Stable integration and expression of mosquito-larvicidal genes from Bacillus thuringiensis subsp. israelensis and Bacillus sphaericus into the chromosome of Enterobacter amnigenus: a potential breakthrough in mosquito biocontrol

Growth-mediated negative feedback shapes quantitative antibiotic response

Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole‐cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth‐mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth‐mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.

Bacterial Growth Inhibition Screen (BGIS): harnessing recombinant protein toxicity for rapid and unbiased interrogation of protein function

In two proof-of-concept studies, we established and validated the Bacterial Growth Inhibition Screen (BGIS), which explores recombinant protein toxicity in Escherichia coli as a largely overlooked and alternative means for basic characterization of functional eukaryotic protein domains. By applying BGIS, we identified an unrecognized RNA-interacting domain in the DEK oncoprotein (this study) and successfully combined BGIS with random mutagenesis as a screening tool for loss-of-function mutants of the DNA modulating domain of DEK [1]. Collectively, our findings shed new light on the phenomenon of recombinant protein toxicity in E. coli. Given the easy and rapid implementation and wide applicability, BGIS will extend the repertoire of basic methods for the identification, analysis and unbiased manipulation of proteins.

Spurious regulatory connections dictate the expression-fitness landscape of translation factors

During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts.

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

Maximization of growth rate is an important fitness strategy for bacteria. Bacteria can achieve this by expressing proteins at optimal concentrations, such that resources are not wasted. This is exemplified for Escherichia coli by the increase of its ribosomal protein-fraction with growth rate, which precisely matches the increased protein synthesis demand. These findings and others have led to the hypothesis that E. coli aims to maximize its growth rate in environments that support growth. However, what kind of regulatory strategy is required for a robust, optimal adjustment of the ribosome concentration to the prevailing condition is still an open question. In the present study, we analyze the ppGpp-controlled mechanism of ribosome expression used by E. coli and show that this mechanism maintains the ribosomes saturated with its substrates. In this manner, overexpression of the highly abundant ribosomal proteins is prevented, and limited resources can be redirected to the synthesis of other growth-promoting enzymes. It turns out that the kinetic conditions for robust, optimal protein-partitioning, which are required for growth rate maximization across conditions, can be achieved with basic biochemical interactions. We show that inactive ribosomes are the most suitable ‘signal’ for tracking the intracellular nutritional state and for adjusting gene expression accordingly, as small deviations from optimal ribosome concentration cause a huge fractional change in ribosome inactivity. We expect to find this control logic implemented across fast-growing microbial species because growth rate maximization is a common selective pressure, ribosomes are typically highly abundant and thus costly, and the required control can be implemented by a small, simple network.

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

A central aim of cell biology was to understand the strategy of gene expression in response to the environment. Here, we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector's total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth rate-dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies.

A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase

Synthetic genetic systems share resources with the host, including machinery for transcription and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors and activators) that enable switching between different promoters and modulation of activity. Here, we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be co-expressed to function. The DNA-binding loop is encoded in a C-terminal 285-aa ‘σ fragment’, and fragments with different specificity can direct the remaining 601-aa ‘core fragment’ to different promoters. Using these parts, we have built a resource allocator that sets the core fragment concentration, which is then shared by multiple σ fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional capacity available to a synthetic system. Further, positive and negative regulation is implemented using a 67-aa N-terminal ‘α fragment’ and a null (inactivated) σ fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via different schemes, which we demonstrate by building a system which adjusts promoter activity to compensate for the difference in copy number of two plasmids.

The bacterium, Lysinibacillus sphaericus, as an insect pathogen

Since the first bacteria with insecticidal activity against mosquito larvae were reported in the 1960s, many have been described, with the most potent being isolates of Bacillus thuringiensis or Lysinibacillus sphaericus (formerly and best known as Bacillus sphaericus). Given environmental concerns over the use of broad spectrum synthetic chemical insecticides and the evolution of resistance to these, industry placed emphasis on the development of bacteria as alternative control agents. To date, numerous commercial formulations of B. thuringiensis subsp. israelensis (Bti) are available in many countries for control of nuisance and vector mosquitoes. Within the past few years, commercial formulations of L. sphaericus (Ls) have become available. Because Bti has been in use for more than 30 years, its properties are well know, more so than those of Ls. Thus, the purpose of this review is to summarise the most critical aspects of Ls and the various proteins that account for its insecticidal properties, especially the mosquitocidal activity of the most common isolates studied. Data are reviewed for the binary toxin, which accounts for the activity of sporulated cells, as well as for other toxins produced during vegetative growth, including sphaericolysin (active against cockroaches and caterpillars) and the different mosquitocidal Mtx and Cry toxins. Future studies of these could well lead to novel potent and environmentally compatible insecticidal products for controlling a range of insect pests and vectors of disease.

Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli

Stochastic switching of a bistable genetic circuit represents a potential cost-saving strategy for adaptation to environmental challenges. This study reports that stochastic switching of a monostable circuit can be sufficient to mediate reversible adaptation in E. coli.

Stochastic switching of a monostable circuit mediated the adaptation of the engineered OSU12-hisC Escherichia coli strain to histidine starvation.

The population shift of OSU12-hisC was accompanied by growth recovery and was reversible upon histidine addition. This is the first report of adaptation mediated by stochastic switching based on a monostable structure.

Weak directionality in stochastic switching initiated the population shift and the fast growth of the occasionally appearing fit cells drove the later stages of adaptation.

Adaptation of OSU12-hisC was resulted from the enhanced expression of the structural genes within the native His operon, along with the transcriptional reorganization of a large number of genes.

The fundamental mechanisms underlying adaptations can be divided into responsive switching and stochastic switching (Kussell and Leibler, 2005). Responsive switching is generally considered as resulting from evolved regulatory units, such as operons and regulons, which enable immediate adaptation (Jacob and Monod, 1961). However, as cells are subject to a wide range of both genetic and environmental perturbations that damage the specificity or efficiency of regulatory systems (Carroll, 2005; Crombach and Hogeweg, 2008), the limited number of regulatory units that can evolve and remain functional may not be sufficient to completely protect cell populations from the danger of extinction. Whether and how cells are able to survive external perturbations, when the corresponding regulatory units are absent or have been genetically disrupted, is an open question of great importance.

Recent studies showed the stochastic switching provided cells a huge potential for sustenance under severe conditions via a so-called ‘bet-hedging' strategy. The experimental evidence was generally based on a bistable genetic structure that fixed stochastically appearing fit state thus limiting further random switching (Kussell and Leibler, 2005; Acar et al, 2008). In contrast to bistable gene expression, monostable gene expression is much more common (Newman et al, 2006) and does not rely on a specific complex genetic architecture. Since a monostable structure has no fixation effect, the fit cells that would appear stochastically tend to return to the original steady state (i.e., unfit state). To achieve a population shift from a maladaptive state (but stable) to an adaptive state (but unstable), a significant increase in fitness (i.e., growth rate) of the fit cells is necessary. Otherwise, the random switching will mask occasionally occurring adaptive transitions and lead to an unchanged population at the stable but maladaptive state. Whether adaptation can be achieved by stochastic switching based on a monostable structure is however an open issue.

To address this question, we applied an engineered E. coli strain, OSU12-hisC, carrying a foreign gene circuit encompassing a physiologically functional gene, hisC, replaced from its native chromosomal locus (Figure 1A). Consequently, hisC in OSU12-hisC is no longer responsive to the native regulation (His operon) that senses histidine depletion. Instead, the foreign gene circuit provided a monostable structure for hisC's stochastic switching. The green fluorescent protein (gfpuv5) was co-expressed with hisC for the quantitative evaluation of HisC in single cells. The upstream regulation of TetR, whose expression level was reported by the red fluorescent protein (dsred.T4), was introduced to achieve the inducible GFP (HisC) level. The full induction of TetR by IPTG was applied to avoid any possible upstream noise that caused by the abundance of endogenous LacI.

Microscopic observation revealed that the OSU12-hisC cells showed stronger green fluorescence after histidine depletion (Figure 1B), which suggested an increased expression level of hisC. Population analysis using flow cytometry showed that the distributions of both GFP concentration and GFP bias (GFP/RFP ratio) in OSU12-hisC shifted towards a higher level in histidine-free conditions (Figure 1C and D), whereas, the depletion caused only a slight change in distributions of OSU11, a control strain carrying both the same engineered genetic circuit and an intact His operon, including the hisC gene in its native context. Repeated experiments revealed that the increases in both GFP concentration (∼2.1 folds) and GFP bias (∼1.5 folds) due to histidine depletion were highly significant (P<0.005, N=6) in OSU12-hisC. In particular, the increased GFP bias strongly suggested that the change in gene expression occurred specifically in the rewired hisC (i.e., GFP) but not in all genes (e.g., RFP). Furthermore, both the growth recovery accompanied population shift and the stress relaxation triggered restoration were clearly observed. It strongly indicated that the adaptation was mediated by stochastic switching of hisC under the monostable control.

Analysis on microcolonies' formation (Figure 4A) showed stochastic behaviour and directionality in individual cells. Variation in cellular GFP level was clearly observed in individual cells. Stochastic switching of hisC was verified according to the random changes in GFP bias along with the cell division under histidine-rich conditions (Figure 4B). On the other hand, the microcolonies formed under the histidine-free conditions tended to the higher level of GFP bias were observed (Figure 4B). The directional tendency favoured the high GFP (HisC) level was evidently detected in the first 2 h after histidine depletion, which resulted in a population shift (Figure 4C). In contrast, the distributions of microcolonies grown in histidine-rich conditions kept steady, due to the randomized directions of stochastic switching (Figure 4C). Further analysis showed that the stochastic fluctuations in the initial state had an important role not only in fate decision (i.e., whether to grow) but also in the directionality of the stochastic switch.

Microarray analysis showed the adaptation of OSU12-hisC was resulted from the enhanced expression of the structural genes within the native His operon, along with the transcriptional reorganization of a large number of genes. In summary, in contrast to bistable structures, the monostable structure used here did not fix the phenotype but allowed the cells to decide where to go. Taken together, the findings suggest that bacteria do not necessarily need to evolve signalling mechanisms to control gene expression appropriately, even for essential genes.

Stochastic switching is considered as a cost-saving strategy for adaptation to environmental challenges. We show here that stochastic switching of a monostable circuit can mediate the adaptation of the engineered OSU12-hisC Escherichia coli strain to histidine starvation. In this strain, the hisC gene was deleted from the His operon and placed under the control of a monostable foreign promoter. In response to histidine depletion, the OSU12-hisC population shifted to a higher HisC expression level, which is beneficial under starving conditions but is not favoured by the monostable circuit. The population shift was accompanied by growth recovery and was reversible upon histidine addition. A weak directionality in stochastic switching of hisC was observed in growing microcolonies under histidine-free conditions. Directionality and fate decision were in part dependent on the initial cellular status. Finally, microarray analysis indicated that OSU12-hisC reorganized its transcriptome to reach the appropriate physiological state upon starvation. These findings suggest that bacteria do not necessarily need to evolve signalling mechanisms to control gene expression appropriately, even for essential genes.

Ribosome degradation in growing bacteria

Ribosomes are large ribozymes that synthesize all cellular proteins. As protein synthesis is rate-limiting for bacterial growth and ribosomes can comprise a large portion of the cellular mass, elucidation of ribosomal turnover is important to the understanding of cellular physiology. Although ribosomes are widely believed to be stable in growing cells, this has never been rigorously tested, owing to the lack of a suitable experimental system in commonly used bacterial model organisms. Here, we develop an experimental system to directly measure ribosomal stability in Escherichia coli. We show that (i) ribosomes are stable when cells are grown at a constant rate in the exponential phase; (ii) more than half of the ribosomes made during exponential growth are degraded during slowing of culture growth preceding the entry into stationary phase; and (iii) ribosomes are stable for many hours in the stationary phase. Ribosome degradation occurs in growing cultures that contain almost no dead cells and coincides with a reduction of comparable magnitude in the cellular RNA concentration.

Variations in the mosquito larvicidal activities of toxins from Bacillus thuringiensis ssp. israelensis

Comparing activities of purified toxins from Bacillus thuringiensis ssp. israelensis against larvae of seven mosquito species (vectors of tropical diseases) that belong to three genera, gleaned from the literature, disclosed highly significant variations in the levels of LC(50) as well as in the hierarchy of susceptibilities. Similar toxicity comparisons were performed between nine transgenic Gram-negative species, four of which are cyanobacterial, expressing various combinations of cry genes, cyt1Aa and p20, against larvae of four mosquito species as potential agents for biological control. Reasons for inconsistencies are listed and discussed. Standard conditions for toxin isolation and presentation to larvae are sought. A set of lyophilized powders prepared identically from six Escherichia coli clones expressing combinations of four genes displayed toxicities against larvae of three mosquito species, with levels that differed between them but with identical hierarchy.

A plasmid encoding a combination of mosquito-larvicidal genes fromBacillus thuringiensissubsp.israelensisandBacillus sphaericusconfers toxicity against a broad range of mosquito larvae when expressed in Gram-negative bacteria

A recombinant plasmid harboring cry4A, cry4B and cry11A from Bacillus thuringiensis subsp. israelensis and binary toxin genes from Bacillus sphaericus has been constructed. The three cry genes were placed under the control of the cry4B promoter whereas the binary toxin gene was controlled by its native promoter. The expression of toxins in Escherichia coli harboring the resulting plasmid, p4BDA-5142, was investigated. Cry4B expression was highest compared to other toxins. Although the level of toxin expression was low compared with E. coli expressing single toxins, the recombinant E. coli strain harboring p4BDA-5142 exhibited broad range mosquito-larvicidal activity against all Aedes, Culex and Anopheles larvae. This work has shown that the development of the recombinant plasmid can be used to broaden the host range spectrum of the appropriate bacterial host for mosquito control.