Daniel B. Kearns

Daniel B. Kearns
Indiana University Bloomington | IUB · Department of Biology

PhD

About

154
Publications
19,322
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7,874
Citations
Additional affiliations
November 2005 - present
Indiana University Bloomington
January 2001 - September 2005
Harvard University
September 1995 - December 2000
University of Georgia

Publications

Publications (154)
Preprint
Many bacterial species typically live in complex three-dimensional biofilms, yet little is known about systematic changes to gene function between non-biofilm and biofilm lifestyles. Here, we created a CRISPRi library of knockdown strains covering all known essential genes in the biofilm-forming Bacillus subtilis strain 3610. We show that gene esse...
Article
Bacillus subtilis exhibits swarming motility, a flagellar-mediated form of surface motility. Here, we use transposon mutagenesis and sequencing (TnSeq) to perform a high-throughput screen for candidate genes required for swarming. The TnSeq approach identified all of the known genes required for flagellar biosynthesis and nearly all of the previous...
Article
Full-text available
Transposon mutagenesis is a powerful tool for random mutagenesis, as insertion of a transposon and accompanying antibiotic resistance cassette often disrupt gene function. Here, we present a series of transposons with fluorescent protein genes which, when integrated in frame, may be selected with a fluorescence activated cell sorter (FACS).
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Full-text available
Regulatory proteolysis targets properly-folded clients via a combination of cis-encoded degron sequences and trans-expressed specificity factors called adaptors. SmiA of Bacillus subtilis was identified as the first adaptor protein for the Lon family of proteases, but the mechanism of SmiA-dependent proteolysis is unknown. Here we develop a fluores...
Preprint
Bacillus subtilis exhibits swarming motility, a flagellar-mediated form of surface motility. Here we use high-throughput transposon mutagenesis and sequencing (TnSeq) to identify candidate genes required for swarming. The TnSeq approach identified all of the known genes required for flagellar biosynthesis as well as nearly all of the previously rep...
Article
Full-text available
Bacillus subtilis can form structurally complex biofilms on solid or liquid surfaces, which requires expression of genes for matrix production. The transcription of these genes is activated by regulatory protein RemA, which binds to poorly conserved, repetitive DNA regions but lacks obvious DNA-binding motifs or domains. Here, we present the struct...
Article
During growth, bacteria increase in size and divide. Division is initiated by the formation of the Z-ring, a ring-like cytoskeletal structure formed by treadmilling protofilaments of the tubulin homolog FtsZ. FtsZ localization is thought to be controlled by the Min and Noc systems, and here, we explore why cell division fails at high temperature wh...
Article
Swarming motility is flagellar-mediated movement over a solid surface and Bacillus subtilis cells require an increase in flagellar density to swarm. SwrB is a protein of unknown function required for swarming that is necessary to increase the number of flagellar hooks but not basal bodies. Previous work suggested that SwrB activates flagellar type...
Preprint
During growth, bacteria increase in size and divide. Division is initiated by the formation of the Z-ring, an intense ring-like cytoskeletal structure formed by treadmilling protofilaments of the tubulin homolog FtsZ. FtsZ localization is thought to be controlled by the Min and Noc systems, and here, we explore why cell division fails at high tempe...
Preprint
Swarming motility is flagellar-mediated movement over a solid surface and Bacillus subtilis cells require an increase in flagellar density to swarm. SwrB is a protein of unknown function required for swarming that is necessary to increase the number of flagellar hooks but not basal bodies. Previous work suggested that SwrB activates flagellar type...
Article
Lytic enzymes play an essential role in the remodeling of bacterial peptidoglycan (PG), an extracellular mesh-like structure that retains the membrane in the context of high internal osmotic pressure. Peptidoglycan (PG) must be unfailingly stable to preserve cell integrity but must also be dynamically remodeled for the cell grow, divide and insert...
Article
Background and Aims Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. This study aims to define a role for bacterial swarmers in amelioration of intestinal stress. Methods We developed a polymicrobial plate agar assay to detect swarming and screened mice and humans with intestinal stress...
Article
Full-text available
Bacteria that divide by binary fission form FtsZ rings at the geometric midpoint of the cell between the bulk of the replicated nucleoids. In Bacillus subtilis , the DNA- and membrane-binding Noc protein is thought to participate in nucleoid occlusion by preventing FtsZ rings from forming over the chromosome. To explore the role of Noc, we used tim...
Preprint
Hydrolytic enzymes play an essential role in the remodeling of bacterial peptidoglycan (PG), an extracellular mesh-like structure that retains the membrane in the context of high internal osmotic pressure. Peptidoglycan (PG) integrity must be unfailingly stable to preserve cell integrity but must also be dynamically remodeled for the cell grow, div...
Article
Full-text available
RNA-DNA hybrids form throughout the chromosome during normal growth and under stress conditions. When left unresolved, RNA-DNA hybrids can slow replication fork progression, cause DNA breaks and increase mutagenesis. To remove hybrids, all organisms use ribonuclease H (RNase H) to specifically degrade the RNA portion. Here we show that, in addition...
Article
CsrA is a small dimeric protein that binds RNA and is one of the few known examples of transcript-specific protein regulators of translation in bacteria. A protein called FliW binds to and antagonizes CsrA to govern flagellin homeostasis and flagellar assembly. Despite having a high-resolution three-dimensional structure of the FliW-CsrA complex, t...
Preprint
Bacteria that divide by binary fission form FtsZ rings at the geometric midpoint of the cell between the bulk of the replicated nucleoids. In B. subtilis , the DNA- and membrane-binding Noc protein is thought to mediate nucleoid occlusion to prevent FtsZ rings from forming over the chromosome. To explore the role of Noc, we used time-lapse fluoresc...
Preprint
NusA and NusG are transcription elongation factors that stimulate RNA polymerase pausing in Bacillus subtilis. While NusA was known to function as an intrinsic termination factor, the role of NusG in this process had not been explored. To examine the individual and combinatorial roles that NusA and NusG play in intrinsic termination, Term-seq was c...
Preprint
Full-text available
The RNA-binding protein CsrA is a post-transcriptional regulator that is encoded in genomes throughout the bacterial phylogeny. In the gamma-proteobacteria, the activity of CsrA is inhibited by small RNAs that competitively sequester CsrA binding. In contrast, the firmicute Bacillus subtilis encodes a protein inhibitor of CsrA called FliW, that non...
Article
The ancestral strain of Bacillus subtilis NCIB3610 (3610) encodes a large, low copy number plasmid called pBS32 that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been due to the fact that it encodes a potent inhibitor of natural genetic competence (ComI), as lab strains were selected for high...
Article
Group A Streptococcus (GAS) displays cell-surface proteins that resemble human collagen. We find that a fluorophore-labeled collagen mimetic peptide (CMP) labels GAS cells but not Escherichia coli or Bacillus subtilis cells, which lack such proteins. The CMP likely engages in a heterotrimeric helix with endogenous collagen, as the nonnatural D en...
Article
Full-text available
Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize surfaces. Physically, swarming is a natural example for active particles that use energy to generate motion. Accordingly, understanding the constraints physics imposes on these dynamics is essential for understanding the mechanisms underlying s...
Article
Full-text available
Many bacteria grow and divide by binary fission in which a mother cell divides into two identical daughter cells. To produce two equally sized daughters, the division machinery, guided by FtsZ, must dynamically localize to the midcell each cell cycle. Here, we quantitatively analyzed FtsZ dynamics during growth and found that the Min system of Baci...
Article
Random transposon mutagenesis is a powerful and unbiased genetic approach to answer fundamental biological questions. Here, we introduce an improved mariner -based transposon system with an enhanced stability during propagation and versatile applications in mutagenesis. We used a low copy number plasmid as a transposon delivery vehicle that affords...
Article
Selective chemical probes enable individual investigation of penicillin-binding proteins (PBPs) and provide critical information about their enzymatic activity with spatial and temporal resolution. To identify scaffolds for novel probes to study peptidoglycan biosynthesis in Bacillus subtilis, we evaluated the PBP inhibition profiles of 21 β-lactam...
Article
Translation elongation factor P (EF-P) is conserved in all three domains of life (called eIF5A and aIF5A in eukaryotes and archaea, respectively) and functions to alleviate ribosome pausing during the translation of specific sequences, including consecutive proline residues. EF-P was identified in 1975 as a factor that stimulated the peptidyltransf...
Article
The presence or absence of oxygen in the environment is a strong effector of cellular metabolism and physiology. Like many eukaryotes and some bacteria, Bacillus subtilis primarily utilizes oxygen during respiration to generate ATP. Despite the importance of oxygen for B. subtilis survival, we know little about how populations adapt to shifts in ox...
Preprint
Selective chemical probes enable individual investigation of penicillin-binding proteins (PBPs) and provide critical information about their enzymatic activity with spatial and temporal resolution. To identify scaffolds for novel probes to study peptidoglycan biosynthesis in Bacillus subtilis, we evaluated the PBP inhibition profiles of 21 β-lactam...
Preprint
A microfluidic system coupled with fluorescence microscopy is a powerful approach for quantitative analysis of bacterial growth. Here, we measure parameters of growth and dynamic localization of the cell division initiation protein FtsZ in Bacillus subtilis . Consistent with previous reports, we find that after division FtsZ rings remain at the cel...
Preprint
Full-text available
Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize a surface. Physically, swarming is a natural example of active particles that use energy to generate motion. Accordingly, understanding the constraints physics imposes on the dynamics is essential to understand the mechanisms underlying the swa...
Preprint
Random transposon mutagenesis is a powerful genetic tool to answer fundamental biological questions in an unbiased approach. Here, we introduce an improved mariner-based transposon system with higher stability, and with versatile applications. We take advantage of the lower frequency of unintended recombination during vector construction and propag...
Article
Full-text available
Laboratory strains of Bacillus subtilis encode many alternative sigma factors, each dedicated to expressing a unique regulon such as those involved in stress resistance, sporulation, and motility. The ancestral strain of B. subtilis also encodes an additional sigma factor homolog, ZpdN, not found in lab strains due to being encoded on the large, lo...
Article
Bacteria move by a variety of mechanisms, but the best understood types of motility are powered by flagella (72). Flagella are complex machines embedded in the cell envelope with a long extracellular helical filament and rotates like a propeller to push cells through the environment. The flagellum is one of relatively few biological machines that e...
Preprint
Bacterial swarming is a conserved and distinct form of bacterial motility that allows for rapid migration over a surface. Swarming motility is often oppositely regulated and antagonistic to biofilm formation. To-date, while bacterial biofilms have been associated with pathogenesis and pathobiology of human diseases (e.g., infections, inflammation a...
Article
Bacteria have developed numerous protection strategies to ensure survival in harsh environments, with perhaps the most robust method being the formation of a protective biofilm. In biofilms, bacterial cells are embedded within a matrix that is composed of a complex mixture of polysaccharides, proteins and DNA. The Gram-positive bacterium Bacillus s...
Preprint
The presence or absence of oxygen in the environment is a strong effector of cellular metabolism and physiology. Like many eukaryotes and some bacteria, Bacillus subtilis is an obligate aerobe that primarily utilizes oxygen during respiration to generate ATP. Despite the importance of oxygen for B. subtilis survival, we know little about how oxygen...
Article
Full-text available
Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues, and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviates ribosome pausing at sequences encoding tandem prolines and ribosomes paused within several essential genes without a co...
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Full-text available
The intracellular concentration of flagellar filament protein Hag is restricted by the Hag-FliW-CsrA system in B. subtilis . Here we show that the Hag-FliW-CsrA dimer system functions at nearly 1:1:1 stoichiometry and that the system is both robust with respect to perturbation and hypersensitive to the Hag intracellular concentration. Moreover, res...
Preprint
Laboratory strains of Bacillus subtilis encodes as many as 16 alternative sigma factors, each dedicated to expressing a unique regulon such as those involved in stress resistance, sporulation, and motility. The ancestral strain of B. subtilis also encodes an additional sigma factor homolog, ZpdN, not found in lab strains due to it being encoded on...
Article
The bacterial secondary metabolite cyclic di-GMP is a widespread, cytoplasmic signal that promotes a physiological transition in which motility is inhibited and biofilm formation is activated. A paper published in this issue (A. E. Baker, S. S. Webster, A. Diepold, S. L. Kuchma, E. Bordeleau, et al., J Bacteriol 201:e00741-18, 2019, https://doi.org...
Article
Flagellar motility plays key roles in the survival of many bacteria and in the harmful action of many pathogens. Bacterial flagella rotate; the direction of flagellar rotation is controlled by a multisubunit protein complex termed the switch complex. This complex has been extensively studied in Gram-negative model species, but little is known about...
Article
Bacterial flagella contain an axle-like rod that transits the cell envelope and connects the transmembrane basal body to the extracellular hook and filament. Although the rod is a crucial component of the flagellum, its structure and assembly are poorly understood. Previous reports defining the order of rod assembly in Gram-negative bacteria sugges...
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Full-text available
Flagellin is amongst the most abundant proteins in flagellated bacterial species and constitutes the major building block of the flagellar filament. The proteins FliW and FliS serve in the post-transcriptional control of flagellin and guide the protein to the flagellar type III secretion system (fT3SS), respectively. Here, we present the high-resol...
Article
Full-text available
Elongation factor P (EF-P) is a ubiquitous translation factor that facilitates translation of polyproline motifs. In order to perform this function, EF-P generally requires posttranslational modification (PTM) on a conserved residue. Although the position of the modification is highly conserved, the structure can vary widely between organisms. In B...
Article
Full-text available
SwrA is the master activator of flagellar biosynthesis in Bacillus subtilis and SwrA activity is restricted by regulatory proteolysis in liquid environments. SwrA is proteolyzed by the LonA protease but requires a proteolytic adaptor protein, SmiA. Here we show that SwrA and SmiA interact directly. To better understand SwrA activity, SwrA was rando...
Article
Full-text available
Enteric viruses encounter diverse environments as they migrate through the gastrointestinal tract to infect their hosts. The interaction of eukaryotic viruses with members of the host microbiota can greatly impact various aspects of virus biology, including the efficiency with which viruses can infect their hosts. Mammalian orthoreovirus, a human e...
Data
Effects of temperature on reovirus virion and ISVP stability. (A) Reovirus T1L and T3D were incubated in PBS at 28°C for indicated times, adsorbed on HeLa cells at an MOI of 5×103 particles/cell, and assessed for infectivity at 18 hpi by indirect immunofluorescence. (B, C, D) Reovirus T1L and T3D ISVPs were incubated in PBS at (B) RT, (C) 28°C, or...
Data
Lipopolysaccharide and peptidoglycan protect reovirus from loss of attachment and infectivity of colonic epithelial cells. Reovirus T1L and T3D were not incubated, incubated with PBS, detoxified LPS (dLPS), LPS, or PG for 2 h at room temperature. (A) Caco2 cells were adsorbed with A633-labeled reovirus at an MOI of 5×103 particles/cell and assessed...
Data
Lipopolysaccharide and peptidoglycan enhance reovirus thermostability at multiple temperatures. Reovirus T3D (A) virions or (B) ISVPs were not incubated, incubated with PBS, 50 μg/ml LPS, or 50 μg/ml PG for 2 h at RT, 28°C, or 37°C. HeLa cells were adsorbed with reovirus at an MOI of (A) 5×103 particles/cell for virions or (B) 1×103 particles/cell...
Data
Lipopolysaccharide and peptidoglycan do not enhance reovirus infectivity. Reovirus T1L and T3D (A) virions or (B) ISVPs were not incubated, incubated with PBS, LPS, or PG for 2 h at 4°C. HeLa cells were adsorbed with reovirus at an MOI of (A) 5×103 particles/cell with virions or (B) 1×103 particles/cell with ISVPs, incubated for 18 h, and scored fo...
Article
Full-text available
Stator elements consisting of MotA4MotB2 complexes are anchored to the cell wall, extend through the cell membrane, and interact with FliG in the cytoplasmic C ring rotor of the flagellum. The cytoplasmic loop of MotA undergoes proton-driven conformational changes that drive flagellar rotation. Functional regulators inhibit motility by either disen...
Article
The bacterium Bacillus subtilis is capable of two methods of flagellar mediated motility: swimming, which occurs in liquid, and swarming, which occurs on a surface. Swarming is distinct from swimming in that it requires secretion of a surfactant, an increase in flagellar density, and perhaps additional factors. Here we report a new gene, swrD , enc...
Article
Full-text available
The bacterial flagellar filament has long been studied to understand how a polymer composed of a single protein can switch between different supercoiled states with high cooperativity. Here we present near-atomic resolution cryo-EM structures for flagellar filaments from both Gram-positive Bacillus subtilis and Gram-negative Pseudomonas aeruginosa....
Article
Bacillus subtilis flagella are not only required for locomotion but also act as sensors that monitor environmental changes. Although how the signal transmission takes place is poorly understood, it has been shown that flagella play an important role in surface sensing by transmitting a mechanical signal to control the DegS-DegU two-component system...
Article
Translation elongation factor P (EF‐P) in Bacillus subtilis is required for a form of surface migration called swarming motility. Furthermore, B. subtilis EF‐P is post‐translationally modified with a 5‐aminopentanol group but the pathway necessary for the synthesis and ligation of the modification is unknown. Here we determine that the protein YmfI...
Article
Translation elongation factor P (EF-P) in Bacillus subtilis is required for a form of surface migration called swarming motility. Furthermore, B. subtilis EF-P is post-translationally modified with a 5-aminopentanol group but the pathway necessary for the synthesis and ligation of the modification is unknown. Here we determine that the protein YmfI...
Article
Bacterial swimming in confined two-dimensional environments is ubiquitous in nature and in clinical settings. Characterizing individual interactions between swimming bacteria in 2D confinement will help to understand diverse microbial processes, such as bacterial swarming and biofilm formation. Here we report a novel motion pattern displayed by fla...
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Full-text available
Bacillus subtilis is a Gram-positive bacterium that serves as an important experimental system. B. subtilis NCIB 3610 is an undomesticated strain that exhibits phenotypes lost from the more common domesticated laboratory strains. Here, we announce the complete genome sequence of DK1042, a genetically competent derivative of NCIB 3610.
Article
Swarming bacteria collectively migrate on surfaces using flagella, forming dynamic whirls and jets that consist of millions of individuals. Because some swarming bacteria elongate prior to actual motion, cell aspect ratio may play a significant role in the collective dynamics. Extensive research on self-propelled rodlike particles confirms that elo...
Article
CsrA (carbon storage regulator A) is a widely distributed bacterial RNA binding protein that regulates translation initiation and mRNA stability of target transcripts. In γ-proteobacteria, CsrA activity is competitively antagonized by one or more small RNAs (sRNAs) containing multiple CsrA binding sites, but CsrA in bacteria outside the γ-proteobac...
Article
Importance: Prophages are phage genomes stably integrated into the host bacterium's chromosome and less frequently into extrachromosomal plasmids. Here we report that the extrachromosomal plasmid pBS32 of Bacillus subtilis encodes a prophage which, when activated, kills the host. pBS32 also encodes a sigma factor homolog, ZpdN that is necessary an...
Article
Full-text available
Following the success of the inaugural games, the Microbial Olympics return with a new series of events and microbial competitors. The games may have moved to a new hosting venue, but the dedication to training, fitness, competition (and yes, education and humour) lives on.
Article
Recent advances in cryo-electron tomography (cryo-ET) have allowed direct visualization of the initial interactions between bacteriophages and their hosts. Previous studies focused on phage infection in Gram-negative bacteria but it is of particular interest how phages penetrate the thick, highly cross-linked Gram-positive cell wall. Here we detail...
Article
Full-text available
Elongation factor P (EF-P) accelerates diprolyl synthesis and requires a posttranslational modification (PTM) to maintain proteostasis. Two phylogenetically distinct EF-P modification pathways have been described and are encoded in the majority of Gram-negative bacteria, but neither is present in Gram-positive bacteria. Prior work suggested the EF-...