A5068627804- Bacterial Genetics and Biotechnology
- Enzyme Structure and Function
- Bacteriophages and microbial interactions
- DNA Repair Mechanisms
- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Bacterial biofilms and quorum sensing
- RNA and protein synthesis mechanisms
- Advanced Biosensing Techniques and Applications
- Biochemical and Molecular Research
- Advanced Fluorescence Microscopy Techniques
- Protein Structure and Dynamics
- Amino Acid Enzymes and Metabolism
- Porphyrin Metabolism and Disorders
- DNA and Nucleic Acid Chemistry
- Heat shock proteins research
- Polyamine Metabolism and Applications
- Chromosomal and Genetic Variations
- Antimicrobial Resistance in Staphylococcus
- Mitochondrial Function and Pathology
- Chemical Synthesis and Analysis
- Antibiotic Resistance in Bacteria
- Probiotics and Fermented Foods
- Coenzyme Q10 studies and effects
University of Wisconsin–Madison
2015-2025
Shandong Provincial Hospital
2024
Shandong University
2024
Sun Yat-sen Memorial Hospital
2024
Sun Yat-sen University
2024
University of Freiburg
2016
Baylor College of Medicine
2007-2014
Massachusetts Institute of Technology
2004-2007
National Institutes of Health
2007
Zhejiang University of Technology
2007
Whole-genome sequencing is a powerful technique for obtaining the reference sequence information of multiple organisms. Its use can be dramatically expanded to rapidly identify genomic variations, which linked with phenotypes obtain biological insights. We explored these potential applications using emerging next-generation platform Solexa Genome Analyzer, and well-characterized model bacterium Bacillus subtilis. Combining experimental verification, we first improved accuracy published B....
In many bacteria, there is a genome-wide bias towards co-orientation of replication and transcription, with essential and/or highly-expressed genes further enriched co-directionally. We previously found that reversing this in the bacterium Bacillus subtilis slows elongation, we proposed effect contributes to evolutionary pressure selecting transcription-replication bias. This selection might have been based purely on for speedy replication; alternatively, slowed actually represent an average...
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,...
ABSTRACT The stringent response (SR), mediated by the alarmone (p)ppGpp, is a conserved bacterial adaptation system controlling broad metabolic alterations necessary for survival under adverse conditions. In Enterococcus faecalis , production of (p)ppGpp controlled bifunctional protein RSH (for “Rel SpoT homologue”; also known as RelA) and monofunctional synthetase RelQ. Previous characterization E. strains lacking rsh relQ or both revealed that responsible activation SR in negatively impact...
The bacterial stringent response (SR) is a conserved stress tolerance mechanism that orchestrates physiological alterations to enhance cell survival. This mediated by the intracellular accumulation of alarmones pppGpp and ppGpp, collectively called (p)ppGpp. In Enterococcus faecalis, (p)ppGpp metabolism carried out bifunctional synthetase/hydrolase E. faecalis Rel (RelEf) small alarmone synthetase (SAS) RelQEf. Although main enzyme responsible for SR activation in Firmicutes, there emerging...
ABSTRACT Gluconeogenesis, the reciprocal pathway of glycolysis, is an energy-consuming process that generates glycolytic intermediates from non-carbohydrate sources. In this study, we demonstrate robust and efficient gluconeogenesis in bacteria relies on allosteric inactivation pyruvate kinase, enzyme responsible for irreversible final step glycolysis. Using model bacterium Bacillus subtilis as example, discovered kinase activity inhibited during via its extra C-terminal domain (ECTD), which...
In many bacteria, there is a strong bias for genes to be encoded on the leading strand of DNA, resulting in coorientation replication and transcription. Bacillus subtilis, transcription majority (75%) cooriented with replication. By using genome-wide profiling DNA microarrays, we found that this reduces adverse effects We wild-type cells, did not appear affect rate elongation. However, mutants reversed an extended region chromosome, elongation was slower. This reduced depended limited which...
The nucleotide (p)ppGpp inhibits GTP biosynthesis in the Gram-positive bacterium Bacillus subtilis. Here we examined how this regulation allows cells to grow absence of amino acids. We showed that B. subtilis lacking (p)ppGpp, due either deletions or point mutations all three synthetase genes, yjbM, ywaC, and relA, strongly require supplementation leucine, isoleucine, valine, methionine, threonine modestly additional This polyauxotrophy is rescued by reducing levels. Reduction levels...
DNA replication in Escherichia coli is normally initiated at a single origin, oriC, dependent on initiation protein DnaA. However, can be elsewhere the chromosome multiple ectopic oriK sites. Genetic evidence indicates that from depends RNA-DNA hybrids (R-loops), which are removed by enzymes such as RNase HI to prevent misfiring during normal growth. Initiation sites occurs HI-deficient mutants, and possibly wild-type cells under certain unusual conditions. Despite previous work, locations...
Abstract The alarmone nucleotides guanosine tetraphosphate and pentaphosphate, commonly referred to as (p)ppGpp, regulate bacterial responses nutritional other stresses. There is evidence for potential existence of a third alarmone, guanosine-5′-monophosphate-3′-diphosphate (pGpp), with less-clear functions. Here, we demonstrate the presence pGpp in cells, perform comprehensive screening identify proteins that interact respectively pGpp, ppGpp pppGpp Bacillus species. Both involved...
DNA damage and perturbations in replication can induce global transcriptional responses that help organisms repair the survive. RecA is known to mediate several bacterial species by inactivating repressor LexA phage repressors. To gain insight into how Bacillus subtilis responds various types of damage, we measured effects on mRNA levels using microarrays. We perturbed either directly with p-hydroxyphenylazo-uracil (HPUra), an inhibitor polymerase, or indirectly DNA-damaging reagents...