Jörg Vogel

Summary

Affiliation: Max-Planck-Institute for Infection Biology
Country: Germany

Publications

  1. ncbi How to find small non-coding RNAs in bacteria
    Jörg Vogel
    Max Planck Institute for Infection Biology, RNA Biology, Schumannstr 21 22, D 10117 Berlin, Germany
    Biol Chem 386:1219-38. 2005
  2. pmc Identification of cyanobacterial non-coding RNAs by comparative genome analysis
    Ilka M Axmann
    Humboldt University, Department of Biology Genetics, Chausseestrasse, D Berlin, Germany
    Genome Biol 6:R73. 2005
  3. doi A rough guide to the non-coding RNA world of Salmonella
    Jörg Vogel
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Mol Microbiol 71:1-11. 2009
  4. ncbi Target identification of small noncoding RNAs in bacteria
    Jörg Vogel
    Max Planck Institute for Infection Biology, Chariteplatz 1, 10117 Berlin, Germany
    Curr Opin Microbiol 10:262-70. 2007
  5. ncbi Small non-coding RNAs and the bacterial outer membrane
    Jörg Vogel
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Curr Opin Microbiol 9:605-11. 2006
  6. ncbi The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide
    Jörg Vogel
    Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
    Curr Biol 14:2271-6. 2004
  7. doi Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level
    Kai Papenfort
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Res Microbiol 160:278-87. 2009
  8. pmc Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation
    Johannes H Urban
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    PLoS Biol 6:e64. 2008
  9. doi Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
    Verena Pfeiffer
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    Nat Struct Mol Biol 16:840-6. 2009
  10. pmc Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
    Alexandra Sittka
    Max Planck Institute for Infection Biology, RNA Biology, Berlin, Germany
    PLoS Genet 4:e1000163. 2008

Collaborators

Detail Information

Publications35

  1. ncbi How to find small non-coding RNAs in bacteria
    Jörg Vogel
    Max Planck Institute for Infection Biology, RNA Biology, Schumannstr 21 22, D 10117 Berlin, Germany
    Biol Chem 386:1219-38. 2005
    ..Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs...
  2. pmc Identification of cyanobacterial non-coding RNAs by comparative genome analysis
    Ilka M Axmann
    Humboldt University, Department of Biology Genetics, Chausseestrasse, D Berlin, Germany
    Genome Biol 6:R73. 2005
    ..Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria...
  3. doi A rough guide to the non-coding RNA world of Salmonella
    Jörg Vogel
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Mol Microbiol 71:1-11. 2009
    ....
  4. ncbi Target identification of small noncoding RNAs in bacteria
    Jörg Vogel
    Max Planck Institute for Infection Biology, Chariteplatz 1, 10117 Berlin, Germany
    Curr Opin Microbiol 10:262-70. 2007
    ..These include the pulse-expression of sRNAs followed by global transcriptome analysis (microarrays), new biocomputational prediction algorithms, and novel gfp reporter gene fusions to validate candidate target gene regulation...
  5. ncbi Small non-coding RNAs and the bacterial outer membrane
    Jörg Vogel
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Curr Opin Microbiol 9:605-11. 2006
    ..An sRNA-OMP network is emerging in which some sRNAs act specifically on a single omp mRNA, whereas others control multiple omp mRNA targets...
  6. ncbi The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide
    Jörg Vogel
    Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
    Curr Biol 14:2271-6. 2004
    ..Our study adds the SOS regulon to the growing list of global regulatory circuits controlled by sRNA genes...
  7. doi Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level
    Kai Papenfort
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Res Microbiol 160:278-87. 2009
    ..This review summarizes how and when several such regulators (CyaR, DsrA, GcvB, OmrAB, RNAIII, RybB, RyhB) act upon multiple targets...
  8. pmc Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation
    Johannes H Urban
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    PLoS Biol 6:e64. 2008
    ..Our study reveals hierarchical action of two well-conserved sRNAs in a complex regulatory cascade that controls the glmS mRNA. Similar cascades of noncoding RNA regulators may operate in other organisms...
  9. doi Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
    Verena Pfeiffer
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    Nat Struct Mol Biol 16:840-6. 2009
    ..The discovery of CDS targeting markedly expands the sequence space for sRNA target predictions in bacteria...
  10. pmc Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
    Alexandra Sittka
    Max Planck Institute for Infection Biology, RNA Biology, Berlin, Germany
    PLoS Genet 4:e1000163. 2008
    ..We present a generic strategy that is ideal for the systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range of bacteria...
  11. doi Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA
    Kai Papenfort
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    Mol Microbiol 74:139-58. 2009
    ..Deep sequencing detected a dramatically changed profile of Hfq-bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post-transcriptional regulation...
  12. pmc A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD
    Kathrin S Fröhlich
    RNA Biology Group, Institute for Molecular Infection Biology, University of Wurzburg, Josef Schneider Strasse 2, D 97080 Wurzburg, Germany
    Nucleic Acids Res 40:3623-40. 2012
    ..The SdsR-binding site in ompD was localized by 3'-RACE, an experimental approach that promises to be of use in predicting other sRNA-target interactions in bacteria...
  13. ncbi A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis
    Johannes H Urban
    Max Planck Institute for Infection Biology, RNA Biology, Chariteplatz 1, 10117 Berlin, Germany
    J Mol Biol 373:521-8. 2007
    ..Our data suggest that Gram-negative bacteria evolved a mechanism of glmS riboregulation that is distinct from the glmS riboswitch mechanism of Gram-positive bacteria...
  14. doi Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis
    Kai Papenfort
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Mol Microbiol 68:890-906. 2008
    ..This represents a new link between porin repression and nutrient availability that is likely to be widely conserved among enterobacteria...
  15. ncbi A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome
    Verena Pfeiffer
    Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Mol Microbiol 66:1174-91. 2007
    ..This study identifies the first regulatory RNA of an enterobacterial pathogenicity island, and new roles for Hfq and HilD in SPI-1 gene expression...
  16. pmc The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair
    Kai Papenfort
    RNA Biology Group, Institute for Molecular Infection Biology, University of Wurzburg, D 97080 Wurzburg, Germany
    Proc Natl Acad Sci U S A 109:E757-64. 2012
    ....
  17. ncbi Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes
    Alexandra Sittka
    Max Planck Institute for Infection Biology, Berlin, Germany
    RNA Biol 6:266-75. 2009
    ..It also suggests that the expression of heterologous RNA-binding proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo...
  18. doi The primary transcriptome of the major human pathogen Helicobacter pylori
    Cynthia M Sharma
    Max Planck Institute for Infection Biology, RNA Biology Group, D 10117 Berlin, Germany
    Nature 464:250-5. 2010
    ..Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species...
  19. doi Small RNA binding to 5' mRNA coding region inhibits translational initiation
    Marie Bouvier
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin D 10117, Germany
    Mol Cell 32:827-37. 2008
    ..This "five codon window" for translational control in the 5' coding region of mRNA not only has implications for sRNA target predictions but might also apply to cis-regulatory systems such as RNA thermosensors and riboswitches...
  20. pmc Translational control and target recognition by Escherichia coli small RNAs in vivo
    Johannes H Urban
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117 Berlin, Germany
    Nucleic Acids Res 35:1018-37. 2007
    ..We expect our GFP fusion approach to be applicable to sRNA targets of other bacteria, and also demonstrate that Vibrio RyhB sRNA represses a Vibrio sodB fusion when co-expressed in E.coli...
  21. pmc RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq
    Liron Argaman
    Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
    Proc Natl Acad Sci U S A 109:4621-6. 2012
    ....
  22. doi A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo
    Johannes H Urban
    Max Planck Institute for Infection Biology, RNA Biology Group, Chariteplatz 1, 10117, Berlin, Germany
    Methods Mol Biol 540:301-19. 2009
    ..The specialized reporter plasmid series also provides a suitable platform to study the function of cis-encoded riboregulators such as natural riboswitches, thermosensors, or engineered aptamer-based regulatory switches...
  23. pmc SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay
    Kai Papenfort
    Max Planck Institute for Infection Biology, Chariteplatz 1, 10117 Berlin, Germany
    Mol Microbiol 62:1674-88. 2006
    ..In unstressed bacterial cells, the two oE-dependent small RNAs function within a surveillance loop to maintain envelope homeostasis and to achieve autoregulation of oE...
  24. pmc A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites
    Cynthia M Sharma
    RNA Biology Group, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
    Genes Dev 21:2804-17. 2007
    ..Taken together, our study suggests highly conserved regions in sRNAs and mRNA regions distant from Shine-Dalgarno sequences as important elements for the identification of sRNA targets...
  25. doi Experimental approaches for the discovery and characterization of regulatory small RNA
    Cynthia Mira Sharma
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Curr Opin Microbiol 12:536-46. 2009
    ..We will also review the available toolbox for wet lab-based research, including in vivo and in vitro reporter systems, genetic methods and biochemical co-purification of sRNA interaction partners...
  26. doi Regulatory RNA in bacterial pathogens
    Kai Papenfort
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Cell Host Microbe 8:116-27. 2010
    ..This review covers the versatile regulatory RNA mechanisms employed by bacterial pathogens and highlights the dynamic interplay between riboregulation and virulence factor expression...
  27. doi The role of Hfq in bacterial pathogens
    Yanjie Chao
    RNA Biology Group, Max Planck Institute for Infection Biology, Berlin, Germany
    Curr Opin Microbiol 13:24-33. 2010
    ..Hfq also facilitates post-transcriptional cross-talk between the core and variable genome regions of bacterial pathogens, and might help integrate horizontally acquired virulence genes into existing regulatory networks...
  28. pmc A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly
    Ana Eulalio
    RNA Biology Group, Max Planck Institute for Infection Biology, Berlin, Germany
    PLoS ONE 6:e17296. 2011
    ..P-body disruption is also induced by the related pathogen, Shigella flexneri, arguing that this might be a new mechanism by which intracellular bacterial pathogens subvert host cell function...
  29. pmc The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium
    Alexandra Sittka
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin, Germany
    Mol Microbiol 63:193-217. 2007
    ..In addition, the hfq mutation appears to cause a chronic activation of the RpoE-mediated envelope stress response which is likely due to a misregulation of membrane protein expression...
  30. pmc Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4
    Jörg Vogel
    Department of Molecular Genetics and Biotechnology, Faculty of Medicine, Hebrew University, Jerusalem, Israel
    Nucleic Acids Res 31:2890-9. 2003
    ..Using a scoring matrix of the -10 element, more than 3000 TSS were predicted, about 40% of which were estimated to be functional. This is the first systematic study of transcription initiation sites in a cyanobacterium...
  31. doi Activation of gene expression by small RNA
    Kathrin S Fröhlich
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Curr Opin Microbiol 12:674-82. 2009
    ..Indirect activation includes cases of RNA mimicry in which degradation of the activating GlmZ sRNA is suppressed by the highly similar GlmY sRNA, or where a pseudo-target mRNA traps MicM sRNA to derepress porin synthesis...
  32. doi A glimpse at the evolution of virulence control
    Alexandra Sittka
    Max Planck Institute for Infection Biology, Chariteplatz 1, D 10117 Berlin, Germany
    Cell Host Microbe 4:310-2. 2008
    ..2008) reported on RNAIII-independent gene regulation in highly virulent, community-associated S. aureus and proposed that two independent regulatory systems were integrated during the pathogenic evolution of S. aureus...
  33. pmc Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing
    Leon N Schulte
    RNA Biology Group, Institute for Molecular Infection Biology, University of Wurzburg, Josef Schneider Strasse 2 D15, D 97080 Wurzburg, Germany
    Nucleic Acids Res 41:542-53. 2013
    ..We predict that dose-dependent responses to environmental stimuli may involve functional specialization of seemingly co-induced miRNAs in other cellular circuitries as well...
  34. doi An RNA trap helps bacteria get the most out of chitosugars
    Jörg Vogel
    Max Planck Institute for Infection Biology, Berlin, Germany
    Mol Microbiol 73:737-41. 2009
    ..The results suggest that 'target' mRNAs might be both prey and also predators of sRNAs...
  35. pmc In vivo expression and purification of aptamer-tagged small RNA regulators
    Nelly Said
    RNA Biology Group, Max Planck Institute for Infection Biology, Chariteplatz 1, 10117 Berlin, Germany
    Nucleic Acids Res 37:e133. 2009
    ..The presented affinity purification strategy may facilitate the isolation of in vivo assembled sRNA-protein complexes in a wide range of bacteria...