Papers by Sine Svenningsen
PRX Life
Safe experimentation addressing the spread of epidemic disease requires extreme care. Risks can b... more Safe experimentation addressing the spread of epidemic disease requires extreme care. Risks can be avoided through the development of model systems where analogs of epidemic processes can be manipulated in the laboratory and compared with predictions from mathematical models. Here we describe an integrated mathematical and experimental analysis of a vector-borne disease. The experimental system we developed, "malaria in a Petri dish," requires alternating host bacteria to propagate a dimorphic virus. Unlike typical vector-borne diseases, this model system uses only nonhazardous and inexpensive materials. We quantified the growth properties of the hosts and viral forms and examined the spread of the virus between independent bacterial microcolonies in an immobilized suspension. The combined model and experiment found the spatial constraints imposed by alternating microcolony infections strongly inhibited the spread of the disease. Our mathematical model allowed us to mimic the propagation of the infections and predicted how propagation increased when the spatial heterogeneity was decreased. The model also correctly predicted the efficiency of herd immunity when immunizing a fraction of the bacterial population.
tRNAs Are Stable After All: Pitfalls in Quantification of tRNA from Starved Escherichia coli Cultures Exposed by Validation of RNA Purification Methods
mBio
We show that E. coli tRNAs are remarkably stable during several days of nutrient starvation, alth... more We show that E. coli tRNAs are remarkably stable during several days of nutrient starvation, although rRNA is degraded extensively under these conditions. The levels of these two major RNA classes are considered to be strongly coregulated at the level of transcription.
Strain‐specific quorum‐sensing responses determine virulence properties in Vibrio anguillarum
Environmental Microbiology
Bacterial populations communicate using quorum‐sensing (QS) molecules and switch on QS regulation... more Bacterial populations communicate using quorum‐sensing (QS) molecules and switch on QS regulation to engage in coordinated behaviour such as biofilm formation or virulence. The marine fish pathogen Vibrio anguillarum harbours several QS systems, and our understanding of its QS regulation is still fragmentary. Here, we identify the VanT‐QS regulon and explore the diversity and trajectory of traits under QS regulation in Vibrio anguillarum through comparative transcriptomics of two wildtype strains and their corresponding mutants artificially locked in QS‐on (ΔvanO) or QS‐off (ΔvanT) states. Intriguingly, the two wildtype populations showed different QS responses to cell density changes and operated primarily in the QS‐on and QS‐off spectrum, respectively. Examining 27 V. anguillarum strains revealed that ~11% were QS‐negative, and GFP‐reporter measurements of nine QS‐positive strains revealed a highly strain‐specific nature of the QS responses. We showed that QS controls a plethora o...
Microbiology Spectrum, 2022
Horizontal transfer of DNA between bacterial cells contributes to the spread of virulence and ant... more Horizontal transfer of DNA between bacterial cells contributes to the spread of virulence and antibiotic resistance genes in human pathogens. For Staphylococcus aureus , bacterial viruses play a major role in facilitating the horizontal transfer.
Viruses, 2021
Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free φ919TP p... more Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of V. cholerae and its interaction with a modified lytic variant of the induced prophage (φ919TP cI-). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage φ919TP cI-. Further, the comparative genomic analysis of wild-type and φ919TP cI--resistant mutant predicted that phage φ919TP cI- selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene gmd. Our study showed that the gmd-mediated O-antigen defect can cause pleiot...
Bacteriophage-mediated transduction of bacterial DNA is a major route of horizontal gene transfer... more Bacteriophage-mediated transduction of bacterial DNA is a major route of horizontal gene transfer in the human pathogen, Staphylococcus aureus. Transduction involves packaging of bacterial DNA by viruses and enables transmission of virulence and resistance genes between cells. To learn more about transduction in S. aureus, we searched a transposon mutant library for genes and mutations that enhanced transfer mediated by the temperate phage, φ11. Using a novel screening strategy, we performed multiple rounds of transduction of transposon mutant pools selecting for an antibiotic resistance marker within the transposon element. When determining the locations of transferred mutations, we found that, within each pool of 96 mutants the screen had selected for just 1 or 2 transposon mutant(s). Subsequent analysis showed that the position of the transposon, rather than inactivation of bacterial genes, was responsible for the phenotype. Interestingly, from multiple rounds we identified a pat...
Viruses, 2020
Zonula occludens toxin (Zot) is a conserved protein in filamentous vibriophages and has been repo... more Zonula occludens toxin (Zot) is a conserved protein in filamentous vibriophages and has been reported as a putative toxin in Vibrio cholerae. Recently, widespread distribution of zot-encoding prophages was found among marine Vibrio species, including environmental isolates. However, little is known about the dynamics of these prophages beyond V. cholerae. In this study, we characterized and quantified the zot-encoding filamentous phage VAIϕ, spontaneously induced from the fish pathogen V. anguillarum. VAIϕ contained 6117 bp encoding 11 ORFs, including ORF8pVAI, exhibiting 27%–73% amino acid identity to Inovirus Zot-like proteins. A qPCR method revealed an average of four VAIϕ genomes per host genome during host exponential growth phase, and PCR demonstrated dissemination of induced VAIϕ to other V. anguillarum strains through re-integration in non-lysogens. VAIϕ integrated into both chromosomes of V. anguillarum by recombination, causing changes in a putative ORF in the phage genome...
The ISME Journal, 2020
Temperate ϕH20-like phages are repeatedly identified at geographically distinct areas as free pha... more Temperate ϕH20-like phages are repeatedly identified at geographically distinct areas as free phage particles or as prophages of the fish pathogen Vibrio anguillarum. We studied mutants of a lysogenic isolate of V. anguillarum locked in the quorumsensing regulatory modes of low (ΔvanT) and high (ΔvanO) cell densities by in-frame deletion of key regulators of the quorum-sensing pathway. Remarkably, we find that induction of the H20-like prophage is controlled by the quorum-sensing state of the host, with an eightfold increase in phage particles per cell in high-cell-density cultures of the quorum-sensingdeficient ΔvanT mutant. Comparative studies with prophage-free strains show that biofilm formation is promoted at low cell density and that the H20-like prophage stimulates this behavior. In contrast, the high-cell-density state is associated with reduced prophage induction, increased proteolytic activity, and repression of biofilm. The proteolytic activity may dually function to disperse the biofilm and as a quorum-sensing-mediated antiphage strategy. We demonstrate an intertwined regulation of phage-host interactions and biofilm formation, which is orchestrated by host quorum-sensing signaling, suggesting that increased lysogeny at high cell density is not solely a strategy for phages to piggy-back the successful bacterial hosts but is also a host strategy evolved to take control of the lysis-lysogeny switch to promote host fitness.
Small RNA-Based Regulation of Bacterial Quorum Sensing and Biofilm Formation
Microbiology Spectrum, 2018
Quorum sensing is a vital property of bacteria that enables community-wide coordination of collec... more Quorum sensing is a vital property of bacteria that enables community-wide coordination of collective behaviors. A key example of such a behavior is biofilm formation, in which groups of bacteria invest in synthesizing a protective, joint extracellular matrix. Quorum sensing involves the production, release, and subsequent detection of extracellular signaling molecules called autoinducers. The architecture of quorum-sensing signal transduction pathways is highly variable among different species of bacteria, but frequently involves posttranscriptional regulation carried out by small regulatory RNA molecules. This review illustrates the diverse roles small trans -acting regulatory RNAs can play, from constituting a network’s core to auxiliary roles in adjusting the rate of autoinducer synthesis, mediating cross talk among different parts of a network, or integrating different regulatory inputs to trigger appropriate changes in gene expression. The emphasis is on describing how the stu...
Trends in Microbiology, 2019
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Proceedings of the National Academy of Sciences, 2018
Significance Virtually all organisms require vitamin B1, including bacterioplankton that impact n... more Significance Virtually all organisms require vitamin B1, including bacterioplankton that impact nutrient cycling and productivity in aquatic systems and Earth’s climate. Here, we show that B1 auxotrophy, the need for exogenous B1 or precursors for survival, is widespread among wild bacterioplankton. Genetic analyses of wild bacterioplankton revealed that most are B1 auxotrophs and the abundance of several B1-related genotypes changes temporally at an estuarine monitoring station, suggesting that B1/precursor availability influences bacterioplankton succession. Complementarily, in-field nutrient-amendment experiments and bioassays indicate that B1/precursor bioavailability periodically limits bulk growth of bacterioplankton. Together the presented data highlight the prevalent reliance of bacterioplankton upon exogenous B1/precursors and suggest a hitherto overlooked influence of B1/precursor availability on aquatic biochemical cycling.
FEMS Microbiology Ecology, 2019
The study highlights the diversity of phage defense mechanisms in the fish pathogen Vibrio anguil... more The study highlights the diversity of phage defense mechanisms in the fish pathogen Vibrio anguillarum, and demonstrates that phage resistance affects the fitness and virulence of this pathogen.
Frontiers in microbiology, 2017
Bacteriophages are the most abundant organisms on the planet and both lytic and temperate phages ... more Bacteriophages are the most abundant organisms on the planet and both lytic and temperate phages play key roles as shapers of ecosystems and drivers of bacterial evolution. Temperate phages can choose between (i) lysis: exploiting their bacterial hosts by producing multiple phage particles and releasing them by lysing the host cell, and (ii) lysogeny: establishing a potentially mutually beneficial relationship with the host by integrating their chromosome into the host cell's genome. Temperate phages exhibit lysogeny propensities in the curiously narrow range of 5-15%. For some temperate phages, the propensity is further regulated by the multiplicity of infection, such that single infections go predominantly lytic while multiple infections go predominantly lysogenic. We ask whether these observations can be explained by selection pressures in environments where multiple phage variants compete for the same host. Our models of pairwise competition, between phage variants that diff...
Journal of Visualized Experiments, 2017
Nucleic acids research, Jan 29, 2016
Due to its long half-life compared to messenger RNA, bacterial transfer RNA is known as stable RN... more Due to its long half-life compared to messenger RNA, bacterial transfer RNA is known as stable RNA. Here, we show that tRNAs become highly unstable as part of Escherichia coli's response to amino acid starvation. Degradation of the majority of cellular tRNA occurs within twenty minutes of the onset of starvation for each of several amino acids. Both the non-cognate and cognate tRNA for the amino acid that the cell is starving for are degraded, and both charged and uncharged tRNA species are affected. The alarmone ppGpp orchestrates the stringent response to amino acid starvation. However, tRNA degradation occurs in a ppGpp-independent manner, as it occurs with similar kinetics in a relaxed mutant. Further, we also observe rapid tRNA degradation in response to rifampicin treatment, which does not induce the stringent response. We propose a unifying model for these observations, in which the surplus tRNA is degraded whenever the demand for protein synthesis is reduced. Thus, the t...
On the role of Cro in l prophage induction
Proceedings of the National Academy of Sciences of the United States of America, 2005
mBio, 2015
ABSTRACTSelection for phage resistance is a key driver of bacterial diversity and evolution, and ... more ABSTRACTSelection for phage resistance is a key driver of bacterial diversity and evolution, and phage-host interactions may therefore have strong influence on the genetic and functional dynamics of bacterial communities. In this study, we found that an important, but so far largely overlooked, determinant of the outcome of phage-bacterial encounters in the fish pathogenVibrio anguillarumis bacterial cell-cell communication, known as quorum sensing. Specifically,V. anguillarumPF430-3 cells locked in the low-cell-density state (ΔvanTmutant) express high levels of the phage receptor OmpK, resulting in a high susceptibility to phage KVP40, but achieve protection from infection by enhanced biofilm formation. By contrast, cells locked in the high-cell-density state (ΔvanΟmutant) are almost completely unsusceptible due to quorum-sensing-mediated downregulation of OmpK expression. The phenotypes of the two quorum-sensing mutant strains are accurately reflected in the behavior of wild-typeV...
Redundant small RNAs and feedback control in Vibrio cholerae and Vibrio harveyi quorum sensing
Small RNA target genes and regulatory connections in the Vibrio cholerae quorum sensing system
The two-component quorum sensing (QS) system, first described in the marine bacterium Vibrio harv... more The two-component quorum sensing (QS) system, first described in the marine bacterium Vibrio harveyi and evolutionarily conserved among members of the genus Vibrio, has been best studied in the human pathogen Vibrio cholerae (1, 2). In the V. cholerae QS system, the response to the accumulation of extracellular autoinducers triggers a signaling cascade resulting in the transcription of four small regulatory RNAs (sRNAs). Our results support the model that the QS sRNAs bind to the 5' untranslated region of multiple mRNAs and alter the fate of one in a positive manner and several others in a negative manner. This mechanism ensures the proper timing of the QS response, which includes the expression of traits critical for virulence and for the formation of biofilms (2-6).
A key event in development is the irreversible commitment to a particular cell fate, which may be... more A key event in development is the irreversible commitment to a particular cell fate, which may be concurrent with or delayed with respect to the initial cell fate decision. In this work, we use the paradigmatic bacteriophage lysis-lysogeny decision circuit to study the timing of commitment. The lysis-lysogeny decision is made based on the expression trajectory of CII. The chosen developmental strategy is manifested by repression of the pR and pL promoters by CI (lysogeny) or by antitermination of late gene expression by Q (lysis). We found that expression of Q in trans from a plasmid at the time of infection resulted in a uniform lytic decision. Furthermore, expression of Q up to 50 min after infection results in lysis of the majority of cells which initially chose lysogenic development. In contrast, expression of Q in cells containing a single chromosomal prophage had no effect on cell growth, indicating commitment to lysogeny. Notably, if the prophage was present in 10 plasmid-borne copies, Q expression resulted in lytic development, suggesting that the cellular phage chromosome number is the critical determinant of the timing of lysogenic commitment. Based on our results, we conclude that (i) the lysogenic decision made by the CI-Cro switch soon after infection can be overruled by ectopic Q expression at least for a time equivalent to one phage life cycle, (ii) the presence of multiple chromosomes is a prerequisite for a successful Q-mediated switch from lysogenic to lytic development, and (iii) phage chromosomes within the same cell can reach different decisions.
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Papers by Sine Svenningsen