High-Density Sequencing Applications in Microbial Molecular Genetics

Agamemnon James (A.J.) Carpousis is a Research Director in the CNRS. He graduated with honors in Biochemistry from the University of Pennsylvania and then did his doctoral studies in the Molecular Biology program at UCLA. His PhD work was on the mechanism of transcription initiation by Escherichia coli RNA polymerase. After postdoctoral research at UC Santa Barbara and the University of Geneva, A.J. Carpousis joined the LMGM, which is a CNRS Microbial Molecular Genetics Laboratory at the University of Toulouse. His research in Geneva contributed to the discovery that RNase E, which is an essential ribonuclease in E. coli, is a key enzyme in the initiation of mRNA degradation. In subsequent research, he purified RNase E and showed that it associates with other proteins involved in mRNA degradation forming a multienzyme complex, which is now known as the RNA degradosome. His group in Toulouse showed that RNase E has a composite structure consisting of a catalytic domain and a large non-catalytic region that serves as the scaffold for interactions with other components of the RNA degradosome. Other work includes studies on the role of RhlB, PNPase and poly(A) polymerase in mRNA degradation, and identification and characterization of beta-CASP ribonucleases in the Archaea. More recently, A.J. Carpousis and his colleagues showed that the RNA degradosome is localized to the inner cytoplasmic membrane of E. coli. They characterized a conserved element in the non-catalytic region of RNase E that directly anchors the RNA degradosome to the phospholipid bilayer of the inner membrane. RNA degradosomes on the inner membrane are highly dynamic forming short-lived clusters that are hypothesized to be centers of mRNA degradation. His group currently uses molecular genetics, biochemistry, high-density sequencing methods and super-resolution microscopy to address the question of the composition and supramolecular structure of the RNA degradosome clusters.

• 1. Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-SeqVânia Pobre and Cecília M. Arraiano2. Conformational Studies of Bacterial Chromosomes by High-Throughput Sequencing MethodsVirginia S. Lioy and Frédéric Boccard3. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to DelaySandrine Laguerre, Ignacio González, Sébastien Nouaille, Annick Moisan, Nathalie Villa-Vialaneix, Christine Gaspin, Marie Bouvier, Agamemnon J. Carpousis, Muriel Cocaign-Bousquet and Laurence Girbal4. FASTBAC-Seq: Functional AnalysiS of Toxin–Antitoxin Systems in BACteria by Deep SequencingSara Masachis, Nicolas J. Tourasse, Sandrine Chabas, Olivier Bouchez and Fabien Darfeuille5. The Challenges of Genome-Wide Studies in a Unicellular Eukaryote With Two Nuclear GenomesSandra Duharcourt and Linda Sperling6. CLIP-Seq in Bacteria: Global Recognition Patterns of Bacterial RNA-Binding ProteinsLiis Andresen and Erik Holmqvist7. High-Resolution Profiling of NMD Targets in YeastFeng He, Alper Celik, Richard Baker and Allan Jacobson8. Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut MicrobiotaThéo Foutel-Rodier, Agnès Thierry, Romain Koszul and Martial Marbouty9. Genome-Wide Mapping of Yeast Retrotransposon Integration Target SitesAnastasia Barkova, Amna Asif-Laidin and Pascale Lesage10. Genome-Wide Quantitation of Protein Synthesis Rates in BacteriaGrace E. Johnson and Gene-Wei Li11. On the Prowl: An In Vivo Method to Identify RNA Partners of a sRNAMarie-Claude Carrier, Claire Morin and Eric Massé12. Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTERIrina O. Vvedenskaya, Seth R. Goldman and Bryce E. Nickels13. Transcriptomic Approaches for Studying Quorum Sensing in Vibrio choleraeRoman Herzog and Kai Papenfort14. In Vitro Study of the Major Bacillus subtilis Ribonucleases Y and JLiliana Mora, Saravuth Ngo, Soumaya Laalami and Harald Putzer15. Mapping 5′-Ends and Their Phosphorylation State With EMOTE, TSS-EMOTE, and nEMOTEPeter Redder16. MS2-Affinity Purification Coupled With RNA Sequencing Approach in the Human Pathogen Staphylococcus aureusDavid Lalaouna, Emma Desgranges, Isabelle Caldelari and Stefano Marzi17. Noncoding RNAs in Archaea: Genome-Wide Identification and Functional ClassificationAnne Buddeweg, Michael Daume, Lennart Randau and Ruth A. Schmitz18. Methodology for Ribosome Profiling of Key Stages of the Caulobacter crescentus Cell CycleJames R. Aretakis, Nadra Al-Husini and Jared M. Schrader19. Transcriptome-Wide Analysis of Protein–RNA and RNA–RNA Interactions in Pathogenic BacteriaJai J. Tree, Kenn Gerdes and David Tollervey20. Profiling RNA Polymerase II Phosphorylation Genome-Wide in Fission YeastTea Kecman, Dong-Hyuk Heo and Lidia Vasiljeva21. Toward Cell Type-Specific In Vivo Dual RNA-SeqLutz Frönicke, Denise N. Bronner, Mariana X. Byndloss, Bridget McLaughlin, Andreas J. Bäumler and Alexander J. Westermann22. Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coliA.M. Mahedi Hasan, Benura Azeroglu and David R.F. Leach