[Show abstract][Hide abstract] ABSTRACT: Amphiphilic aminoglycoside antibiotics kill bacteria by disruption of their highly negatively charged membrane. In their Communication (DOI:10.1002/anie.201200761), M. Fridman and co-workers report the synthesis of 6''-thioether tobramycin derivatives and show that their aliphatic chain acts as a drill bit that can rupture bacterial cells. These potent compounds evade many of the common bacterial resistance mechanisms, thereby opening a new avenue for the discovery of membrane-targeting antibiotics.
Angewandte Chemie International Edition 05/2012; · 11.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Amphiphilic tobramycin analogues with potent antibacterial activity against tobramycin-resistant bacteria were synthesized. Most analogues were found to be less prone to deactivation by aminoglycoside-modifying enzymes than tobramycin. These compounds target the bacterial membrane rather than the ribosome. The lipophilic residue of these analogues is key to their antibacterial potency and selectivity towards bacterial membranes.
Angewandte Chemie International Edition 04/2012; 51(23):5652-6. · 11.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Signaling photoreceptors mediate diverse organismal adaptations in response to light. As light-gated protein switches, signaling photoreceptors provide the basis for optogenetics, a term that refers to the control of organismal physiology and behavior by light. We establish as novel optogenetic tools the plasmids pDusk and pDawn, which employ blue-light photoreceptors to confer light-repressed or light-induced gene expression in Escherichia coli with up to 460-fold induction upon illumination. Key features of these systems are low background activity, high dynamic range, spatial control on the 20-μm scale, independence from exogenous factors, and ease of use. In optogenetic experiments, pDusk and pDawn can be used to specifically perturb individual nodes of signaling networks and interrogate their role. On the preparative scale, pDawn can induce by light the production of recombinant proteins and thus represents a cost-effective and readily automated alternative to conventional induction systems.
Journal of Molecular Biology 03/2012; 416(4):534-42. · 3.91 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Amphiphilic aminoglycoside antibiotics kill bacteria by disruption of their highly negatively charged membrane. In their Communication on page 5652 ff., M. Fridman, S. Garneau‐Tsodikova, and co‐workers report the synthesis of 6′′‐thioether tobramycin derivatives and show that their aliphatic chain acts as a drill bit that can rupture bacterial cells. These potent compounds evade many of the common bacterial resistance mechanisms, thereby opening a new avenue for the discovery of membrane‐targeting antibiotics.
Angewandte Chemie International Edition 01/2012; 51(23). · 11.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Amphiphile Aminoglycosid‐Antibiotika töten Bakterien durch Zerstörung ihrer hoch negativ geladenen Membran. In der Zuschrift auf S. 5750 ff. beschreiben M. Fridman, S. Garneau‐Tsodikova et al. 6′′‐Thioether‐Tobramycin‐Derivate und zeigen, dass deren aliphatische Kette wie ein Bohrer wirkt, der Bakterienzellen aufbrechen kann. Diese wirksamen Verbindungen umgehen viele der gewöhnlichen bakteriellen Abwehrmechanismen und ebnen so einen neuen Weg für die Erforschung von Antibiotika, die die Membran angreifen.
[Show abstract][Hide abstract] ABSTRACT: Bacterial phenotypic variability--the display of multiple distinct phenotypes in a genetically homogenous population of bacteria-emerges as an adaptive response to conflicting challenges. This creates an opportunity for social interactions which are able to dynamically redistribute cell fates within a community and to directly share the benefits of the different fates. While social interactions between cell fates can optimize community behavior, they also make the community vulnerable to exploitation. The aim of this review is to emphasize the social roles of phenotypic variability and introduce it as a communal rather than a single-cell property. Specifically, we present two prevalent perspectives on the forces shaping social interactions between cell fates--engineering optimality and social stability--and review recent works combining engineering, developmental and social evolution analyses in light of this distinction.
Current opinion in genetics & development 12/2011; 21(6):759-67. · 8.99 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In microbial "quorum sensing" (QS) communication systems, microbes produce and respond to a signaling molecule, enabling a cooperative response at high cell densities. Many species of bacteria show fast, intraspecific, evolutionary divergence of their QS pathway specificity--signaling molecules activate cognate receptors in the same strain but fail to activate, and sometimes inhibit, those of other strains. Despite many molecular studies, it has remained unclear how a signaling molecule and receptor can coevolve, what maintains diversity, and what drives the evolution of cross-inhibition. Here I use mathematical analysis to show that when QS controls the production of extracellular enzymes--"public goods"--diversification can readily evolve. Coevolution is positively selected by cycles of alternating "cheating" receptor mutations and "cheating immunity" signaling mutations. The maintenance of diversity and the evolution of cross-inhibition between strains are facilitated by facultative cheating between the competing strains. My results suggest a role for complex social strategies in the long-term evolution of QS systems. More generally, my model of QS divergence suggests a form of kin recognition where different kin types coexist in unstructured populations.
Proceedings of the National Academy of Sciences 08/2011; 108(33):13635-40. · 9.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The hindguts of wood-feeding termites typically contain hundreds of microbial species. Together with their insect host, these gut microbes degrade lignocellulose into usable catabolites. Although past research revealed many facets of the stepwise flow of metabolites in this scheme, not much is known about the breadth of interactions occurring between termite-gut microbes. Most of these microbes are thought to depend on, and to have co-speciated with, their host and each other for millions of years. In this study, we explored the interactions of two spirochetes previously isolated from the very same termite species. As hydrogen (H(2)) is the central free intermediate in termite-gut lignocellulose digestion, we focused on interactions between two closely related termite-gut spirochetes possessing complementary H(2) physiologies: one produces H(2), while the other consumes it. In vitro, these two Treponema species markedly enhanced each other's growth. RNA sequencing resolved the transcriptomes of these two closely related organisms, revealing that co-cultivation causes comprehensive changes in global gene expression. The expression of well over a 100 genes in each species was changed >twofold, with over a dozen changed >10-fold. Several changes implicating synergistic cross-feeding of known metabolites were validated in vitro. Additionally, certain activities beneficial to the host were preferentially expressed during consortial growth. However, the majority of changes in gene expression are not yet understandable, but indicate a broad, comprehensive and mutualistic interaction between these closely related, co-resident gut symbionts. The results suggest that staggeringly intricate networks of metabolic and gene interactions drive lignocellulose degradation and co-evolution of termite gut microbiota.
The ISME Journal 02/2011; 5(7):1133-42. · 8.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Compartmentalization of the activities of RNA polymerase sigma factors is a hallmark of formation of spores by Bacillus subtilis. It is initiated soon after the asymmetrically located sporulation division takes place with the activation of σ(F) in the smaller cell, the prespore. σ(F) then directs a signal via the membrane protease SpoIIGA to activate σ(E) in the larger mother cell by processing of pro-σ(E). Here, we show that σ(E) can be activated in the prespore with little effect on sporulation efficiency, implying that complete compartmentalization of σ(E) activity is not essential for spore formation. σ(E) activity in the prespore can be obtained by inducing transcription in the prespore of spoIIGA or of sigE*, which encodes a constitutively active form of σ(E), but not of spoIIGB, which encodes pro-σ(E). We infer that σ(E) compartmentalization is partially attributed to a competition between the compartments for the activation signaling protein SpoIIR. Normally, SpoIIGA is predominantly located in the mother cell and as a consequence confines σ(E) activation to it. In addition, we find that CsfB, previously shown to inhibit σ(G), is independently inhibiting σ(E) activity in the prespore. CsfB thus appears to serve a gatekeeper function in blocking the action of two sigma factors in the prespore: it prevents σ(G) from becoming active before completion of engulfment and helps prevent σ(E) from becoming active at all.
Journal of bacteriology 11/2010; 192(21):5616-24. · 3.94 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The genetic circuits that regulate cellular functions are subject to stochastic fluctuations, or 'noise', in the levels of their components. Noise, far from just a nuisance, has begun to be appreciated for its essential role in key cellular activities. Noise functions in both microbial and eukaryotic cells, in multicellular development, and in evolution. It enables coordination of gene expression across large regulons, as well as probabilistic differentiation strategies that function across cell populations. At the longest timescales, noise may facilitate evolutionary transitions. Here we review examples and emerging principles that connect noise, the architecture of the gene circuits in which it is present, and the biological functions it enables. We further indicate some of the important challenges and opportunities going forward.
[Show abstract][Hide abstract] ABSTRACT: Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fates of individual organisms differently. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve. Here we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an intercompartmental signalling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable 'twin' spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we can systematically tune the penetrance of each mutant fate. Furthermore, signalling and replication perturbations synergize to significantly increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum shows a strong resemblance to twin sporulation in these B. subtilis mutants. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.
[Show abstract][Hide abstract] ABSTRACT: The Bacillus subtilis SpoVE integral membrane protein is essential for the heat resistance of spores, probably because of its involvement in spore peptidoglycan synthesis. We found that an SpoVE-yellow fluorescent protein (YFP) fusion protein becomes localized to the forespore during the earliest stages of engulfment, and this pattern is maintained throughout sporulation. SpoVE belongs to a well-conserved family of proteins that includes the FtsW and RodA proteins of B. subtilis. These proteins are involved in bacterial shape determination, although their function is not known. FtsW is necessary for the formation of the asymmetric septum in sporulation, and we found that an FtsW-YFP fusion localized to this structure prior to the initiation of engulfment in a nonoverlapping pattern with SpoVE-cyan fluorescent protein. Since FtsW and RodA are essential for normal growth, it has not been possible to identify loss-of-function mutations that would greatly facilitate analysis of their function. We took advantage of the fact that SpoVE is not required for growth to obtain point mutations in SpoVE that block the development of spore heat resistance but that allow normal protein expression and targeting to the forespore. These mutant proteins will be invaluable tools for future experiments aimed at elucidating the function of members of the SEDS ("shape, elongation, division, and sporulation") family of proteins.
Journal of bacteriology 02/2008; 190(1):363-76. · 3.94 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Why do cells of the same type, grown in the same conditions, look and behave so differently? Studying fluctuations in a well-characterized genetic pathway in yeast hints at how such variation arises.
[Show abstract][Hide abstract] ABSTRACT: Generating clones of mutated cells within a wild-type tissue is a powerful experimental paradigm for elucidating gene function. Recently, this approach was employed for identifying genes that shape morphogen profiles in the Drosophila wing-imaginal disc. Interpreting such experiments poses a theoretical challenge. We present a general framework that links specific features of the morphogen profile in the clone vicinity to three basic morphogen properties: diffusion, degradation, and binding to immobile elements. Our results provide rigorous criteria to examine existing data and can facilitate the design and interpretation of future clone experiments.
[Show abstract][Hide abstract] ABSTRACT: Morphogen gradients play a pivotal role in most phases of developmental patterning. To ensure proper patterning, reproducible gradients are established under diverse environmental conditions and genetic backgrounds. We refer to the capacity to buffer fluctuations in gene dosage or environmental conditions as 'robustness'. By theoretical analysis of mechanisms that facilitate robustness, it is possible to unravel the machinery responsible for generating the spatial distribution of morphogens.
Current Opinion in Genetics & Development 09/2004; 14(4):435-9. · 7.47 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Morphogen gradients provide long-range positional information by extending across a developing field. To ensure reproducible patterning, their profile is invariable despite genetic or environmental fluctuations. Common models assume a morphogen profile that decays exponentially. Here, we show that exponential profiles cannot, at the same time, buffer fluctuations in morphogen production rate and define long-range gradients. To comply with both requirements, morphogens should decay rapidly close to their source but at a significantly slower rate over most of the field. Numerical search revealed two network designs that support robustness to fluctuations in morphogen production rate. In both cases, morphogens enhance their own degradation, leading to a higher degradation rate close to their source. This is achieved through reciprocal interactions between the morphogen and its receptor. The two robust networks are consistent with properties of the Wg and Hh morphogens in the Drosophila wing disc and provide novel insights into their function.
[Show abstract][Hide abstract] ABSTRACT: Developmental patterning relies on morphogen gradients, which generally involve feedback loops to buffer against perturbations caused by fluctuations in gene dosage and expression. Although many gene components involved in such feedback loops have been identified, how they work together to generate a robust pattern remains unclear. Here we study the network of extracellular proteins that patterns the dorsal region of the Drosophila embryo by establishing a graded activation of the bone morphogenic protein (BMP) pathway. We find that the BMP activation gradient itself is robust to changes in gene dosage. Computational search for networks that support robustness shows that transport of the BMP class ligands (Scw and Dpp) into the dorsal midline by the BMP inhibitor Sog is the key event in this patterning process. The mechanism underlying robustness relies on the ability to store an excess of signalling molecules in a restricted spatial domain where Sog is largely absent. It requires extensive diffusion of the BMP-Sog complexes, coupled with restricted diffusion of the free ligands. We show experimentally that Dpp is widely diffusible in the presence of Sog but tightly localized in its absence, thus validating a central prediction of our theoretical study.