5th Meeting of Regulating with
RNA in Bacteria & Archaea

March 19-22, 2018 • Seville/Spain

5th Meeting of Regulating with
RNA in Bacteria & Archaea

March 19-22, 2018 • Seville/Spain

Congress details

Abstract submission


Scientific programme

Please find the preliminary programme here:

Invited Speakers

The following invited speakers will present their latest work and results:

Plenary speakers

Emmanuelle Charpentier, Ph.D., is a French microbiologist, geneticist and biochemist. She is Scientific Member of the Max Planck Society, Director at the Max Planck Institute for Infection Biology in Berlin, Germany, Honorary Professor at Humboldt University, and recipient of an Alexander von Humboldt Professorship. Prior to her current appointments, she was Head of Department at the Helmholtz Centre for Infection Research, Professor at the Hannover Medical School in Germany, Visiting and Associate Professor at the Laboratory for Molecular Infection Medicine Sweden at Umeå University in Sweden, and Assistant and Associate Professor at the Max F. Perutz Laboratories, University of Vienna, Austria. Before becoming an independent investigator, she held several research associate positions in the US. Prof. Charpentier’s research on the RNA- and protein-based CRISPR-Cas9 prokaryotic immune system laid the foundation for the ground-breaking CRISPR-Cas9 genome engineering technology. She has received numerous prestigious awards and distinctions, and is an elected member of several academies of sciences. She is co-founder of CRISPR Therapeutics and ERS Genomics.

Gisela Storz is an NIH Distinguished Investigator in the Eunice Kennedy Shriver National Institute of Child Health and Human Development in Bethesda, Maryland.  She received her Ph.D. from the University of California, Berkeley, and then carried out postdoctoral work at the National Cancer Institute and Harvard Medical School.  As a result of the serendipitous discovery of the peroxide-induced OxyS RNA in E. coli, one of the first small, regulatory RNAs to be found, much of the work in her lab has focused on the genome-wide identification of small RNAs and their characterization.  More recently, work in the Storz lab has extended to the detection and characterization of proteins of less than 50 amino acids sometimes encoded by small RNAs.

Prof. Rotem Sorek received his PhD in Human Genetics from Tel Aviv University on 2006, and conducted his post-doctoral studies at the Berkeley National Laboratories in Berkeley, CA. Since 2008 he is a Professor at the Weizmann Institute of Science.
Prof. Sorek’s investigates microbial transcriptomes, with an interest in understanding RNA-mediated regulation in bacteria and archaea. He also studies CRISPR-Cas, the adaptive “immune” system that bacteria use to defend themselves against viruses, as well as additional, new anti-viral defense systems discovered at the Sorek lab. His studies also discovered that viruses can use small molecules to communicate among themselves and coordinate the dynamics of infection. Prof. Sorek received numerous prestigious awards, including the 2006 RNA Society/Scaringe Young Scientist Award, the 2008 Sir Charles Clore Prize, the 2012 Rubinowitz-Grossman Prize for outstanding young scientists and the 2014 FEBS Anniversary Prize. Sorek was recently elected to the European Academy of Microbiology.

Invited speakers

Prof. Magnar Bjørås is a Principle Investigator of the research group of Cellular responses to DNA damage at Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim and at Oslo University Hospital/University of Oslo. Bjørås is an expert on genome dynamics with particular emphasis on oxidative stress, DNA base lesion repair and maintenance of epigenetic DNA methylation (epigenome stability).
Cellular genomes are continuously challenged by physical, chemical and biological agents that introduce changes of the chemical structure of the DNA. Intracellular reactive metabolites such as reactive oxygen species and alkylating compounds are important inducers of such changes. Nevertheless, mutation frequencies are low because of very efficient pathways for DNA repair and DNA recombination, which remove DNA damage and conserve at least one functional copy of the genome.


  • Molecular mechanisms of DNA base lesion repair
  • Role of oxidative DNA base lesion repair in cancer
  • Impact of oxidative DNA base lesion repair and epigenetics on brain function (cognition, behavior and neurogenesis)
  • Small peptides in biological responses to DNA damage
  • Impact of Oxidation resistance gene 1 (Oxr1) in stress signaling

Helge B. Bode studied chemistry and biology in Göttingen, Germany, and obtained his PhD in organic chemistry from Göttingen University in 2000. After a first Postdoc at the German Research Center for Biotechnology (GBF) in Braunschweig (Germany) from 2001-2002 and a second one at the Stanford University (USA) from 2002-2003 he became an assistant professor (Juniorprofessor) for natural product biotechnology at the Saarland University in Saarbrücken (Germany) from 2005-2006. From 2006-2010 he was a group leader within the Emmy Noether program of the Deutsche Forschungsgemeinschaft (DFG) and since 2008 he is the Merck endowed chair for Molecular Biotechnology at the Goethe-University Frankfurt. His research is centred around all aspects of microbial natural products with a special focus on their natural function and underlying regulation including RNA-based mechanisms.

After completing his PhD at Harvard in 2004 in the lab of David Liu, Dr. Allen Buskirk began studying pauses that occur during translation and how they are resolved by the cell. Using genetic selections, he identified nascent polypeptide sequences that inhibit their own synthesis on the ribosome. Together with Rachel Green, he used kinetic methods to tease out the molecular mechanism of ribosome stalling by these peptides and how ribosomes are rescued by tmRNA. His group moved to Johns Hopkins in 2014, where he has made significant contributions to improving the ribosome profiling protocol in bacteria in order to obtain high resolution data that accurately reflect the translational landscape in vivo.

Agamemnon J. (A.J.) Carpousis is a Research Director in the CNRS. He received his PhD in Molecular Biology from UCLA for his work on transcription initiation in E. coli. After postdoctoral research at UC Santa Barbara and the University of Geneva, he joined the LMGM, which is a Molecular Microbiology laboratory in Toulouse, France. His work in Geneva contributed to the discovery that RNase E, which is an essential endo-ribonuclease in E. coli, is a key enzyme in the initiation of mRNA degradation. In subsequent work, his group showed that RNase E is part of a large multienzyme RNA-degrading complex, which is now known as the RNA degradosome. Other work includes studies on the role of RhlB, PNPase and poly(A) polymerase in mRNA degradation, and identification of beta-CASP ribonucleases in the Archaea. His current research is based on the recent discovery that the RNA degradosome is localized to the inner cytoplasmic membrane of E. coli. His group characterized a conserved element in the non-catalytic region of RNase E that directly anchors the RNA degradosome to the phospholipid bilayer. They are now addressing the question of how association of the RNA degradosome with the inner membrane impacts RNA processing and degradation.

Sean Crosson received his B.A. in Biology in 1996 from Earlham College and Ph.D. in Biochemistry and Molecular Biophysics from the University of Chicago in 2002.  From 2003 to 2005 he was a postdoctoral fellow at Stanford University School of Medicine, where he began to investigate mechanisms bacterial sensory transduction.  He is currently Professor of Biochemistry and Molecular Biology and Chair of the Committee on Microbiology at the University of Chicago.  Since joining the Chicago faculty in 2006, he has developed an interdisciplinary research program focused on understanding regulatory mechanisms that control bacterial cell physiology and infection biology.  His studies center on the model freshwater bacterium Caulobacter crescentus and the related mammalian pathogen Brucella abortus, which is a causative agent of the global zoonotic disease, brucellosis.

Emma Denham completed a BSc in Genetics at the University of Leicester. Having discovered a passion for microbiology during the year she spent at the University of the Algarve, Portugal investigating autolysins in Helicobacter pylori, she moved to the then Institute for Animal Health, Compton, UK to complete her PhD under the supervision of Jamie Leigh and Phil Ward. There she investigated the lipoprotein processing enzymes in Streptococcus uberis. After completion of her PhD she moved to the lab of Jan Maarten van Dijl, University Medical Center Groningen, the Netherlands for her post-doctoral period. She switched bacterial species again, to study the Gram-positive model organism Bacillus subtilis and the pathogen Staphylococcus aureus. She was involved in several EU consortia, including BaSysBio and BaSynthec and became interested in all levels of regulation. During this time she developed a fascination with RNA and set about trying to understand how sRNAs fit within the B. subtilis regulatory network. In 2013 she was made an Assistant Professor of Molecular Bacteriology at Warwick Medical School, University of Warwick, UK where she continues to study RNA regulation in Gram-positive species.

Petra Dersch graduated in Microbiology at the University of Konstanz and at the Max-Planck-Institute for Terrestrial Microbiology Marburg. She worked as a postdoc at the Tufts Medical School, Boston/USA, started her own group at the Freie Universität Berlin, and was Junior Research Group Leader at the Robert Koch Institute Berlin. 2005 she was appointed at the Technische Universität Braunschweig as Associate Professor in Microbiology, and since 2008, she is Head of the Department of Molecular Infection Biology at the Helmholtz Centre for Infection Research in Braunschweig. Petra Dersch is member of various boards, and a current member of the study section „Microbiology, Virology and Immunology“ of the DFG. Since 2016 she is one of the Vice Presidents of the German Society for Hygiene and Microbiology. Her main research field is molecular pathogenesis of enteric pathogens. She published more than 90 original papers in peer-reviewed international journals, reviews and book chapters.

Michael Ibba is a Professor and Chair of the Department of Microbiology at Ohio State University, USA. Research in the Ibba lab is directed towards understanding the mechanisms that determine how cells ensure the accurate translation of the genetic code, and how changes in the underlying processes impact cellular health, stress responses, and long-term survival.

School of Life Sciences, University of Dundee, Dundee, UK
Visiting Professor Xiamen University and the University of the Chinese Academy of Sciences.

Professor Lilley has a long-standing interest in nucleic acid structure and function (both DNA and RNA) going back more than forty years. He was the first to solve the structure of the Holliday junction in DNA, and has made extensive studies of its interaction with junction-resolving enzymes. He has solved the crystal structure of a complex with eukaryotic GEN1 resolving enzyme.
Lilley has had a long interest in the mechanisms of RNA catalysis, including with the hairpin and VS ribozymes. More recently he has solved crystal structures of the twister and TS ribozymes, and defined the detailed mechanism of the former.
He is also interested in RNA structure, and has made a detailed study of the structure and folding k-turn motif. This is arguably now the best understood structural motif in RNA. Most recently he has shown how N6-methylation of a critical adenine blocks the key first stages of box C/D snoRNP assembly.
Lilley has very recently solved crystal structures of the guanine II- and III-riboswitches.

Stephen Lory received his Bachelor’s degree in 1974 in Bacteriology and a PhD, in 1980, in Microbiology, both from the University of California in Los Angeles. Between 1980 and 1984 he was a Post-doctoral Research Fellow at Harvard Medical School in Boston. Subsequently, he joined the faculty in the Department of Microbiology at the University of Washington, Seattle. In 2000 he relocated to Harvard Medical School in Boston,  where he is currently a Professor in the Department of Microbiology and Immunobiology.
Since establishing his independent laboratory, his research program covered the areas of P. aeruginosa genome evolution, bacterial physiology, comparative genomics and more recently, on the use of modern molecular technologies to gain new insights into the genetic basis of bacterial virulence. He was involved in several projects that resulted in the discovery of small molecule inhibitors of virulence, working with academic and industrial collaborators. Currently, the focus of his laboratory is on the development of new tools and their application to post-translation regulation of gene expression by small regulatory RNAs, identification of regulatory circuits controlling virulence traits of bacterial pathogens and the discovery of biomarkers of infections for a range of opportunistic human pathogens.

Hanah Margalit is a Professor of Computational Molecular Biology at the Hebrew University of Jerusalem. She received her BSc in Mathematics and Biology and her PhD in Computational Biology from the Hebrew University.  Her PhD research concerned mathematical modeling and simulation of molecular control mechanisms in bacteria. For her postdoc she went to NIH, where she specialized in bioinformatics. When she returned to Israel she was among the first to develop this scientific field in Israel. The studies in her group have focused mainly on cellular regulatory mechanisms, from individual interactions up to the network level. Her more recent studies concern integration of various types of large-scale data, in order to understand the intertwining of different regulation levels in the cell. These include transcription regulation, post-transcriptional regulation by small RNAs, and post-transcriptional regulation by endoribonucleases. Among the recent contributions of the group is the RIL-seq experimental-computational protocol for in vivo detection of small RNA-target interactions in bacteria.


After completing my BSc in 1994, I started my PhD at the Université de Montréal under the supervision of Dr Marc Drolet. There, I studied the role of topoisomerases in the regulation of RNA-DNA hybrids (R-loops) behind the RNA polymerase during transcription elongation. I was able to show that RNase H and topoisomerase I are able to prevent R-loops formation and help bacterial growth. After graduating with honours in 2000, I started my post-doctoral training at the Laboratory of Molecular Biology, NIH, in Bethesda where I trained under the supervision of Dr. Susan Gottesman. During those years, I worked on a small regulatory RNA, called RyhB, which controls the expression of mRNAs encoding iron-using proteins and is regulated by intracellular iron concentration. In 2004, I joined the Biochemistry Dept at University of Sherbrooke in Canada to start my own laboratory. With my group we have studied the role of RNase E and Hfq in the regulation of sRNA targets. We demonstrated that Hfq can be recruited by a sRNA to block translation of a target mRNA. We recently showed that certain sRNAs are regulated by tRNA fragments acting as a sponge.

Isabella Moll received her doctorate in Microbiology in 2000 from the University of Vienna for her studies on translation initiation on leaderless mRNAs in E. coli. After her postdoctoral research, which focused on the post-transcriptional control of gene expression by Hfq and sRNAs in E. coli, she was funded by an EMBO fellowship to pursue studies on ribosome heterogeneity in the laboratory of Knud Nierhaus at the Max Planck Institute for Molecular Genetics, Berlin. In 2005, she received the Hertha-Firnberg Award and became principal investigator at the Centre of Molecular Biology in Vienna. After her Habilitation in 2012, she was appointed Associate Professor at the Max F. Perutz Laboratories, University of Vienna. Her current research addresses various aspects of the modulation of protein synthesis during bacterial stress adaptation with a particular focus on molecular mechanisms governing ribosome heterogeneity.

Bryce Nickels is a Professor of Genetics at Rutgers University. He received his Ph.D. in Microbiology from Harvard University and then remained at Harvard to carry out his post-doctoral studies in Ann Hochschild’s laboratory. His research focus is the study of transcription mechanism and transcription regulation in bacteria. His lab utilizes a range of approaches including molecular biology, genetics, biochemistry and high-throughput sequencing to obtain a detailed understanding of the mechanism and regulation of transcription. Amoung his lab’s discoveries was that of a functional role for 2- to 4-nucleotide RNA products, “nanoRNAs,” in modulating gene expression and biofilm formation in bacteria by serving as primers for transcription initiation. More recently, his lab identified an “ab initio” mechanism of RNA 5'-end capping whereby a nucleoside-containing metabolite such as nicotinamide adenine dinucleotide (NAD+) is added at the RNA 5' end by serving as a “non-canonical initiating nucleotide” (NCIN) for transcription initiation by RNA polymerase.

Kai Papenfort studied biology at the Phillips University of Marburg (Germany), where he graduated in 2005. In 2006 he moved to the laboratory of Jörg Vogel at the Max Planck Institute for Infection Biology in Berlin to study gene regulation by small noncoding RNAs in Salmonella Typhimurium. In the same year, he also worked as a Marie Curie fellow at the Institute of Food Research in Norwich (UK). He obtained his PhD from the Humboldt University of Berlin in 2010. Since then, he has worked as a postdoctoral research fellow with Jörg Vogel at the Institute for Molecular Infection Biology in Würzburg (Germany) and as an HFSP postdoctoral researcher with Bonnie Bassler at Princeton University (USA). In 2015, he was appointed Professor of Microbiology at the Ludwig Maximilians University of Munich, Germany. Work in his group focusses on gene regulation by bacterial noncoding RNAs in Vibrio cholerae and intercellular communication among microbes.

Anna Marie Pyle is the William Edward Gilbert Professor of Molecular, Cellular and Developmental Biology and Professor of Chemistry at Yale University. She has been a Howard Hughes Medical Institute Investigator since 1997. Dr. Pyle obtained her undergraduate degree in Chemistry from Princeton University and received her Ph.D. in Chemistry from Columbia University in 1990, where she worked with Professor Jacqueline K. Barton. Dr. Pyle was a postdoctoral fellow in the laboratory of Thomas Cech at the University of Colorado. Dr. Pyle formed her own research group in 1992 in the Department of Biochemistry and Molecular Biophysics at Columbia University Medical Center. In 2002, she moved to Yale University, where she leads a research group that specializes in determining the structure and function of large RNA molecules and protein enzymes that operate on RNA. Dr. Pyle teaches the undergraduate Molecular Biology course at Yale, she is Chair of the Building Committee for the Yale Science Building and she serves on the University Budget Committee. Dr. Pyle was Chair of the MSFA Study Section at the NIH, and previously served as a permanent member on the MSFE, and MGB Study Sections. At Brookhaven National labs, she serves on the Science and Technology Steering Committee and on Beamline Advisory Teams at the NSLSII light source. Dr. Pyle is the Co-Editor of Methods in Enzymology and serves on the Editorial Board of the Journal of Molecular Biology. Dr. Pyle is the author of over 160 publications and has mentored more than 40 graduate students and postdocs.

Lennart Randau holds a diploma degree in Biology from the Technical University Braunschweig. He finished his PhD under the supervision of Prof. Dieter Jahn in 2006. Thereafter, he worked as a Postdoctoral Associate in the group of Prof. Dieter Söll at the Yale University in New Haven (USA) and investigated transfer RNA processing pathways.
Since December 2010, he is head of the Max Planck Research Group for Prokaryotic Small RNA Biology at the Max Planck Institute for Terrestrial Microbiology in Marburg. His present research is focused on studying small RNA-mediated processes in prokaryotes, in particular non-coding RNA gene fragmentation mechanisms in hyperthermophilic archaea and minimal CRISPR-Cas antiviral defense systems in proteobacteria.

Dr. Pascale Romby, PhD, is Director of the CNRS Unit “Architecture and Reactivity of RNA” (100 persons) at the Institute of Molecular and Cellular Biology (IBMC) since 2016. She also leads the research team “mRNA and regulatory RNAs in bacteria” and has produced 130 publications in peer-reviewed journals. Her team is studying the roles of RNAs in gene regulation and deep mechanistic analysis in various bacteria. Two major themes are focusing on (i) the analysis of the translation initiation of structured mRNAs in bacteria, and (ii) the characterization of the function of regulatory RNAs and their networks in the opportunistic pathogen Staphylococcus aureus. She is member of several editorial boards: RNA Biology, Pathogens and Diseases, Biochemistry, Virulence. She has organized several international meetings related to the non coding genome in gene regulation. She received various awards, such as the silver CNRS medal in 2016 and the Langevin prize of the Academy of Sciences in 2010.

Renée Schroeder was born and grew up in Brazil and has been living in Austria since she was 14 years old. She studied biochemistry at the University of Vienna and completed her postdoctoral studies in Munich, Paris and Albany New York. Since 1989, she is leading a research group at the University of Vienna. Since 2005 she is the Head of Department of Biochemistry and Cellbiology. Her research topics center around the diverse functions of RNA, from RNA-binding antibiotics, RNA chaperones, RNA catalysis and regulatory RNAs. The current research focus of her group are genomic aptamers that regulate transcription by direct interaction with RNA polymerase demonstrating that RNA can control its own synthesis. She is the recipient of many research awards, including the Wittgenstein and the Eduard Buchner Prize. She is the author of over 100 scientific articles and 3 popular science books on evolution. Since 2007 she is Editor in Chief of the Journal “RNA Biology”.

Scarlet Shell is an Assistant Professor of Biology and Biotechnology at Worcester Polytechnic Institute in Worcester, Massachusetts. She received a B.A. in Biological Sciences at Smith College in 2001, and then conducted her graduate studies at the University of California, San Diego where she studied DNA mismatch repair under the supervision of Richard Kolodner and received a Ph.D. in Biomedical Sciences in 2008. Scarlet then received postdoctoral training in the lab of Sarah Fortune at the Harvard T. H. Chan School of Public Health, where she investigated the role of DNA methylation in Mycobacterium tuberculosis and developed methodology to map mycobacterial transcription start sites and RNA cleavage sites transcriptome-wide.

Scarlet launched her independent research program at WPI in 2014.  The central goal of the Shell lab is to understand the regulatory mechanisms that underlie mycobacterial stress tolerance. They combine genetics, genomics, transcriptomics and biochemistry to understand how mycobacteria respond to, and ultimately survive, stressful conditions. Current efforts, funded by a CAREER award from NSF, are focused on the mechanisms of regulation of mRNA stability.

Dr. Virginijus Siksnys holds the position of Professor of Vilnius University since 2002 and is Chief scientist/Department head at the Institute of Biotechnology of Vilnius University. Dr. Siksnys has made a major and sustained contribution to the understanding of the structure and function of restriction enzymes. His current research on the CRISPR system for antiviral defense has had a major impact on the field. His studies of the Cas9 protein paved the way for development of novel tools for genome editing applications.

Sarah Woodson is the T. C. Jenkins Professor of Biophysics at Johns Hopkins University.  She received her PhD in Biophysical Chemistry in 1987 with Donald Crothers at Yale University, and did postdoctoral research in the laboratory of Thomas Cech at the University of Colorado Boulder from 1987-1990.  Her research group studies how RNA molecules fold into specific three-dimensional structures, and how the RNA and proteins components of cellular complexes such as the ribosome come together. In addition to biophysical methods such as X-ray scattering and single-molecule fluorescence, her group has pioneered the application of X-ray hydroxyl radical footprinting to RNA. Dr. Woodson received a Pew Scholar Award in the Biomedical Sciences in 1993, a Camille Dreyfus Teacher-Scholar Award in 1995, was elected a AAAS Fellow in 2010 and the President of the RNA Society (2016-2017).