The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

Workflow for quantitative proteomic analysis of Clostridium acetobutylicum ATCC 824 using iTRAQ tags

(2013) Shuyu Hou et al.   METHODS

Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

(2013) Olga A. Soutourina et al.   PLoS Genetics

The redox-sensing protein Rex, a transcriptional regulator of solventogenesis in Clostridium acetobutylicum

(2012) Mandy Wietzke et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

(2012) Nadja Patenge et al.   BMC GENOMICS

Multiple factors dictate target selection by Hfq-binding small RNAs

(2012) Chase L Beisel et al.   EMBO JOURNAL

Transcription Factor Family-Based Reconstruction of Singleton Regulons and Study of the Crp/Fnr, ArsR, and GntR Families in Desulfovibrionales Genomes

(2012) A. E. Kazakov et al.   JOURNAL OF BACTERIOLOGY

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum – Cellular behavior in adaptation to n-butanol

(2012) Katrin M. Schwarz et al.   JOURNAL OF BIOTECHNOLOGY

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum—Solvent stress caused by a transient n-butanol pulse

(2012) Holger Janssen et al.   JOURNAL OF BIOTECHNOLOGY

Global transcriptional changes of Clostridium acetobutylicum cultures with increased butanol:acetone ratios

(2012) Daniel Hönicke et al.   New Biotechnology

Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens

(2012) Ina Wilms et al.   RNA Biology

The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail

(2012) H. Ishikawa et al.   RNA

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

(2011) Atsuko Shinhara et al.   BMC GENOMICS

Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications

(2011) Bryan P Tracy et al.   CURRENT OPINION IN BIOTECHNOLOGY

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages

(2011) Mobarak A. Mraheil et al.   NUCLEIC ACIDS RESEARCH

Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis

(2011) Amy T. Cavanagh et al.   NUCLEIC ACIDS RESEARCH

Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes

(2011) Sergios A. Nicolaou et al.   NUCLEIC ACIDS RESEARCH

PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action

(2011) Hironori Otaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

E. coli6S RNA: A universal transcriptional regulator within the centre of growth adaptation

(2011) René Geißen et al.   RNA Biology

The RpoS-Mediated General Stress Response inEscherichia coli

(2010) Aurelia Battesti et al.   Annual Review of Microbiology

Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA

(2010) Pierre Mandin et al.   EMBO JOURNAL

Rho-dependent Termination ofssrS(6S RNA) Transcription inEscherichia coli

(2010) Huiseok Chae et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing

(2010) Jacob R. Borden et al.   METABOLIC ENGINEERING

A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation

(2010) Sergios A. Nicolaou et al.   METABOLIC ENGINEERING

Glucose uptake regulation in E. coli by the small RNA SgrS: comparative analysis of E. coli K-12 (JM109 and MG1655) and E. coli B (BL21)

(2010) Alejandro Negrete et al.   Microbial Cell Factories

Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli

(2010) Yoshiki Ikeda et al.   MOLECULAR MICROBIOLOGY

Identification of regulatory RNAs in Bacillus subtilis

(2010) Irnov Irnov et al.   NUCLEIC ACIDS RESEARCH

Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA

(2010) K. Papenfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Legionella pneumophila 6S RNA optimizes intracellular multiplication

(2010) S. P. Faucher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Alexandra Sittka et al.   RNA Biology

The tmRNA-tagging mechanism and the control of gene expression: a review

(2010) Sharief Barends et al.   Wiley Interdisciplinary Reviews-RNA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes

(2009) J. S. Byun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biology oftrans-Translation

(2008) Kenneth C. Keiler   Annual Review of Microbiology

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum

(2008) Gaëlle André et al.   NUCLEIC ACIDS RESEARCH

The transcriptional program underlying the physiology of clostridial sporulation

(2008) Shawn W Jones et al.   GENOME BIOLOGY