request reprint Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria
    Mareike Rüdinger
    IZMB Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    J Mol Evol 74:37-51. 2012
    ..We propose that DYW proteins are the key players of RNA editing at the origin of land plants...
  7. doi request reprint Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature
    Henning Lenz
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    Curr Genet 56:189-201. 2010
    ..Finally, binary matrices of editing positions can be produced that may be used for downstream (e.g. phylogenetic) analyses...
  8. doi request reprint Tracing plant Mitochondrial DNA evolution: rearrangements of the ancient mitochondrial gene cluster trnA-trnT-nad7 in liverwort phylogeny
    Ute Wahrmund
    IZMB Institut für Zelluläre und Molekulare Botanik, Abt Molekulare Evolution, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    J Mol Evol 66:621-9. 2008
    ....
  9. doi request reprint Magnesium deficiency phenotypes upon multiple knockout of Arabidopsis thaliana MRS2 clade B genes can be ameliorated by concomitantly reduced calcium supply
    Henning Lenz
    Abteilung Molekulare Evolution, IZMB Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, D 53115 Bonn, Germany
    Plant Cell Physiol 54:1118-31. 2013
    ....
  10. doi request reprint Membrane protein interactions between different Arabidopsis thaliana MRS2-type magnesium transporters are highly permissive
    Johanna Schmitz
    IZMB Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Kirschallee 1, D 53115 Bonn, Germany
    Biochim Biophys Acta 1828:2032-40. 2013
    ..Plant magnesium homeostasis may be influenced by hetero-oligomer channel formation where different plant MRS2 proteins meet in the same membrane naturally or in transgenic approaches. ..
  11. pmc A root-expressed magnesium transporter of the MRS2/MGT gene family in Arabidopsis thaliana allows for growth in low-Mg2+ environments
    Michael Gebert
    Institut für Zelluläre und Molekulare Botanik, Universität Bon, D 53115 Bon, Germany
    Plant Cell 21:4018-30. 2009
    ..Hence, contrary to what is frequently found in analyses of plant gene families, a single gene family member knockout results in a strong, environmentally dependent phenotype...
  12. doi request reprint The phylogeny of mosses - addressing open issues with a new mitochondrial locus: group I intron cobi420
    Ute Wahrmund
    IZMB Institut für Zelluläre und Molekulare Botanik, Abt Molekulare Evolution, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    Mol Phylogenet Evol 54:417-26. 2010
    ..A concatenated 6-loci analysis suggests reconsideration of a Funariidae concept which includes Gigaspermaceae but leaves the isolated genus Timmia at the radiation of arthrodontous mosses unresolved...
  13. ncbi request reprint Introducing intron locus cox1i624 for phylogenetic analyses in Bryophytes: on the issue of Takakia as sister genus to all other extant mosses
    Ute Volkmar
    IZMB Institut für Zelluläre und Molekulare Botanik, Abt Molekulare Evolution, Universitat Bonn, Kirschallee 1, Bonn, Germany
    J Mol Evol 70:506-18. 2010
    ....
  14. ncbi request reprint Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants
    Milena Groth-Malonek
    Institut für Zelluläre und Molekulare Botanik, Abt Molekulare Evolution, Universitat Bonn, Bonn, Germany
    Mol Biol Evol 22:117-25. 2005
    ....
  15. doi request reprint RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal
    Mareike Rüdinger
    Abteilung Molekulare Evolution, IZMB Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Kirschallee 1, 53115, Bonn, Germany
    Mol Genet Genomics 281:473-81. 2009
    ..Furthermore, we here wish to propose a unifying nomenclature to clearly identify and designate RNA editing positions and to facilitate future communication and database annotation...
  16. ncbi request reprint Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts
    Mareike Rüdinger
    Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Bonn, Germany
    Mol Biol Evol 25:1405-14. 2008
    ..Although the presence of modularly extended PPR proteins correlates well with organelle RNA editing, the now apparent complete loss of an entire gene family from one clade of embryophytes, the marchantiid liverworts, remains puzzling...
  17. pmc A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii
    Felix Grewe
    IZMB, Universitat Bonn, Kirschallee 1, 53115 Bonn, Germany
    Nucleic Acids Res 39:2890-902. 2011
    ..We finally investigated the four group II introns of the nad7 gene and could identify 27 sites of editing, most of which improve base pairing for proper secondary structure formation...
  18. doi request reprint Assigning DYW-type PPR proteins to RNA editing sites in the funariid mosses Physcomitrella patens and Funaria hygrometrica
    Mareike Rüdinger
    IZMB Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universitat Bonn, Kirschallee 1, Bonn, Germany
    Plant J 67:370-80. 2011
    ..hygrometrica (rps14eU137SL) is addressed by the DYW protein characterized here and the presence of its orthologue in F. hygrometrica is explained through its simultaneous action on site cox1eU755SL conserved in both mosses...
  19. ncbi request reprint Evolution of a pseudogene: exclusive survival of a functional mitochondrial nad7 gene supports Haplomitrium as the earliest liverwort lineage and proposes a secondary loss of RNA editing in Marchantiidae
    Milena Groth-Malonek
    Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Kirschallee 1, D 53115 Bonn, Germany
    Mol Biol Evol 24:1068-74. 2007
    ....
  20. pmc Plant-type mitochondrial RNA editing in the protist Naegleria gruberi
    Mareike Rüdinger
    Department of Molecular Evolution, IZMB, University of Bonn, Bonn, Germany
    RNA 17:2058-62. 2011
    ....
  21. ncbi request reprint A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype
    Mareike Schallenberg-Rüdinger
    Institut für Zelluläre und Molekulare Botanik IZMB, Abteilung Molekulare Evolution, Universitat Bonn, Kirschallee 1, 53115, Bonn, Germany Faculty of Biology, Department of Cell Biology, University of Marburg, Karl von Frisch Str 8, 35043, Marburg, Germany Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA, 6009, Australia
    Plant J 76:420-32. 2013
    ..Together with the functional characterization of DYW-PPR_65, this completes the assignment of RNA editing factors to all editing sites in the Physcomitrella mitochondrial transcriptome. ..
  22. doi request reprint Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes
    Julia Hecht
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, D 53115 Bonn, Germany
    Genome Biol Evol 3:344-58. 2011
    ....
  23. doi request reprint Slugs' last meals: molecular identification of sequestered chloroplasts from different algal origins in Sacoglossa (Opisthobranchia, Gastropoda)
    Katharina Händeler
    Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany Institut für Zelluläre und Molekulare Botanik, Bonn, Germany
    Mol Ecol Resour 10:968-78. 2010
    ....
  24. pmc PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation
    Henning Lenz
    Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik, Universitat Bonn, Bonn, Germany
    Bioinform Biol Insights 7:1-19. 2013
    ..Enhancements to the BLASTX mode in PREPACT 2.0 allow querying of complete novel organelle genomes within a few minutes, identifying protein genes and candidate RNA editing sites simultaneously without prior user analyses...
  25. pmc The deepest divergences in land plants inferred from phylogenomic evidence
    Yin Long Qiu
    Department of Ecology and Evolutionary Biology, University Herbarium, University of Michigan, Ann Arbor, MI 48109 1048, USA
    Proc Natl Acad Sci U S A 103:15511-6. 2006
    ..In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences...
  26. ncbi request reprint Divergent intron conservation in the mitochondrial nad2 gene: signatures for the three bryophyte classes (mosses, liverworts, and hornworts) and the lycophytes
    Dagmar Pruchner
    Molekulare Botanik, Universitat Ulm, D 89069 Ulm, Germany
    J Mol Evol 55:265-71. 2002
    ..Plant mitochondrial peculiarities such as RNA editing frequency, U-to-C type of RNA editing, and small group II introns appear to be genus-specific rather than gene-specific features...
  27. ncbi request reprint A hypothesis on the identification of the editing enzyme in plant organelles
    Veronique Salone
    URGV, 2 rue Gaston Cremieux, F 91057 Evry Cedex, France
    FEBS Lett 581:4132-8. 2007
    ....
  28. ncbi request reprint Molecular characterization of a seed transmitted clavicipitaceous fungus occurring on dicotyledoneous plants (Convolvulaceae)
    Ulrike Steiner
    Institut für Pflanzenkrankheiten der Universität Bonn, Nussallee 9, 53115 Bonn, Germany
    Planta 224:533-44. 2006
    ..This is the first report of an ergot alkaloid producing clavicipitaceous fungus associated with a dicotyledonous plant...
  29. pmc Primary sooty mangabey simian immunodeficiency virus and human immunodeficiency virus type 2 nef alleles modulate cell surface expression of various human receptors and enhance viral infectivity and replication
    Jan Munch
    Abteilung Virologie, Universitatsklinikum, Albert Einsteinallee 11, D 89081 Ulm, Germany
    J Virol 79:10547-60. 2005
    ..These differences in Nef function might contribute to the relatively low levels of immune activation observed in HIV-2-infected human individuals...