A5071189462- Bacterial Genetics and Biotechnology
- DNA Repair Mechanisms
- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Advanced Fluorescence Microscopy Techniques
- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Advanced Biosensing Techniques and Applications
- RNA and protein synthesis mechanisms
- Genetic factors in colorectal cancer
- Bacterial biofilms and quorum sensing
- Organic Chemistry Cycloaddition Reactions
- Evolution and Genetic Dynamics
- Enzyme Structure and Function
- Organometallic Complex Synthesis and Catalysis
- Antibiotic Resistance in Bacteria
- DNA and Nucleic Acid Chemistry
- Cellular transport and secretion
- Structural and Chemical Analysis of Organic and Inorganic Compounds
- Plant biochemistry and biosynthesis
- Enterobacteriaceae and Cronobacter Research
- Cancer Genomics and Diagnostics
- RNA Research and Splicing
University of Michigan–Ann Arbor
2015-2025
University of Wisconsin–Madison
2017-2023
University of Duisburg-Essen
2013
Bielefeld University
2009
Ohio Northern University
2008
Philipps University of Marburg
1998
University of Münster
1990
University of Göttingen
1988
Bayer (Germany)
1970
Bacterial biofilms are ubiquitous in natural environments and play an important role many clinical, industrial, ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation model bacteria such as Bacillus subtilis , very little of metabolism this complex developmental process. To address knowledge gap, we performed a time-resolved analysis metabolic changes associated with bacterial development B. by combining metabolomic,...
The concentration of ribonucleoside triphosphates (rNTPs) in cells is far greater than the deoxyribonucleoside (dNTPs), and this pool imbalance presents a challenge for DNA polymerases (Pols) to select their proper substrate. This report examines effect nucleotide on rate fidelity Escherichia coli replisome. We find that rNTPs decrease replication fork by competing with dNTPs at active site C-family Pol III replicase step does not require correct base-pairing. generalizes B-family eukaryotic...
The cardiotonic steroid marinobufagenin (MBG) has been implicated in the pathogenesis of experimental uremic cardiomyopathy, which is characterized by progressive cardiac fibrosis. We examined whether transcription factor Friend leukemia integration-1 (Fli-1) might be involved this process. Fli-1-knockdown mice demonstrated greater collagen-1 expression and fibrosis compared with wild-type mice; both developed increased collagen after 5/6 nephrectomy. There was a strong inverse relationship...
Significance We integrated single-molecule superresolution imaging with biochemical and genomic approaches to understand how the mismatch repair protein MutS efficiently identifies DNA mismatches during real time in living cells. show that molecules move fast, exploring entire nucleoid, but can transition a slow-moving population is localized at replisome even before produced. bacterial must initiate binding very close proximity replisome. also detection increases speed, supporting model for...
RecA is central to maintaining genome integrity in bacterial cells. Despite the near-ubiquitous conservation of eubacteria, pathways that facilitate loading and repair center assembly have remained poorly understood Bacillus subtilis. Here, we show rapidly colocalizes with DNA polymerase complex (replisome) immediately following damage or damage-independent replication fork arrest. In Escherichia coli, RecFOR RecBCD serve load choice between these two depends on type under repair. We found...
Bacillus subtilis is a Gram-positive soil-dwelling and endospore-forming bacterium in the phylum Firmicutes. B. strain PY79 prototrophic laboratory that has been highly used for studying wide variety of cellular pathways. Here, we announce complete whole-genome sequence PY79.
The most abundant oxidants controlling bacterial colonization on mucosal barrier epithelia are hypochlorous acid (HOCl), hypobromous (HOBr) and hypothiocyanous (HOSCN). All three highly antimicrobial but little is known about their relative efficacies, respective cellular targets, or what specific responses they elicit in bacteria. To address these important questions, we directly tested the individual virulent Pseudomonas aeruginosa strain PA14. We discovered that HOCl HOBr work almost...
<title>Abstract</title> Persisters describe phenotypically switched cells refractory to antibiotic killing in a genetically susceptible population, while preserving the ability resume growth when antibiotics are discontinued1,2. Since its proposal 70 years ago, great strides were made build framework regarding persistence, including defining triggered, spontaneous and antibiotic-induced persisters. However, challenges remain characterizing molecular determinants underlying phenotypic switch...
Abstract Determining where transcriptional regulators bind within a genome is paramount to understanding how gene expression regulated. Historically, position weight matrices (PWMs) have been used define the binding preferences of DNA proteins 1 . However, PWMs treat identity each base in sequence as an independent and additive measure preference, which can limit their utility 2 Models that consider higher order interactions between nearby bases yield greater success predicting proteins’...
ABSTRACT Bacillus subtilis is a Gram-positive bacterium that serves as an important experimental system. B. NCIB 3610 undomesticated strain exhibits phenotypes lost from the more common domesticated laboratory strains. Here, we announce complete genome sequence of DK1042, genetically competent derivative 3610.
Replicative DNA polymerases misincorporate ribonucleoside triphosphates (rNTPs) into approximately once every 2,000 base pairs synthesized. Ribonucleotide excision repair (RER) removes monophosphates (rNMPs) from genomic DNA, replacing the error with appropriate deoxyribonucleoside triphosphate (dNTP). Ribonucleotides represent a major threat to genome integrity potential cause strand breaks. Furthermore, it has been shown in bacterium Bacillus subtilis that loss of RER increases spontaneous...
Abstract The genomes of organisms from all three domains life harbor endogenous base modifications in the form DNA methylation. In bacterial genomes, methylation occurs on adenosine and cytidine residues to include N6-methyladenine (m6A), 5-methylcytosine (m5C), N4-methylcytosine (m4C). Bacterial has been well characterized context restriction-modification (RM) systems, where regulates incision by cognate restriction endonuclease. Relative RM systems less is known about how m6A contributes...
The nucleotide messenger (p)ppGpp allows bacteria to adapt fluctuating environments by reprogramming the transcriptome. Despite its well-recognized role in gene regulation, is only known directly affect transcription Proteobacteria binding RNA polymerase. Here, we reveal a different mechanism of regulation Firmicutes: binds factor PurR downregulate purine biosynthesis expression upon amino acid starvation. We first identified as receptor Bacillus anthracis. A co-structure with subtilis...
RNA:DNA hybrids compromise replication fork progression and genome integrity in all cells. The overall impacts of naturally occurring on integrity, the relative contributions ribonucleases H to mitigating negative effects hybrids, remain unknown. Here, we investigate RNases HII (RnhB) HIII (RnhC) hybrid removal, DNA replication, mutagenesis wide. Deletion either rnhB or rnhC triggers accumulation but with distinct patterns accumulation. Across cells, accumulate strongly noncoding RNAs...
DNA helicases have important roles in genome maintenance. The RecD helicase has been well studied as a component of the heterotrimeric RecBCD helicase-nuclease enzyme for double-strand break repair Escherichia coli. Interestingly, many bacteria lack RecBC and instead contain RecD2 helicase, which is not known to function part larger complex. Depending on organism studied, shown provide resistance broad range DNA-damaging agents while also contributing mismatch (MMR). Here we investigated...
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform single-cell time-lapse imaging is the mother machine, which enables long-term tracking microbial cells under precisely controlled growth conditions. While several machine pipelines have been developed in past years, adoption by non-expert audience challenge. To fill this gap, we implemented our own software, MM3, as plugin multidimensional viewer...