Prof Jörg Vogel
About
Prof. Jörg Vogel is the founding director of the Helmholtz Institute for RNA-based Infection Research (HIRI) as well as the director of the Institute of Molecular Infection Biology (IMIB) at the University of Würzburg, Germany. As world-leading scientist in the field of RNA biology, Jörg Vogel is considered a pioneer in the application and development of high-throughput sequencing methods for the analysis of individual infected cells as well as interactions between pathogenic bacteria and their hosts.
Prof. Jörg Vogel studied biochemistry at Humboldt University, Berlin, Germany, and at Imperial College, London, UK. In 1999, he received his PhD from Humboldt University with a thesis on Group II intron splicing. He spent his postdoctoral years at Uppsala University, Sweden (2000-2001) and as an EMBO fellow at the Hebrew University, Jerusalem, Israel (2002-2003) before he started an Independent Junior Research Group at the Max Planck Institute for Infection Biology in Berlin, Germany (2004-2010). He became Full Professor and Director of the Institute for Molecular Infection Biology at the University of Würzburg in 2009. As of 2017, he is the Director of the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg.
Jörg Vogel is an elected member of EMBO, the German National Academy of Sciences, as well as the European and American Academies of Microbiology. In 2017, he received a Leibniz Prize, Germany’s most prestigious research award, for his ground-breaking contributions to the understanding of regulatory RNA molecules in infection biology.
Prof. Vogel’s group seek to understand the full (noncoding) RNA world of bacterial pathogens and use RNA-centric approaches to targeting pathogens and manipulating microbiota. A major innovative goal is the comprehensive simultaneous RNA-based profiling of the pathogen and the infected host in real time and at single-cell resolution; where applicable, this should also include co-colonizing microbiota. Researchers at the Vogel lab focus on the mode of action of those noncoding RNA molecules that are crucial for the virulence of the pathogen, differentially expressed upon exposure to the host, or impact gene expression in interacting members of the microbiota. The knowledge obtained will be exploited for therapeutic intervention with clinically relevant bacterial pathogens.
2019
The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells
Heidrich N, Hagmann A, Bauriedl S, Vogel J, Schoen C (2019)
RNA Biol, 16 (4): 390-396DOI: 10.1080/15476286.2018.1486660
The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium
Westermann A, Venturini E, Sellin M, Förstner K, Hardt W, Vogel J (2019)
MBio, 10 (1): 02504-18DOI: 10.1128/mBio.02504-18
Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA
Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J (2019)
Nucleic Acids Res, 47 (4): 2075-2088DOI: 10.1093/nar/gky1243
2018
Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends
Holmqvist E, Li L, Bischler T, Barquist L, Vogel J (2018)
Mol Cell, 70 (5): 971-982DOI: 10.1016/j.molcel.2018.04.017
CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level
El Mouali Y, Gaviria-Cantin T, Sánchez-Romero M, Gibert M, Westermann A, Vogel J, Balsalobre C (2018)
Plos Genet, 14 (6)DOI: 10.1371/journal.pgen.1007401
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes
Yu S, Vogel J, Förstner K (2018)
Gigascience, 7 (9)DOI: 10.1093/gigascience/giy096
Salmonella persisters undermine host immune defenses during antibiotic treatment
Stapels D, Hill P, Westermann A, Fisher R, Thurston T, Saliba A, Blommestein I, Vogel J, Helaine S (2018)
Science, 362 (6419): 1156-1160DOI: 10.1126/science.aat7148
Nuclear lncRNA stabilization in the host response to bacterial infection
Munschauer M, Vogel J (2018)
EMBO J, 37 (13)DOI: 10.15252/embj.201899875
Genome organization and DNA accessibility control antigenic variation in trypanosomes
Müller L, Cosentino R, Förstner K, Guizetti J, Wedel C, Kaplan N, Janzen C, Arampatzi P, Vogel J, Steinbiss S, …, Sebra R, Siegel T (2018)
Nature, 563 (7729): 121-125DOI: 10.1038/s41586-018-0619-8
Bacterial RNA Biology on a Genome Scale
Hör J, Gorski S, Vogel J (2018)
Mol Cell, 70 (5): 785-799DOI: 10.1016/j.molcel.2017.12.023
Host-Pathogen Transcriptomics by Dual RNA-Seq
Westermann A, Vogel J (2018)
In: Arluison V., Valverde C. (eds) Bacterial Regulatory RNA, Methods Mol Biol (Methods in Molecular Biology), 1737: 59-75DOI: 10.1007/978-1-4939-7634-8_4
RNA-binding proteins in bacteria
Holmqvist E, Vogel J (2018)
Nat Rev Microbiol, 16 (10): 601-615DOI: 10.1038/s41579-018-0049-5
Stress-induced host membrane remodeling protects from infection by non-motile bacterial pathogens
Tawk C, Nigro G, Rodrigues Lopes I, Aguilar C, Lisowski C, Mano M, Sansonetti P, Vogel J, Eulalio A (2018)
EMBO J, 37 (23)DOI: 10.15252/embj.201798529
2017
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins
Sharan M, Förstner K, Eulalio A, Vogel J (2017)
Nucleic Acids Res, 45 (11)DOI: 10.1093/nar/gkx137
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins
Tawk C, Sharan M, Eulalio A, Vogel J (2017)
Sci Rep, 7 (1)DOI: 10.1038/s41598-017-09527-0
Global snapshots of bacterial RNA networks
Hör J, Vogel J (2017)
EMBO J, 36 (3): 245-247DOI: 10.15252/embj.201696072
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J (2017)
Nucleic Acids Res, 45 (10): 6147-6167DOI: 10.1093/nar/gkx168
Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA
Smirnov A, Wang C, Drewry L, Vogel J (2017)
EMBO J, 36 (8): 1029-45DOI: 10.15252/embj.201696127
RNA-based recognition and targeting: sowing the seeds of specificity
Gorski S, Vogel J, Doudna J (2017)
Nat Rev Mol Cell Biol, 18 (4): 215-228DOI: 10.1038/nrm.2016.174
Discovery of new RNA classes and global RNA-binding proteins
Smirnov A, Schneider C, Hör J, Vogel J (2017)
Curr Opin Microbiol, 39: 152-160DOI: 10.1016/j.mib.2017.11.016
RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE
Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann A, Gunn J, Vogel J (2017)
Proc Natl Acad Sci U S A, 114 (26): 6824-6829DOI: 10.1073/pnas.1620772114
Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess
Saliba A, Westermann A, Vogel J (2017)
Biospektrum, 23 (5): 525-528DOI: 10.1007/s12268-017-0836-y
Structure of the Escherichia coli ProQ RNA-binding protein
Gonzalez G, Hardwick S, Maslen S, Skehel J, Holmqvist E, Vogel J, Bateman A, Luisi B, Broadhurst R (2017)
RNA (New York, N.Y.C), 23 (5): 696-711DOI: 10.1261/rna.060343.116
New RNA-seq approaches for the study of bacterial pathogens
Saliba A, C Santos S, Vogel J (2017)
Curr Opin Microbiol, 35: 78-87DOI: 10.1016/j.mib.2017.01.001
In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways
Chao Y, Li L, Girodat D, Förstner K, Said N, Corcoran C, Smiga M, Papenfort K, Reinhardt R, Wieden H, Luisi B, Vogel J (2017)
Mol Cell, 65 (1): 39-51DOI: 10.1016/j.molcel.2016.11.002
2016
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
Holmqvist E, Wright P, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)
EMBO J, 35 (9): 991-1011DOI: 10.15252/embj.201593360
Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation
Das S, Lindemann C, Young B, Muller J, Österreich B, Ternette N, Winkler A, Paprotka K, Reinhardt R, Förstner K, …, Wyllie D, Fraunholz M (2016)
Proc Natl Acad Sci U S A, 113 (22): 3101-10DOI: 10.1073/pnas.1520255113
An NK Cell Perforin Response Elicited via IL-18 Controls Mucosal Inflammation Kinetics during Salmonella Gut Infection
Müller A, Dolowschiak T, Sellin M, Felmy B, Verbree C, Gadient S, Westermann A, Vogel J, LeibundGut-Landmann S, Hardt W (2016)
Plos Pathog, 12 (6)DOI: 10.1371/journal.ppat.1005723
A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response
Chao Y, Vogel J (2016)
Mol Cell, 61 (3): 352-363DOI: 10.1016/j.molcel.2015.12.023
Grad-seq guides the discovery of ProQ as a major small RNA-binding protein
Smirnov A, Förstner K, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J (2016)
Proc Natl Acad Sci U S A, 113 (41): 11591-11596DOI: 10.1073/pnas.1609981113
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Jiang Y, Oron T, Clark W, Bankapur A, D'Andrea D, Lepore R, Funk C, Kahanda I, Verspoor K, Ben-Hur A, …, Friedberg I, Radivojac P (2016)
Genome Biol, 17 (1)DOI: 10.1186/s13059-016-1037-6
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella
Saliba A, Li L, Westermann A, Appenzeller S, Stapels D, Schulte L, Helaine S, Vogel J (2016)
Nat Microbiol, 2DOI: 10.1038/nmicrobiol.2016.206
The target spectrum of SdsR small RNA in Salmonella
Fröhlich K, Haneke K, Papenfort K, Vogel J (2016)
Nucleic Acids Res, 44 (21): 10406-22DOI: 10.1093/nar/gkw632
Molecular phenotyping of infection-associated small non-coding RNAs
Barquist L, Westermann A, Vogel J (2016)
Philos Trans R Soc Lond B Biol Sci, 371 (1707)DOI: 10.1098/rstb.2016.0081
cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides
Cao Y, Förstner K, Vogel J, Smith C (2016)
J Bacteriol, 198 (18): 2410-8DOI: 10.1128/JB.00381-16
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions
Westermann A, Forstner K, Amman F, Barquist L, Chao Y, Schulte L, Muller L, Reinhardt R, Stadler P, Vogel J (2016)
Nature, 529 (7587): 496-501DOI: 10.1038/nature16547
The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation
Berger P, Knödler M, Förstner K, Berger M, Bertling C, Sharma C, Vogel J, Karch H, Dobrindt U, Mellmann A (2016)
Sci Rep, 6DOI: 10.1038/srep35307
Emerging roles of RNA modifications in bacteria
Marbaniang C, Vogel J (2016)
Curr Opin Microbiol, 30: 50-57DOI: 10.1016/j.mib.2016.01.001
Gifsy-1 Prophage IsrK with Dual Function as Small and Messenger RNA Modulates Vital Bacterial Machineries
Hershko-Shalev T, Odenheimer-Bergman A, Elgrably-Weiss M, Ben-Zvi T, Govindarajan S, Seri H, Papenfort K, Vogel J, Altuvia S (2016)
Plos Genet, 12 (4)DOI: 10.1371/journal.pgen.1005975
2015
Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells
Afonso-Grunz F, Hoffmeier K, Müller S, Westermann A, Rotter B, Vogel J, Winter P, Kahl G (2015)
BMC Genomics, 16DOI: 10.1186/s12864-015-1489-1
Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella
Papenfort K, Espinosa E, Casadesús J, Vogel J (2015)
Proc Natl Acad Sci U S A, 112 (34): 4772-81DOI: 10.1073/pnas.1507825112
Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies
Barquist L, Vogel J (2015)
Annu Rev Genet, 49: 367-94DOI: 10.1146/annurev-genet-112414-054804
dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42
Fan B, Li L, Chao Y, Förstner K, Vogel J, Borriss R, Wu X (2015)
Plos One, 10 (11)DOI: 10.1371/journal.pone.0142002
Regulatory small RNAs from the 3' regions of bacterial mRNAs
Miyakoshi M, Chao Y, Vogel J (2015)
Curr Opin Microbiol, 24: 132-9DOI: 10.1016/j.mib.2015.01.013
Investigating CRISPR RNA Biogenesis and Function Using RNA-seq
Heidrich N, Dugar G, Vogel J, Sharma C (2015)
In: CRISPR: Methods and protocols (eds Lundgren M, Charpentier E, Fineran PC), Methods Mol Biol (Methods in Molecular Biology), 1311: 1-21DOI: 10.1007/978-1-4939-2687-9_1
Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA
Miyakoshi M, Chao Y, Vogel J (2015)
EMBO J, 34 (11): 1478-92DOI: 10.15252/embj.201490546
The end is not the end: remnants of tRNA precursors live on to sponge up small regulatory RNAs
Ziebuhr W, Vogel J (2015)
Mol Cell, 58 (3): 389-90DOI: 10.1016/j.molcel.2015.04.032
Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
Sass A, van Acker H, Förstner K, van Nieuwerburgh F, Deforce D, Vogel J, Coenye T (2015)
BMC Genomics, 16DOI: 10.1186/s12864-015-1993-3
2014
Differential RNA-seq: the approach behind and the biological insight gained
Sharma C, Vogel J (2014)
Curr Opin Microbiol, 19: 97-105DOI: 10.1016/j.mib.2014.06.010
READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data
Förstner K, Vogel J, Sharma C (2014)
Bioinformatics, 30 (23): 3421-3DOI: 10.1093/bioinformatics/btu533
Recognition of the small regulatory RNA RydC by the bacterial Hfq protein
Dimastrogiovanni D, Fröhlich K, Bandyra K, Bruce H, Hohensee S, Vogel J, Luisi B (2014)
Elife, 3DOI: 10.7554/eLife.05375
A bacterial seek-and-destroy system for foreign DNA
Vogel J (2014)
Science, 344 (6187): 972-3DOI: 10.1126/science.1252962
Small RNA functions in carbon metabolism and virulence of enteric pathogens
Papenfort K, Vogel J (2014)
Front Cell Infect Microbiol, 4DOI: 10.3389/fcimb.2014.00091
Single-cell RNA-seq: advances and future challenges
Saliba A, Westermann A, Gorski S, Vogel J (2014)
Nucleic Acids Res, 42 (14): 8845-60DOI: 10.1093/nar/gku555
Identification and Characterization of Small Non-coding RNAs in Bacteria
Podkaminski D, Bouvier M, Vogel J (2014)
, 136: 719-786DOI: 10.1002/9783527647064.ch33
2013
β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity
Gutierrez A, Laureti L, Crussard S, Abida H, Rodríguez-Rojas A, Blázquez J, Baharoglu Z, Mazel D, Darfeuille F, Vogel J, Matic I (2013)
Nat Commun, 4DOI: 10.1038/ncomms2607
Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA
Göpel Y, Papenfort K, Reichenbach B, Vogel J, Görke B (2013)
Gene Dev, 27 (5): 552-64DOI: 10.1101/gad.210112.112
Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis
Zhang Y, Heidrich N, Ampattu B, Gunderson C, Seifert H, Schoen C, Vogel J, Sontheimer E (2013)
Mol Cell, 50 (4): 488-503DOI: 10.1016/j.molcel.2013.05.001
Same same but different: new structural insight into CRISPR-Cas complexes
Heidrich N, Vogel J (2013)
Mol Cell, 52 (1): 4-7DOI: 10.1016/j.molcel.2013.09.023.
Comparative genomics boosts target prediction for bacterial small RNAs
Wright P, Richter A, Papenfort K, Mann M, Vogel J, Hess W, Backofen R, Georg J (2013)
Proc Natl Acad Sci U S A, 110 (37): 3487-96DOI: 10.1073/pnas.1303248110
Alexander Böhm (1971-2012)
Boos W, Parkinson J, Jenal U, Vogel J, Søgaard-Andersen L (2013)
Mol Microbiol, 88 (2): 219-21DOI: 10.1111/mmi.12198
Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing
Schulte L, Westermann A, Vogel J (2013)
Nucleic Acids Res, 41 (1): 542-53DOI: 10.1093/nar/gks1030
Bacterial regulatory mechanisms: the gene and beyond
Bassler B, Vogel J (2013)
Curr Opin Microbiol, 16 (2): 109-11DOI: 10.1016/j.mib.2013.04.001
CRISPRs extending their reach: prokaryotic RNAi protein Cas9 recruited for gene regulation
Heidrich N, Vogel J (2013)
EMBO J, 32 (13): 1802-4DOI: 10.1038/emboj.2013.141
Small RNA-Mediated Activation of Sugar Phosphatase mRNA Regulates Glucose Homeostasis
Papenfort K, Sun Y, Miyakoshi M, Vanderpool C, Vogel J (2013)
Cell, 153 (2): 426-437DOI: 10.1016/j.cell.2013.03.003
RNA-mediated regulation in pathogenic bacteria
Caldelari I, Chao Y, Romby P, Vogel J (2013)
Cold Spring Harb Perspect Med, 3 (9)DOI: 10.1101/cshperspect.a010298
A small RNA activates CFA synthase by isoform-specific mRNA stabilization
Fröhlich K, Papenfort K, Fekete A, Vogel J (2013)
EMBO J, 32 (22): 2963-79DOI: 10.1038/emboj.2013.222
Regulatory Mechanisms of Special Significance: Role of Small RNAs in Virulence Regulation
Papenfort K, Corcoran C, Gupta S, Miyakoshi M, Heidrich N, Chao Y, Fröhlich K, Ziebuhr W, Böhm A, Vogel J, Sharma C (2013)
In: Regulation of Bacterial Virulence (eds Darwin AJ, Vasil ML): 493-527DOI: 10.1128/9781555818524.ch25
2012
Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis
Madhugiri R, Pessi G, Voss B, Hahn J, Sharma C, Reinhardt R, Vogel J, Hess W, Fischer H, Evguenieva-Hackenberg E (2012)
RNA Biol, 9 (1): 47-58DOI: 10.4161/rna.9.1.18008
Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression
Lioliou E, Sharma C, Caldelari I, Helfer A, Fechter P, Vandenesch F, Vogel J, Romby P (2012)
Plos Genet, 8 (6)DOI: 10.1371/journal.pgen.1002782
The csgD mRNA as a hub for signal integration via multiple small RNAs
Boehm A, Vogel J (2012)
Mol Microbiol, 84 (1): 1-5DOI: 10.1111/j.1365-2958.2012.08033.x
Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs
Corcoran C, Rieder R, Podkaminski D, Hofmann B, Vogel J (2012)
In: Bacterial Regulatory RNA: Methods and protocols (ed Keiler KC), 905: 177-200DOI: 10.1007/978-1-61779-949-5_11
The mammalian microRNA response to bacterial infections
Eulalio A, Schulte L, Vogel J (2012)
RNA Biol, 9 (6): 742-50DOI: 10.4161/rna.20018
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium
Kröger C, Dillon S, Cameron A, Papenfort K, Sivasankaran S, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, …, Vogel J, Hinton J (2012)
Proc Natl Acad Sci U S A, 109 (20): 1277-86DOI: 10.1073/pnas.1201061109
Experimental tools to identify RNA-protein interactions in Helicobacter pylori
Rieder R, Reinhardt R, Sharma C, Vogel J (2012)
RNA Biol, 9 (4): 520-31DOI: 10.4161/rna.20331
Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA
Corcoran C, Podkaminski D, Papenfort K, Urban J, Hinton J, Vogel J (2012)
Mol Microbiol, 84 (3): 428-45DOI: 10.1111/j.1365-2958.2012.08031.x
Dual RNA-seq of pathogen and host
Westermann A, Gorski S, Vogel J (2012)
Nat Rev Microbiol, 10 (9): 618-30DOI: 10.1038/nrmicro2852
Hfq-associated Regulatory Small RNAs
Corcoran C, Papenfort K, Vogel J (2012)
In: Regulatory RNAs in Prokaryotes (eds Marchfelder A, Hess WR): 15-50DOI: 10.1007/978-3-7091-0218-3_2
The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E
Bandyra K, Said N, Pfeiffer V, Górna M, Vogel J, Luisi B (2012)
Mol Cell, 47 (6): 943-53DOI: 10.1016/j.molcel.2012.07.015
Differential RNA Sequencing (dRNA-Seq): Deep-Sequencing-Based Analysis of Primary Transcriptomes
Borries A, Vogel J, Sharma C (2012)
In: Tag-based next generation sequencing (eds Kahl G, Harbers M ), 316: 109-121DOI: 10.1002/9783527644582.ch7
The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA PolymeraseCWOA
Zhelyazkova P, Sharma C, Förstner K, Liere K, Vogel J, Börner T (2012)
Plant Cell, 24 (1): 123-36DOI: 10.1105/tpc.111.089441
An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs
Chao Y, Papenfort K, Reinhardt R, Sharma C, Vogel J (2012)
EMBO J, 31 (20): 4005-19DOI: 10.1038/emboj.2012.229
RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq
Argaman L, Elgrably-Weiss M, Hershko T, Vogel J, Altuvia S (2012)
Proc Natl Acad Sci U S A, 109 (12): 4621-6DOI: 10.1073/pnas.1113113109
The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair
Papenfort K, Podkaminski D, Hinton J, Vogel J (2012)
Proc Natl Acad Sci U S A, 109 (13): 757-64DOI: 10.1073/pnas.1119414109
2011
The transcriptional landscape of Chlamydia pneumoniae
Albrecht M, Sharma C, Dittrich M, Müller T, Reinhardt R, Vogel J, Rudel T (2011)
Genome Biol, 12 (10)DOI: 10.1186/gb-2011-12-10-r98
Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA
Sharma C, Papenfort K, Pernitzsch S, Mollenkopf H, Hinton J, Vogel J (2011)
Mol Microbiol, 81 (5): 1144-65DOI: 10.1111/j.1365-2958.2011.07751.x
Sweet Business: Spot42 RNA networks with CRP to Modulate Catabolite Repression
Papenfort K, Vogel J (2011)
Mol Cell, 41 (3): 245-6DOI: 10.1016/j.molcel.2011.01.011
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
Schmidtke C, Findeiß S, Sharma C, Kuhfuß J, Hoffmann S, Vogel J, Stadler P, Bonas U (2011)
Nucleic Acids Res, 40 (5): 2020-31DOI: 10.1093/nar/gkr904
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
Deltcheva E, Chylinski K, Sharma C, Gonzales K, Chao Y, Pirzada Z, Eckert M, Vogel J, Charpentier E (2011)
Nature, 471 (7340): 602-7DOI: 10.1038/nature09886
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides
Berghoff B, Glaeser J, Sharma C, Zobawa M, Lottspeich F, Vogel J, Klug G (2011)
Mol Microbiol, 80 (6): 1479-95DOI: 10.1111/j.1365-2958.2011.07658.x
Microbes at their best: first Mol Micro Meeting Würzburg
Böhm A, Papenfort K, Lopez D, Vogel J (2011)
Mol Microbiol, 82 (4): 797-806DOI: 10.1111/j.1365-2958.2011.07852.x
Regulation by small RNAs in bacteria: expanding frontiers
Storz G, Vogel J, Wassarman K (2011)
Mol Cell, 43 (6): 880-91DOI: 10.1016/j.molcel.2011.08.022
A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly
Eulalio A, Fröhlich K, Mano M, Giacca M, Vogel J (2011)
Plos One, 6 (3)DOI: 10.1371/journal.pone.0017296
Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression
Belair C, Baud J, Chabas S, Sharma C, Vogel J, Staedel C, Darfeuille F (2011)
Silence, 2 (1)DOI: 10.1186/1758-907X-2-7
Hfq and its constellation of RNA
Vogel J, Luisi B (2011)
Nat Rev Microbiol, 9 (8): 578-89DOI: 10.1038/nrmicro2615
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD
Fröhlich K, Papenfort K, Berger A, Vogel J (2011)
Nucleic Acids Res, 40 (8): 3623-40DOI: 10.1093/nar/gkr1156
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon
Gogol E, Rhodius V, Papenfort K, Vogel J, Gross C (2011)
Proc Natl Acad Sci U S A, 108 (31): 12875-80DOI: 10.1073/pnas.1109379108
Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family
Schulte L, Eulalio A, Mollenkopf H, Reinhardt R, Vogel J (2011)
EMBO J, 30 (10): 1977-89DOI: 10.1038/emboj.2011.94
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803
Mitschke J, Georg J, Scholz I, Sharma C, Dienst D, Bantscheff J, Voss B, Steglich C, Wilde A, Vogel J, Hess W (2011)
Proc Natl Acad Sci U S A, 108 (5): 2124-9DOI: 10.1073/pnas.1015154108
2010
The primary transcriptome of the major human pathogen Helicobacter pylori
Sharma C, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler P, Vogel J (2010)
Nature, 464 (7286): 250-5DOI: 10.1038/nature08756
The role of Hfq in bacterial pathogens
Chao Y, Vogel J (2010)
Curr Opin Microbiol, 13 (1): 24-33DOI: 10.1016/j.mib.2010.01.001
Analysis of A to I editing of miRNA in macrophages exposed to salmonella
Heale B, Eulalio A, Schulte L, Vogel J, O'Connell M (2010)
RNA Biol, 7 (5): 621-7DOI: 10.4161/rna.7.5.13269
Small RNAs promote mRNA stability to activate the synthesis of virulence factors
Podkaminski D, Vogel J (2010)
Mol Microbiol, 78 (6): 1327-31DOI: 10.1111/j.1365-2958.2010.07428.x
Identification of regulatory RNAs in Bacillus subtilis
Irnov I, Sharma C, Vogel J, Winkler W (2010)
Nucleic Acids Res, 38 (19): 6637-51DOI: 10.1093/nar/gkq454
Regulatory RNA in bacterial pathogens
Papenfort K, Vogel J (2010)
Cell Host Microbe, 8 (1): 116-27DOI: 10.1016/j.chom.2010.06.008
Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA
Papenfort K, Bouvier M, Mika F, Sharma C, Vogel J (2010)
Proc Natl Acad Sci U S A, 107 (47): 20435-40DOI: 10.1073/pnas.1009784107
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
Albrecht M, Sharma C, Reinhardt R, Vogel J, Rudel T (2010)
Nucleic Acids Res, 38 (3): 868-77DOI: 10.1093/nar/gkp1032
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
Bohn C, Rigoulay C, Chabelskaya S, Sharma C, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, …, Vogel J, Bouloc P (2010)
Nucleic Acids Res, 38 (19): 6620-36DOI: 10.1093/nar/gkq462
2009
Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
Pfeiffer V, Papenfort K, Lucchini S, Hinton J, Vogel J (2009)
Nat Struct Mol Biol, 16 (8): 840-6DOI: 10.1038/nsmb.1631
Fast mapping of short sequences with mismatches, insertions and deletions using index structures
Hoffmann S, Otto C, Kurtz S, Sharma C, Khaitovich P, Vogel J, Stadler P, Hackermüller J (2009)
PLos Comput Biol, 5 (9)DOI: 10.1371/journal.pcbi.1000502
In vivo expression and purification of aptamer-tagged small RNA regulators
Said N, Rieder R, Hurwitz R, Deckert J, Urlaub H, Vogel J (2009)
Nucleic Acids Res, 37 (20): 133-DOI: 10.1093/nar/gkp719
A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo
Urban J, Vogel J (2009)
In: Riboswitches: Methods and protocols (ed Serganov A), Methods Mol Biol, 540: 301-19DOI: 10.1007/978-1-59745-558-9_22
Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA
Papenfort K, Said N, Welsink T, Lucchini S, Hinton J, Vogel J (2009)
Mol Microbiol, 74 (1): 139-158DOI: 10.1111/j.1365-2958.2009.06857.x
An RNA trap helps bacteria get the most out of chitosugars
Vogel J (2009)
Mol Microbiol, 73 (5): 737-41DOI: 10.1111/j.1365-2958.2009.06806.x
Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability
Jäger D, Sharma C, Thomsen J, Ehlers C, Vogel J, Schmitz R (2009)
Proc Natl Acad Sci U S A, 106 (51): 21878-82DOI: 10.1073/pnas.0909051106
Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level
Papenfort K, Vogel J (2009)
Res Microbiol, 160 (4): 278-87DOI: 10.1016/j.resmic.2009.03.004
Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides
Berghoff B, Glaeser J, Sharma C, Vogel J, Klug G (2009)
Mol Microbiol, 74 (6): 1497-512DOI: 10.1111/j.1365-2958.2009.06949.x
Experimental approaches for the discovery and characterization of regulatory small RNA
Sharma C, Vogel J (2009)
Curr Opin Microbiol, 12 (5): 536-46DOI: 10.1016/j.mib.2009.07.006
A rough guide to the non-coding RNA world of Salmonella
Vogel J (2009)
Mol Microbiol, 71 (1): 1-11DOI: 10.1111/j.1365-2958.2008.06505.x
Activation of gene expression by small RNA
Fröhlich K, Vogel J (2009)
Curr Opin Microbiol, 12 (6): 674-82DOI: 10.1016/j.mib.2009.09.009
Acid stress activation of the sigma(E) stress response in Salmonella enterica serovar Typhimurium
Muller C, Bang I, Velayudhan J, Karlinsey J, Papenfort K, Vogel J, Fang F (2009)
Mol Microbiol, 71 (5): 1228-38DOI: 10.1111/j.1365-2958.2009.06597.x
Regulatory RNAs in prokaryotes: here, there and everywhere
Narberhaus F, Vogel J (2009)
Mol Microbiol, 74 (2): 261-9DOI: 10.1111/j.1365-2958.2009.06869.x
2008
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
Sittka A, Lucchini S, Papenfort K, Sharma C, Rolle K, Binnewies T, Hinton J, Vogel J (2008)
Plos Genet, 4 (8)DOI: 10.1371/journal.pgen.1000163
Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation
Urban J, Vogel J (2008)
PLos Biol, 6 (3)DOI: 10.1371/journal.pbio.0060064
A Glimpse at the Evolution of Virulence Control
Sittka A, Vogel J (2008)
Cell Host Microbe, 4 (4): 310-2DOI: 10.1016/j.chom.2008.09.006
Small RNA binding to 5' mRNA coding region inhibits translational initiation
Bouvier M, Sharma C, Mika F, Nierhaus K, Vogel J (2008)
Mol Cell, 32 (6): 827-37DOI: 10.1016/j.molcel.2008.10.027
A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles
Song T, Mika F, Lindmark B, Liu Z, Schild S, Bishop A, Zhu J, Camilli A, Johansson J, Vogel J, Wai S (2008)
Mol Microbiol, 70 (1): 100-11DOI: 10.1111/j.1365-2958.2008.06392.x
Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis
Papenfort K, Pfeiffer V, Lucchini S, Sonawane A, Hinton J, Vogel J (2008)
Mol Microbiol, 68 (4): 890-906DOI: 10.1111/j.1365-2958.2008.06189.x
RNA: Noncoding
Henry A, Vogel J (2008)
In: Wiley Encyclopedia of Chemical Biology (ed Begley TP), 22DOI: 10.1002/9780470048672.wecb522
Noncoding RNA control of the making and breaking of sugars
Görke B, Vogel J (2008)
Gene Dev, 22 (21): 2914-25DOI: 10.1101/gad.1717808
The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp. PCC 6803
Dienst D, Dühring U, Mollenkopf H, Vogel J, Golecki J, Hess W, Wilde A (2008)
Microbiology, 154 (Pt 10): 3134-3143DOI: 10.1099/mic.0.2008/020222-0.
2007
Translational control and target recognition by Escherichia coli small RNAs in vivo
Urban J, Vogel J (2007)
Nucleic Acids Res, 35 (3): 1018-37DOI: 10.1093/nar/gkl1040
Sensory and regulatory RNAs in prokaryotes: a new German research focus
Narberhaus F, Vogel J (2007)
RNA Biol, 4 (3): 160-4DOI: 10.4161/rna.4.3.5308
An antisense RNA inhibits translation by competing with standby ribosomes
Darfeuille F, Unoson C, Vogel J, Wagner E (2007)
Mol Cell, 26 (3): 381-92DOI: 10.1016/j.molcel.2007.04.003
A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis
Urban J, Papenfort K, Thomsen J, Schmitz R, Vogel J (2007)
J Mol Biol, 373 (3): 521-8DOI: 10.1016/j.jmb.2007.07.035
The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium
Sittka A, Pfeiffer V, Tedin K, Vogel J (2007)
Mol Microbiol, 63 (1): 193-217DOI: 10.1111/j.1365-2958.2006.05489.x
A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome
Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J (2007)
Mol Microbiol, 66 (5): 1174-91DOI: 10.1111/j.1365-2958.2007.05991.x
Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq
Wilson J, Ott C, Höner zu Bentrup K, Ramamurthy R, Quick L, Porwollik S, Cheng P, McClelland M, Tsaprailis G, Radabaugh T, …, Stefanyshyn-Piper H, Nickerson C (2007)
Proc Natl Acad Sci U.S.A., 104 (41): 16299-304DOI: 10.1073/pnas.0707155104
Characterization of the role of ribonucleases in Salmonella small RNA decay
Viegas S, Pfeiffer V, Sittka A, Silva I, Vogel J, Arraiano C (2007)
Nucleic Acids Res, 35 (22): 7651-64DOI: 10.1093/nar/gkm916
A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites
Sharma C, Darfeuille F, Plantinga T, Vogel J (2007)
Gene Dev, 21 (21): 2804-17DOI: 10.1101/gad.447207
Recent advances in the expression, evolution, and dynamics of prokaryotic genomes
Arraiano C, Bamford J, Brüssow H, Carpousis A, Pelicic V, Pflüger K, Polard P, Vogel J (2007)
J Bacteriol, 189 (17): 6093-100DOI: 10.1128/JB.00612-07
Target identification of small noncoding RNAs in bacteria
Vogel J, Wagner E (2007)
Curr Opin Microbiol, 10 (3): 262-70DOI: 10.1016/j.mib.2007.06.001
2006
Experimental approaches to identify non-coding RNAs
Hüttenhofer A, Vogel J (2006)
Nucleic Acids Res, 34 (2): 635-46DOI: 10.1093/nar/gkj469
σE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay
Papenfort K, Pfeiffer V, Mika F, Lucchini S, Hinton J, Vogel J (2006)
Mol Microbiol, 62 (6): 1674-1688DOI: 10.1111/j.1365-2958.2006.05524.x
Small non-coding RNAs and the bacterial outer membrane
Vogel J, Papenfort K (2006)
Curr Opin Microbiol, 9 (6): 605-11DOI: 10.1016/j.mib.2006.10.006
2005
Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: Functional Analysis of Identified Non-mRNAs
Gerhart E, Wagner H, Vogel J (2005)
In: Handbook of RNA Biochemistry (eds Hartmann RK, Bindereif A, Schön A, Westhof E), 2: 614-642DOI: 10.1002/9783527619504.ch37
Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: RNA Mining
Vogel J, Gerhart E, Wagner H (2005)
In: Handbook of RNA Biochemistry (eds Hartmann RK, Bindereif A, Schön A, Westhof E), 2: 595-613DOI: 10.1002/9783527619504.ch36
How to find small non-coding RNAs in bacteria
Vogel J, Sharma C (2005)
Biol Chem, 386 (12): 1219-38DOI: 10.1515/BC.2005.140
Identification of cyanobacterial non-coding RNAs by comparative genome analysis
Axmann I, Kensche P, Vogel J, Kohl S, Herzel H, Hess W (2005)
Genome Biol, 6 (9)DOI: 10.1186/gb-2005-6-9-r73
Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA
Udekwu K, Darfeuille F, Vogel J, Reimegård J, Holmqvist E, Wagner E (2005)
Gene Dev, 19 (19): 2355-66DOI: 10.1101/gad.354405
2004
The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide
Vogel J, Argaman L, Wagner E, Altuvia S (2004)
Curr Biol, 14 (24): 2271-6DOI: 10.1016/j.cub.2004.12.003
2002
Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing
Vogel J, Börner T (2002)
EMBO J, 21 (14): 3794-803DOI: 10.1093/emboj/cdf359
2001
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner E, Margalit H, Altuvia S (2001)
Curr Biol, 11 (12): 941-50