A5048266578- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Salmonella and Campylobacter epidemiology
- Helicobacter pylori-related gastroenterology studies
- CRISPR and Genetic Engineering
- Microbial Community Ecology and Physiology
- Bacterial biofilms and quorum sensing
- Viral gastroenteritis research and epidemiology
- Escherichia coli research studies
- Vibrio bacteria research studies
- RNA regulation and disease
- Legume Nitrogen Fixing Symbiosis
- Veterinary medicine and infectious diseases
- Probiotics and Fermented Foods
- Photosynthetic Processes and Mechanisms
- Antimicrobial Resistance in Staphylococcus
- Aquaculture disease management and microbiota
- Galectins and Cancer Biology
- Metabolomics and Mass Spectrometry Studies
- Synthesis of heterocyclic compounds
- Clostridium difficile and Clostridium perfringens research
- Cancer-related molecular mechanisms research
University of Würzburg
2016-2025
Biology of Infection
2012-2024
University of Puerto Rico at Río Piedras
2024
Max Planck Institute for Infection Biology
2005-2019
Institute of Molecular Biology
2016-2017
Eunice Kennedy Shriver National Institute of Child Health and Human Development
2014
National Institutes of Health
2014
National Center for Infectious Diseases
2012
Kiel University
2012
University of Freiburg
2012
Recent advances in high-throughput pyrosequencing (HTPS) technology now allow a thorough analysis of RNA bound to cellular proteins, and, therefore, post-transcriptional regulons. We used HTPS discover the Salmonella RNAs that are targeted by common bacterial Sm-like protein, Hfq. Initial transcriptomic revealed Hfq controls expression almost fifth all genes, including several horizontally acquired pathogenicity islands (SPI-1, -2, -4, -5), two sigma factor regulons, and flagellar gene...
With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most underlying matching models neglect necessity allow not only mismatches, but also insertions and deletions. Current evaluations indicate, however, that very different error apply novel high-throughput sequencing methods. While most frequent error-type in Illumina reads are produced by 454's GS FLX predominantly contain deletions (indels). Even though 454 sequencers able...
The interactions of numerous regulatory small RNAs (sRNAs) with target mRNAs have been characterized, but how sRNAs can regulate multiple, structurally unrelated is less understood. Here we show that Salmonella GcvB sRNA directly acts on seven commonly encode periplasmic substrate-binding proteins ABC uptake systems for amino acids and peptides. Alignment homologs distantly related bacteria revealed a conserved G/U-rich element strictly required recognition. Analysis gene fusion regulation...
There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and of their potential for the production biofuels. However, exploitation bioengineering requires knowledge transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map 3,527 start sites (TSS) model organism Synechocystis sp. PCC6803. One-third all TSS were located upstream annotated gene; another third on reverse...
ABSTRACT While the model organism Escherichia coli has been subject of intense study for decades, full complement its RNAs is only now being examined. Here we describe a survey E. transcriptome carried out using differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, an automated prediction algorithm transcriptional start sites (TSS). With criterion expression under at least one three growth conditions examined, predicted 14,868 TSS...
Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison multiple strains revealed a high genetic and phenotypic diversity. However, little known about differences transcriptome organization, gene expression, small RNA (sRNA) repertoires. Here we present first comparative primary analysis based on differential RNA-seq (dRNA-seq) four C. isolates. Our approach includes novel, generic method for automated annotation transcriptional start sites...
Significance To our knowledge, this work describes the first genome-wide annotation of transcriptional start sites in Vibrio cholerae and discovery characterization a regulatory RNA, named VqmR, which controls collective behaviors major human pathogen. We show that VqmR is activated by VqmA regulator. represses expression multiple mRNA targets including those encoding Rtx (repeats toxin) toxin VpsT, required for biofilm formation. Indeed, we formation through repression vpsT .
Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and nuclear-encoded phage-type (NEP), which recognize distinct types promoters. The division labor between PEP NEP during plastid development mature chloroplasts unclear due to lack comprehensive information promoter usage. Here, we present thorough investigation into the distribution promoters within genome barley (Hordeum vulgare)....
Cellular RNAs guide CRISPR-Cas9 The Cas9 nuclease widely used for genome editing is derived from natural bacterial defense systems that protect against invading viruses. directed by RNA guides to cut matching viral DNA. Jiao et al. discovered can also originate cellular unassociated with (see the Perspective Abudayyeh and Gootenberg). They rendered this process programmable, linking presence of virtually any cutting DNA Cas9. This capability basis a new CRISPR diagnostic method developed...
Small noncoding RNAs (sRNAs) have predominantly been shown to repress bacterial mRNAs by masking the Shine-Dalgarno (SD) or AUG start codon sequence, thereby preventing 30S ribosome entry and, consequently, translation initiation. However, many recently identified sRNAs lack obvious SD and complementarity, indicating that sRNA-mediated translational control could also take place at other mRNA sites. We report Salmonella RybB sRNA represses ompN pairing with 5′ coding region. Results of...
Chlamydia trachomatis is an obligate intracellular pathogenic bacterium that has been refractory to genetic manipulations. Although the genomes of several strains have sequenced, very little information available on gene structure these bacteria. We used deep sequencing define transcriptome purified elementary bodies (EB) and reticulate (RB) C. L2b, respectively. Using RNA-seq approach, we mapped 363 transcriptional start sites (TSS) annotated genes. Semi-quantitative analysis cDNA reads...
GcvB is one of the most highly conserved Hfq-associated small RNAs in Gram-negative bacteria and was previously reported to repress several ABC transporters for amino acids. To determine full extent GcvB-mediated regulation Salmonella, we combined a genome-wide experimental approach with biocomputational target prediction. Comparative pulse expression wild-type versus mutant sRNA variants revealed that governs large post-transcriptional regulon, impacting ~1% all Salmonella genes via its...
Post-transcriptional regulatory mechanisms are widespread in bacteria. Interestingly, current published data hint that some of these may be non-random with respect to their phylogenetic distribution. Although small, trans -acting RNAs commonly occur bacterial genomes, they have been better characterized Gram-negative bacteria, leaving the impression less important for Firmicutes. It has presumed Gram-positive particular Firmicutes, likely utilize cis located within 5′ mRNA leader region more...
Methanosarcina mazei and related mesophilic archaea are the only organisms fermenting acetate, methylamines, methanol to methane carbon dioxide, contributing significantly greenhouse gas production. The biochemistry of these metabolic processes is well studied, genome sequences available, yet little known about overall transcriptional organization noncoding regions representing 25% 4.01-Mb M. mazei. We present a genome-wide analysis transcription start sites (TSS) in grown under different...
The abundant class of bacterial Hfq-associated small regulatory RNAs (sRNAs) parallels animal microRNAs in their ability to control multiple genes at the posttranscriptional level by short and imperfect base pairing. In contrast universal length seed pairing mechanism microRNAs, sRNAs are heterogeneous size structure, how they regulate targets is not well understood. This paper provides evidence that a 5' located sRNA domain critical element for large regulon. We show conserved end RybB...
Abstract Summary: RNA-Seq has become a potent and widely used method to qualitatively quantitatively study transcriptomes. To draw biological conclusions based on data, several steps, some of which are computationally intensive, have be taken. Our READemption pipeline takes care these individual tasks integrates them into an easy-to-use tool with command line interface. leverage the full power modern computers, most subcommands offer parallel data processing. While was mainly developed for...
Using an experimental approach, we investigated the RNome of pathogen Staphylococcus aureus to identify 30 small RNAs (sRNAs) including 14 that are newly confirmed. Among latter, 10 encoded in intergenic regions, three generated by premature transcription termination associated with riboswitch activities, and one is expressed from complementary strand a transposase gene. The expression four sRNAs increases during transition exponential stationary phase. We focused our study on RsaE, sRNA...
Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping transcriptional start sites (TSSs) and identification novel transcripts. Although transcriptomes diverse bacterial species have been characterized by dRNA-Seq, analysis archaeal still rather limited. Therefore, we used dRNA-Seq to characterize model archaeon Haloferax volcanii. Three independent cultures Hfx. volcanii grown under optimal...