Microbial thermosensors

Fever-like temperature impacts on Staphylococcus aureus and Pseudomonas aeruginosa interaction, physiology, and virulence both in vitro and in vivo

BACKGROUND

Staphylococcus aureus (SA) and Pseudomonas aeruginosa (PA) cause a wide variety of bacterial infections and coinfections, showing a complex interaction that involves the production of different metabolites and metabolic changes. Temperature is a key factor for bacterial survival and virulence and within the host, bacteria could be exposed to an increment in temperature during fever development. We analyzed the previously unexplored effect of fever-like temperatures (39 °C) on S. aureus USA300 and P. aeruginosa PAO1 microaerobic mono- and co-cultures compared with 37 °C, by using RNAseq and physiological assays including in vivo experiments.

RESULTS

In general terms both temperature and co-culturing had a strong impact on both PA and SA with the exception of the temperature response of monocultured PA. We studied metabolic and virulence changes in both species. Altered metabolic features at 39 °C included arginine biosynthesis and the periplasmic glucose oxidation in S. aureus and P. aeruginosa monocultures respectively. When PA co-cultures were exposed at 39 °C, they upregulated ethanol oxidation-related genes along with an increment in organic acid accumulation. Regarding virulence factors, monocultured SA showed an increase in the mRNA expression of the agr operon and hld, pmsα, and pmsβ genes at 39 °C. Supported by mRNA data, we performed physiological experiments and detected and increment in hemolysis, staphyloxantin production, and a decrease in biofilm formation at 39 °C. On the side of PA monocultures, we observed an increase in extracellular lipase and protease and biofilm formation at 39 °C along with a decrease in the motility in correlation with changes observed at mRNA abundance. Additionally, we assessed host-pathogen interaction both in vitro and in vivo. S. aureus monocultured at 39οC showed a decrease in cellular invasion and an increase in IL-8-but not in IL-6-production by A549 cell line. PA also decreased its cellular invasion when monocultured at 39 °C and did not induce any change in IL-8 or IL-6 production. PA strongly increased cellular invasion when co-cultured at 37 and 39 °C. Finally, we observed increased lethality in mice intranasally inoculated with S. aureus monocultures pre-incubated at 39 °C and even higher levels when inoculated with co-cultures. The bacterial burden for P. aeruginosa was higher in liver when the mice were infected with co-cultures previously incubated at 39 °C comparing with 37 °C.

CONCLUSIONS

Our results highlight a relevant change in the virulence of bacterial opportunistic pathogens exposed to fever-like temperatures in presence of competitors, opening new questions related to bacteria-bacteria and host-pathogen interactions and coevolution.

A Molecular Orchestration of Plant Translation under Abiotic Stress

The complexities of translational strategies make this stage of implementing genetic information one of the most challenging to comprehend and, simultaneously, perhaps the most engaging. It is evident that this diverse range of strategies results not only from a long evolutionary history, but is also of paramount importance for refining gene expression and metabolic modulation. This notion is particularly accurate for organisms that predominantly exhibit biochemical and physiological reactions with a lack of behavioural ones. Plants are a group of organisms that exhibit such features. Addressing unfavourable environmental conditions plays a pivotal role in plant physiology. This is particularly evident with the changing conditions of global warming and the irrevocable loss or depletion of natural ecosystems. In conceptual terms, the plant response to abiotic stress comprises a set of elaborate and intricate strategies. This is influenced by a range of abiotic factors that cause stressful conditions, and molecular genetic mechanisms that fine-tune metabolic pathways allowing the plant organism to overcome non-standard and non-optimal conditions. This review aims to focus on the current state of the art in the field of translational regulation in plants under abiotic stress conditions. Different regulatory elements and patterns are being assessed chronologically. We deem it important to focus on significant high-performance techniques for studying the genetic information dynamics during the translation phase.

Fever-like temperature impacts on Staphylococcus aureus and Pseudomonas aeruginosa interaction, physiology, and virulence both in vitro and in vivo

Background

Staphylococcus aureus and Pseudomonas aeruginosa cause a wide variety of bacterial infections and coinfections, showing a complex interaction that involves the production of different metabolites and metabolic changes. Temperature is a key factor for bacterial survival and virulence and within the host, bacteria could be exposed to an increment in temperature during fever development. We analyzed the previously unexplored effect of fever-like temperatures (39°C) on S. aureus USA300 and P. aeruginosa PAO1 microaerobic mono- and co-cultures compared with 37°C, by using RNAseq and physiological assays including in-vivo experiments.

Results

In general terms both temperature and co-culturing had a strong impact on both PA and SA with the exception of the temperature response of monocultured PA. We studied metabolic and virulence changes on both species. Altered metabolic features at 39°C included arginine biosynthesis and the periplasmic glucose oxidation in S. aureus and P. aeruginosa monocultures respectively. When PA co-cultures were exposed at 39°C they upregulated ethanol oxidation related genes along with an increment in organic acid accumulation. Regarding virulence factors, monocultured SA showed an increase in the mRNA expression of the agr operon and hld, pmsα and pmsβ genes at 39°C. Supported by mRNA data, we performed physiological experiments and detected and increment in hemolysis, staphylxantin production and a decrease in biofilm formation at 39°C. On the side of PA monocultures, we observed increase in extracellular lipase and protease and biofilm formation at 39°C along with a decrease in motility in correlation with changes observed at mRNA abundance. Additionally, we assessed host-pathogen interaction both in-vitro and in-vivo . S. aureus monocultured at 39°C showed a decrease in cellular invasion and an increase in IL-8 -but not in IL-6- production by A549 cell line. PA also decreased its cellular invasion when monocultured at 39°C and did not induce any change in IL-8 or IL-6 production. PA strongly increased cellular invasion when co-cultured at 37°C and 39°C. Finally, we observed increased lethality in mice intranasally inoculated with S. aureus monocultures pre-incubated at 39°C and even higher levels when inoculated with co-cultures. The bacterial burden for P. aeruginosa was higher in liver when the mice were infected with co-cultures previously incubated at 39°C comparing with 37°C.

Conclusion

Our results highlight a relevant change in the virulence of bacterial opportunistic pathogens exposed to fever-like temperatures in presence of competitors, opening new questions related to bacteria-bacteria and host-pathogen interactions and coevolution.

Gas and light: triggers of c-di-GMP-mediated regulation

The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.

The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation

Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.

The involvement of CiaR and the CiaR-regulated serine protease HtrA in thermal adaptation of Streptococcus pneumoniae

The in vivo temperature can vary according to the host tissue and the response to infection. Streptococcus pneumoniae has evolved mechanisms to survive these temperature differences, but neither the consequences of different temperatures for pneumococcal phenotype nor the genetic basis of thermal adaptation are known in detail. In our previous study [16], we found that CiaR, which is a part of two-component regulatory system CiaRH, as well as 17 genes known to be controlled by CiaRH, were identified to be differentially expressed with temperature. One of the CiaRH-regulated genes shown to be differentially regulated by temperature is for the high-temperature requirement protein (HtrA), coded by SPD_2068 (htrA). In this study, we hypothesized that the CiaRH system plays an important role in pneumococcal thermal adaptation through its control over htrA. This hypothesis was evaluated by testing strains mutated or overexpressing ciaR and/or htrA, in in vitro and in vivo assays. The results showed that in the absence of ciaR, the growth, haemolytic activity, amount of capsule and biofilm formation were considerably diminished at 40 °C only, while the cell size and virulence were affected at both 34 and 40 °C. The overexpression of htrA in the ∆ciaR background reconstituted the growth at all temperatures, and the haemolytic activity, biofilm formation and virulence of ∆ciaR partially at 40 °C. We also showed that overexpression of htrA in the wild-type promoted pneumococcal virulence at 40 °C, while the increase of capsule was observed at 34 °C, suggesting that the role of htrA changes at different temperatures. Our data suggest that CiaR and HtrA play an important role in pneumococcal thermal adaptation.

Response and regulatory mechanisms of heat resistance in pathogenic fungi

Abstract

Both the increasing environmental temperature in nature and the defensive body temperature response to pathogenic fungi during mammalian infection cause heat stress during the fungal existence, reproduction, and pathogenic infection. To adapt and respond to the changing environment, fungi initiate a series of actions through a perfect thermal response system, conservative signaling pathways, corresponding transcriptional regulatory system, corresponding physiological and biochemical processes, and phenotypic changes. However, until now, accurate response and regulatory mechanisms have remained a challenge. Additionally, at present, the latest research progress on the heat resistance mechanism of pathogenic fungi has not been summarized. In this review, recent research investigating temperature sensing, transcriptional regulation, and physiological, biochemical, and morphological responses of fungi in response to heat stress is discussed. Moreover, the specificity thermal adaptation mechanism of pathogenic fungi in vivo is highlighted. These data will provide valuable knowledge to further understand the fungal heat adaptation and response mechanism, especially in pathogenic heat-resistant fungi.

Key points

• Mechanisms of fungal perception of heat pressure are reviewed.

• The regulatory mechanism of fungal resistance to heat stress is discussed.

• The thermal adaptation mechanism of pathogenic fungi in the human body is highlighted.

Robust network topologies for temperature-inducible bioswitches

BACKGROUND

Thermoinducible bioswitches are unique in that the all-or-none switch response is triggered by temperature, which is a global factor that impacts all biochemical reaction processes. To date, temperature-inducible bioswitches rely exclusively on special thermal sensing biomolecules of DNA, RNA, proteins and lipids whose conformations are critically temperature dependent.

METHOD

This paper extends the traditional thermal switch by utilizing purposely designed network topologies of biomolecular interactions to achieve the switching function. By assuming the general Arrhenius law for biochemical reactions, we explore the full space of all three-node genetic interaction networks to screen topologies capable of thermal bioswitches. Three target bioswitches, i.e., thermal-inducible Off-On, cold-inducible On-Off, and hybrid Off-On-Off double switches, are considered separately.

CONCLUSIONS

We identify the minimal and core network skeletons that are basic and essential for building robust high-performance bioswitches: three Off-On motifs, three On-Off motifs, and an incoherent feedforward motif for an Off-On-Off double switch. Functional topologies are implicitly preferential in choosing parameter values to achieve the target functions. The scenario of the topology-based bioswitch we propose here is an extension of molecule-based bioswitches and would be valuable in aiding the rational design and synthesis of efficient high-performance thermal bioswitches.

Degron-mediated proteolysis of CrhR-like DEAD-box RNA helicases in cyanobacteria

Conditional proteolytic degradation is an irreversible and highly regulated process that fulfills crucial regulatory functions in all organisms. As proteolytic targets tend to be critical metabolic or regulatory proteins, substrates are targeted for degradation only under appropriate conditions through the recognition of an amino acid sequence referred to as a “degron”. DEAD-box RNA helicases mediate all aspects of RNA metabolism, contributing to cellular fitness. However, the mechanism by which abiotic-stress modulation of protein stability regulates bacterial helicase abundance has not been extensively characterized. Here, we provide in vivo evidence that proteolytic degradation of the cyanobacterial DEAD-box RNA helicase CrhR is conditional, being initiated by a temperature upshift from 20 to 30 °C in the model cyanobacterium, Synechocystis sp. PCC 6803. We show degradation requires a unique, highly conserved, inherently bipartite degron located in the C-terminal extension found only in CrhR-related RNA helicases in the phylum Cyanobacteria. However, although necessary, the degron is not sufficient for proteolysis, as disruption of RNA helicase activity and/or translation inhibits degradation. These results suggest a positive feedback mechanism involving a role for CrhR in expression of a crucial factor required for degradation. Furthermore, AlphaFold structural prediction indicated the C-terminal extension is a homodimerization domain with homology to other bacterial RNA helicases, and mass photometry data confirmed that CrhR exists as a dimer in solution at 22 °C. These structural data suggest a model wherein the CrhR degron is occluded at the dimerization interface but could be exposed if dimerization was disrupted by nonpermissive conditions.

Microbial Mechanisms of Heat Sensing

Temperature is one of the ubiquitous signals that control both the development as well as virulence of various microbial species. Therefore their survival is dependent upon initiating appropriate response upon temperature fluctuations. In particular, pathogenic microbes exploit host-temperature sensing mechanisms for triggering the expression of virulence genes. Many studies have revealed that the biomolecules within a cell such as DNA, RNA, lipids and proteins help in sensing change in temperature, thereby acting as thermosensors. This review shall provide an insight into the different mechanisms of thermosensing and how they aid pathogenic microbes in host invasion.

Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene

Global change is a defining feature of the Anthropocene, the current human-dominated epoch, and poses imminent threats to ecosystem dynamics and services such as plant productivity, biodiversity, and environmental regulation. In this era, terrestrial ecosystems are experiencing perturbations linked to direct habitat modifications as well as indirect effects of global change on species distribution and extreme abiotic conditions. Microorganisms represent an important reservoir of biodiversity that can influence macro-organisms as they face habitat loss, rising atmospheric CO₂ concentration, pollution, global warming, and increased frequency of drought. Plant-microbe interactions in the phyllosphere have been shown to support plant growth and increase host resistance to biotic and abiotic stresses. Here, we review how plant-microbe interactions in the phyllosphere can influence host survival and fitness in the context of global change. We highlight evidence that plant-microbe interactions (1) improve urban pollution remediation through the degradation of pollutants such as ultrafine particulate matter, black carbon, and atmospheric hydrocarbons, (2) have contrasting impacts on plant species range shifts through the loss of symbionts or pathogens, and (3) drive plant host adaptation to drought and warming. Finally, we discuss how key community ecology processes could drive plant-microbe interactions facing challenges of the Anthropocene.

RNA thermometers and other regulatory elements: Diversity and importance in bacterial pathogenesis

Survival of microorganisms depends to a large extent on environmental conditions and the occupied host. By adopting specific strategies, microorganisms can thrive in the surrounding environment and, at the same time, preserve their viability. Evading the host defenses requires several mechanisms compatible with the host survival which include the production of RNA thermometers to regulate the expression of genes responsible for heat or cold shock as well as of those involved in virulence. Microorganisms have developed a variety of molecules in response to the environmental changes in temperature and even more specifically to the host they invade. Among all, RNA-based regulatory mechanisms are the most common ones, highlighting the importance of such molecules in gene expression control and novel drug development by suitable structure-based alterations. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.

Design of a Toolbox of RNA Thermometers

RNA thermometers are RNA regulatory elements that convert temperature into a functional biological response through a temperature-induced conformational change. These regulatory elements have been investigated in numerous natural contexts and have been designed for synthetic biology as well. A basic challenge has been the design of an RNA thermometer whose final activity in response to temperature matches a prespecified response, in terms of its sensitivity, threshold, and leakiness. This chapter provides a methodology for the design of a toolbox of RNA thermometers. We describe considerations for the conceptual design, a computational assessment, and strategies for experimental synthesis and measurement.

Glutamate Dehydrogenase (GdhA) of Streptococcus pneumoniae Is Required for High Temperature Adaptation

During its progression from the nasopharynx to other sterile and nonsterile niches of its human host, Streptococcus pneumoniae must cope with changes in temperature. We hypothesized that the temperature adaptation is an important facet of pneumococcal survival in the host. Here, we evaluated the effect of temperature on pneumococcus and studied the role of glutamate dehydrogenase (GdhA) in thermal adaptation associated with virulence and survival. Microarray analysis revealed a significant transcriptional response to changes in temperature, affecting the expression of 252 genes in total at 34°C and 40°C relative to at 37°C. One of the differentially regulated genes was gdhA, which is upregulated at 40°C and downregulated at 34°C relative to 37°C. Deletion of gdhA attenuated the growth, cell size, biofilm formation, pH survival, and biosynthesis of proteins associated with virulence in a temperature-dependent manner. Moreover, deletion of gdhA stimulated formate production irrespective of temperature fluctuation. Finally, ΔgdhA grown at 40°C was less virulent than other temperatures or the wild type at the same temperature in a Galleria mellonella infection model, suggesting that GdhA is required for pneumococcal virulence at elevated temperature.

Effect of Low Temperature on the Aggressiveness of Rhizoctonia solani AG 2-2 Isolates on Sugar Beet (Beta vulgaris) Seedlings

Rhizoctonia solani anastomosis group (AG) 2-2 can cause seedling damping-off in sugar beets and substantial losses may occur in all regions where beets are grown. Sugar beets are planted early in the season when soil temperatures are low in order to maximize the length of the growing season and minimize the risk of damping-off. However, predictive models that indicate there is little to no risk of Rhizoctonia damping-off at temperatures <15°C may not be entirely reliable. We tested this possibility by inoculating sugar beet seedlings in a growth chamber at 11°C with 35 R. solani AG 2-2 isolates that were representative of the genetic diversity present in AG 2-2. Although disease progress and growth rate were greatly reduced at 11°C, considerable disease symptoms did develop in inoculated plants. Three weeks after inoculation, 16% of the plants were dead and 77% of the isolates tested had average disease severity scores that were significantly greater than those of the mock inoculated control. This confirms our concern about the possibility for low-temperature infection of sugar beets and indicates that waiting until the soil warms up to above 15°C to apply fungicide could leave the crop at risk. Aggressiveness does not appear to be related to subgroup or growth rate but rather depends on the response of the specific isolate to low temperature.

Feeling the Heat: The Campylobacter jejuni HrcA Transcriptional Repressor Is an Intrinsic Protein Thermosensor

The heat-shock response, a universal protective mechanism consisting of a transcriptional reprogramming of the cellular transcriptome, results in the accumulation of proteins which counteract the deleterious effects of heat-stress on cellular polypeptides. To quickly respond to thermal stress and trigger the heat-shock response, bacteria rely on different mechanisms to detect temperature variations, which can involve nearly all classes of biological molecules. In Campylobacter jejuni the response to heat-shock is transcriptionally controlled by a regulatory circuit involving two repressors, HspR and HrcA. In the present work we show that the heat-shock repressor HrcA acts as an intrinsic protein thermometer. We report that a temperature upshift up to 42 °C negatively affects HrcA DNA-binding activity to a target promoter, a condition required for de-repression of regulated genes. Furthermore, we show that this impairment of HrcA binding at 42 °C is irreversible in vitro, as DNA-binding was still not restored by reversing the incubation temperature to 37 °C. On the other hand, we demonstrate that the DNA-binding activity of HspR, which controls, in combination with HrcA, the transcription of chaperones' genes, is unaffected by heat-stress up to 45 °C, portraying this master repressor as a rather stable protein. Additionally, we show that HrcA binding activity is enhanced by the chaperonin GroE, upon direct protein-protein interaction. In conclusion, the results presented in this work establish HrcA as a novel example of intrinsic heat-sensing transcriptional regulator, whose DNA-binding activity is positively modulated by the GroE chaperonin.

Precision of Protein Thermometry

Temperature sensing is a ubiquitous cell behavior, but the fundamental limits to the precision of temperature sensing are poorly understood. Unlike in chemical concentration sensing, the precision of temperature sensing is not limited by extrinsic fluctuations in the temperature field itself. Instead, we find that precision is limited by the intrinsic copy number, turnover, and binding kinetics of temperature-sensitive proteins. Developing a model based on the canonical TlpA protein, we find that a cell can estimate temperature to within 2%. We compare this prediction with in vivo data on temperature sensing in bacteria.

Exploiting RNA thermometer-driven molecular bioprocess control as a concept for heterologous rhamnolipid production

A key challenge to advance the efficiency of bioprocesses is the uncoupling of biomass from product formation, as biomass represents a by-product that is in most cases difficult to recycle efficiently. Using the example of rhamnolipid biosurfactants, a temperature-sensitive heterologous production system under translation control of a fourU RNA thermometer from Salmonella was established to allow separating phases of preferred growth from product formation. Rhamnolipids as bulk chemicals represent a model system for future processes of industrial biotechnology and are therefore tied to the efficiency requirements in competition with the chemical industry. Experimental data confirms function of the RNA thermometer and suggests a major effect of temperature on specific rhamnolipid production rates with an increase of the average production rate by a factor of 11 between 25 and 38 °C, while the major part of this increase is attributable to the regulatory effect of the RNA thermometer rather than an unspecific overall increase in bacterial metabolism. The production capacity of the developed temperature sensitive-system was evaluated in a simple batch process driven by a temperature switch. Product formation was evaluated by efficiency parameters and yields, confirming increased product formation rates and product-per-biomass yields compared to a high titer heterologous rhamnolipid production process from literature.

RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection

Bacterial processes necessary for adaption to stressful host environments are potential targets for new antimicrobials. Here, we report large-scale transcriptomic analyses of 32 human bacterial pathogens grown under 11 stress conditions mimicking human host environments. The potential relevance of the in vitro stress conditions and responses is supported by comparisons with available in vivo transcriptomes of clinically important pathogens. Calculation of a probability score enables comparative cross-microbial analyses of the stress responses, revealing common and unique regulatory responses to different stresses, as well as overlapping processes participating in different stress responses. We identify conserved and species-specific 'universal stress responders', that is, genes showing altered expression in multiple stress conditions. Non-coding RNAs are involved in a substantial proportion of the responses. The data are collected in a freely available, interactive online resource (PATHOgenex).

RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures

Thermoregulation of virulence genes in bacterial pathogens is essential for environment-to-host transition. However, the mechanisms governing cold adaptation when outside the host remain poorly understood. Here, we found that the production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches. Through in silico prediction, enzymatic probing and site-directed mutagenesis, we demonstrated that cspB and cspC 5′UTRs adopt alternative RNA structures that shift from one another upon temperature shifts. The open (O) conformation that facilitates mRNA translation is favoured at ambient temperatures (22°C). Conversely, the alternative locked (L) conformation, where the ribosome binding site (RBS) is sequestered in a double-stranded RNA structure, is folded at host-related temperatures (37°C). These structural rearrangements depend on a long RNA hairpin found in the O conformation that sequesters the anti-RBS sequence. Notably, the remaining S. aureus CSP, CspA, may interact with a UUUGUUU motif located in the loop of this long hairpin and favour the folding of the L conformation. This folding represses CspB and CspC production at 37°C. Simultaneous deletion of the cspB/cspC genes or their RNA thermoswitches significantly decreases S. aureus growth rate at ambient temperatures, highlighting the importance of CspB/CspC thermoregulation when S. aureus transitions from the host to the environment.

Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications

Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.

Lanthanide doped luminescence nanothermometers in the biological windows: strategies and applications

The development of lanthanide-doped non-contact luminescent nanothermometers with accuracy, efficiency and fast diagnostic tools attributed to their versatility, stability and narrow emission band profiles has spurred the replacement of conventional contact thermal probes. The application of lanthanide-doped materials as temperature nanosensors, excited by ultraviolet, visible or near infrared light, and the generation of emissions lying in the biological window regions, I-BW (650 nm-950 nm), II-BW (1000 nm-1350 nm), III-BW (1400 nm-2000 nm) and IV-BW (centered at 2200 nm), are notably growing due to the advantages they present, including reduced phototoxicity and photobleaching, better image contrast and deeper penetration depths into biological tissues. Here, the different mechanisms used in lanthanide ion-doped nanomaterials to sense temperature in these biological windows for biomedical and other applications are summarized, focusing on factors that affect their thermal sensitivity, and consequently their temperature resolution. Comparing the thermometric performance of these nanomaterials in each biological window, we identified the strategies that allow boosting of their sensing properties.

Molecular and Physiological Adaptations to Low Temperature in Thioalkalivibrio Strains Isolated from Soda Lakes with Different Temperature Regimes

The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of two Thioalkalivibrio strains to low (10°C) and high (30°C) temperatures. For this, the strains were grown under controlled conditions in chemostats and analyzed for their gene expression (RNA sequencing [RNA-Seq]), membrane lipid composition, and glycine betaine content. The strain Thioalkalivibrio versutus AL2^T originated from a soda lake in southeast Siberia that is exposed to strong seasonal temperature differences, including freezing winters, whereas Thioalkalivibrio nitratis ALJ2 was isolated from an East African Rift Valley soda lake with a constant warm temperature the year round. The strain AL2^T grew faster than ALJ2 at 10°C, likely due to its 3-fold-higher concentration of the osmolyte glycine betaine. Moreover, significant changes in the membrane lipid composition were observed for both strains, leading to an increase in their unsaturated fatty acid content via the Fab pathway to avoid membrane stiffness. Genes for the transcriptional and translational machinery, as well as for counteracting cold-induced hampering of nucleotides and proteins, were upregulated. Oxidative stress was reduced by induction of vitamin B₁₂ biosynthesis genes, and growth at 10°C provoked downregulation of genes involved in the second half of the sulfur oxidation pathway. Genes for intracellular signal transduction were differentially expressed, and interestingly, AL2^T upregulated flagellin expression, whereas ALJ2 downregulated it.

IMPORTANCE In addition to their haloalkaline conditions, soda lakes can also harbor a variety of other extreme parameters, to which their microbial communities need to adapt. However, for most of these supplementary stressors, it is not well known yet how haloalkaliphiles adapt and resist. Here, we studied the strategy for adaptation to low temperature in the haloalkaliphilic genus Thioalkalivibrio by using two strains isolated from soda lakes with different temperature regimes. Even though the strains showed a strong difference in growth rate at 10°C, they exhibited similar molecular and physiological adaptation responses. We hypothesize that they take advantage of resistance mechanisms against other stressors commonly found in soda lakes, which are therefore maintained in the bacteria living in the absence of low-temperature pressure. A major difference, however, was detected for their glycine betaine content at 10°C, highlighting the power of this osmolyte to also act as a key compound in cryoprotection.

Author Video: An author video summary of this article is available.

Thermoinducible expression system for producing recombinant proteins in Escherichia coli: advances and insights

Recombinant protein (RP) production from Escherichia coli has been extensively studied to find strategies for increasing product yields. The thermoinducible expression system is commonly employed at the industrial level to produce various RPs which avoids the addition of chemical inducers, thus minimizing contamination risks. Multiple aspects of the molecular origin and biotechnological uses of its regulatory elements (pL/pR promoters and cI857 thermolabile repressor) derived from bacteriophage λ provide knowledge to improve the bioprocesses using this system. Here, we discuss the main aspects of the potential use of the λpL/pR-cI857 thermoinducible system for RP production in E. coli, focusing on the approaches of investigations that have contributed to the advancement of this expression system. Metabolic and physiological changes that occur in the host cells caused by heat stress and by RP overproduction are also described. Therefore, the current scenario and the future applications of systems that use heat to induce RP production is discussed to understand the relationship between the activation of the bacterial heat shock response, RP accumulation, and its possible aggregation to form inclusion bodies.

Modulating the Heat Stress Response to Improve Hyperthermia-Based Anticancer Treatments

Simple Summary

Hyperthermia is a method to expose a tumor to elevated temperatures. Heating of the tumor promotes the effects of various treatment regimens that are based on chemo and radiotherapy. Several aspects, however, limit the efficacy of hyperthermia-based treatments. This review provides an overview of the effects and limitations of hyperthermia and discusses how current drawbacks of the therapy can potentially be counteracted by inhibiting the heat stress response—a mechanism that cells activate to defend themselves against hyperthermia.

Abstract

Cancer treatments based on mild hyperthermia (39–43 °C, HT) are applied to a widening range of cancer types, but several factors limit their efficacy and slow down more widespread adoption. These factors include difficulties in adequate heat delivery, a short therapeutic window and the acquisition of thermotolerance by cancer cells. Here, we explore the biological effects of HT, the cellular responses to these effects and their clinically-relevant consequences. We then identify the heat stress response—the cellular defense mechanism that detects and counteracts the effects of heat—as one of the major forces limiting the efficacy of HT-based therapies and propose targeting this mechanism as a potentially universal strategy for improving their efficacy.

Response of psychrophilic plant endosymbionts to experimental temperature increase

Countless uncertainties remain regarding the effects of global warming on biodiversity, including the ability of organisms to adapt and how that will affect obligate symbiotic relationships. The present study aimed to determine the consequences of temperature increase in the adaptation of plant endosymbionts (endophytes) that grow better at low temperatures (psychrophilic). We isolated fungal endophytes from a high-elevation (paramo) endemic plant, Chusquea subtessellata. Initial growth curves were constructed at different temperatures (4-25°C). Next, experiments were carried out in which only the psychrophilic isolates were subjected to repeated increments in temperature. After the experiments, the final growth curves showed significantly slower growth than the initial curves, and some isolates even ceased to grow. While most studies suggest that the distribution of microorganisms will expand as temperatures increase because most of these organisms grow better at 25°C, the results from our experiments demonstrate that psychrophilic fungi were negatively affected by temperature increases. These outcomes raise questions concerning the potential adaptation of beneficial endosymbiotic fungi in the already threatened high-elevation ecosystems. Assessing the consequences of global warming at all trophic levels is urgent because many species on Earth depend on their microbial symbionts for survival.

VdNop12, containing two tandem RNA recognition motif domains, is a crucial factor for pathogenicity and cold adaption in Verticillium dahliae

Previous studies have reported the ability of fungi to overwinter in soil or on crop debris under different environmental conditions, but how fungi adapt to chilling is still largely unknown. In this study, we have identified and characterized the RNA binding protein (RBP) (VdNop12) by screening an Agrobacterium tumefaciens-mediated transformation-mediated insertional mutational library of Verticillium dahliae. We determined that this protein was essential to the pathogen for virulence on cotton plants. VdNop12 contains two tandem RNA recognition motif domains, and its orthologs are widely distributed in filamentous fungi. Mutants produced by disruption of VdNop12 showed defects in vegetative growth, conidiation and cell wall integrity. The mutant also showed an increase in sensitivity to low temperature, as compared to the wildtype and complementation strains. Yeast complementation assay showed that VdNop12 could functionally restore the growth phenotype of ΔScNop12 mutant of Saccharomyces cerevisiae at 15°C. We demonstrated that the VdNop12 is localized in the nucleus, and its loss resulted in the downregulated expression of several genes related to cAMP-PKA and MAPK pathways in V. dahliae. Our results demonstrated a crucial role of RBPs in the regulation of morphology, cold adaption, and pathogenic development in V. dahliae.

Temperature-regulated heterogeneous extracellular matrix gene expression defines biofilm morphology in Clostridium perfringens

Cells in biofilms dynamically adapt to surrounding environmental conditions, which alters biofilm architecture. The obligate anaerobic pathogen Clostridium perfringens shows different biofilm structures in different temperatures. Here we find that the temperature-regulated production of extracellular polymeric substance (EPS) is necessary for morphological changes in biofilms. We identify BsaA proteins as an EPS matrix necessary for pellicle biofilm formation at lower temperature and find that extracellularly secreted BsaA protein forms filamentous polymers. We show that sipW-bsaA operon expression is bimodal, and the EPS-producing population size is increased at a lower temperature. This heterogeneous expression of the EPS gene requires a two-component system. We find that EPS-producing cells cover EPS-nonproducing cells attaching to the bottom surface. In the deletion mutant of pilA2, encoding a type IV pilin, the EPS gene expression is ON in the whole population. This heterogeneity is further regulated by the cleavage of the pilA2 mRNA by RNase Y, causing temperature-responsive EPS expression in biofilms. As temperature is an environmental cue, C. perfringens may modulate EPS expression to induce morphological changes in biofilm structure as a strategy for adapting to interhost and external environments.

Interlocked DNA Nanojoints for Reversible Thermal Sensing

The ability to precisely measure and monitor temperature at high resolution at the nanoscale is an important task for better understanding the thermodynamic properties of functional entities at the nanoscale in complex systems, or at the level of a single cell. However, the development of high-resolution and robust thermal nanosensors is challenging. The design, assembly, and characterization of a group of thermal-responsive deoxyribonucleic acid (DNA) joints, consisting of two interlocked double-stranded DNA (dsDNA) rings, is described. The DNA nanojoints reversibly switch between the static and mobile state at different temperatures without a special annealing process. The temperature response range of the DNA nanojoint can be easily tuned by changing the length or the sequence of the hybridized region in its structure, and because of its interlocked structure the temperature response range of the DNA nanojoint is largely unaffected by its own concentration; this contrasts with systems that consist of separated components.

A tight cold-inducible switch built by coupling thermosensitive transcriptional and proteolytic regulatory parts

Natural organisms have evolved intricate regulatory mechanisms that sense and respond to fluctuating environmental temperatures in a heat- or cold-inducible fashion. Unlike dominant heat-inducible switches, very few cold-inducible genetic switches are available in either natural or engineered systems. Moreover, the available cold-inducible switches still have many shortcomings, including high leaky gene expression, small dynamic range (<10-fold) or broad transition temperature (>10°C). To address these problems, a high-performance cold-inducible switch that can tightly control target gene expression is highly desired. Here, we introduce a tight and fast cold-inducible switch that couples two evolved thermosensitive variants, TF_ts and TEV_ts, as well as an additional Mycoplasma florum Lon protease (mf-Lon) to effectively turn-off target gene expression via transcriptional and proteolytic mechanisms. We validated the function of the switch in different culture media and various Escherichia coli strains and demonstrated its tightness by regulating two morphogenetic bacterial genes and expressing three heat-unstable recombinant proteins, respectively. Moreover, the additional protease module enabled the cold-inducible switch to actively remove the pre-existing proteins in slow-growing cells. This work establishes a high-performance cold-inducible system for tight and fast control of gene expression which has great potential for basic research, as well as industrial and biomedical applications.

High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in E. coli

Controlling metabolism of engineered microbes is important to modulate cell growth and production during a bioprocess. For example, external parameters such as light, chemical inducers, or temperature can act on metabolism of production strains by changing the abundance or activity of enzymes. Here, we created temperature-sensitive variants of an essential enzyme in arginine biosynthesis of Escherichia coli (argininosuccinate synthetase, ArgG) and used them to dynamically control citrulline overproduction and growth of E. coli. We show a method for high-throughput enrichment of temperature-sensitive ArgG variants with a fluorescent TIMER protein and flow cytometry. With 90 of the thus derived ArgG variants, we complemented an ArgG deletion strain showing that 90% of the strains exhibit temperature-sensitive growth and 69% of the strains are auxotrophic for arginine at 42 °C and prototrophic at 30 °C. The best temperature-sensitive ArgG variant enabled precise and tunable control of cell growth by temperature changes. Expressing this variant in a feedback-dysregulated E. coli strain allowed us to realize a two-stage bioprocess: a 33 °C growth-phase for biomass accumulation and a 39 °C stationary-phase for citrulline production. With this two-stage strategy, we produced 3 g/L citrulline during 45 h cultivation in a 1-L bioreactor. These results show that temperature-sensitive enzymes can be created en masse and that they may function as metabolic valves in engineered bacteria.

•

Method to enrich temperature-sensitive enzymes en masse.

•

Temperature-sensitive enzymes function as metabolic valve.

•

Temperature controlled two-stage production of citrulline.

Proteomic analysis of Aspergillus niger 3.316 under heat stress

β‐Glucosidase production by Aspergillus niger is accompanied by an inevitable temperature increase in the industrial fermentation environment. Hence, the synthetic process of β‐glucosidase is negatively affected. However, our understanding of the heat stress response (HSR) mechanism in A. niger is still incomplete. The current study explored the intracellular proteome profile of A. niger 3.316 in group T (50°C stress) and group C (30°C control) using two proteomic approaches (isobaric tags for relative and absolute quantitation [iTRAQ] and label‐free) and examined the expression of four proteins using a parallel reaction monitoring (PRM) approach. Based on the result of the iTRAQ proteomic analysis, 1,025 proteins were differentially expressed in group T compared to group C. Using the label‐free approach, we only focused on 77 proteins with significant changes in their protein expression levels. In addition, we performed bioinformatics analysis on all these proteins and obtained detailed gene ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway results. Under heat stress conditions, the relative expression levels of proteins with protection and repair functions were upregulated in A. niger 3.316. These proteins were involved in metabolic pathways, oxidative phosphorylation, porphyrin and chlorophyll metabolism, pyruvate metabolism, and the citrate cycle (TCA cycle). The insights obtained from the presented proteomics and bioinformatics analyses can be used to further explore the HSR mechanism of A. niger.

An RNA thermometer dictates production of a secreted bacterial toxin

Frequent transitions of bacterial pathogens between their warm-blooded host and external reservoirs are accompanied by abrupt temperature shifts. A temperature of 37°C serves as reliable signal for ingestion by a mammalian host, which induces a major reprogramming of bacterial gene expression and metabolism. Enteric Yersiniae are Gram-negative pathogens accountable for self-limiting gastrointestinal infections. Among the temperature-regulated virulence genes of Yersinia pseudotuberculosis is cnfY coding for the cytotoxic necrotizing factor (CNF_Y), a multifunctional secreted toxin that modulates the host’s innate immune system and contributes to the decision between acute infection and persistence. We report that the major determinant of temperature-regulated cnfY expression is a thermo-labile RNA structure in the 5’-untranslated region (5’-UTR). Various translational gene fusions demonstrated that this region faithfully regulates translation initiation regardless of the transcription start site, promoter or reporter strain. RNA structure probing revealed a labile stem-loop structure, in which the ribosome binding site is partially occluded at 25°C but liberated at 37°C. Consistent with translational control in bacteria, toeprinting (primer extension inhibition) experiments in vitro showed increased ribosome binding at elevated temperature. Point mutations locking the 5’-UTR in its 25°C structure impaired opening of the stem loop, ribosome access and translation initiation at 37°C. To assess the in vivo relevance of temperature control, we used a mouse infection model. Y. pseudotuberculosis strains carrying stabilized RNA thermometer variants upstream of cnfY were avirulent and attenuated in their ability to disseminate into mesenteric lymph nodes and spleen. We conclude with a model, in which the RNA thermometer acts as translational roadblock in a two-layered regulatory cascade that tightly controls provision of the CNF_Y toxin during acute infection. Similar RNA structures upstream of various cnfY homologs suggest that RNA thermosensors dictate the production of secreted toxins in a wide range of pathogens.

Bacterial pathogens closely survey the ambient conditions and induce virulence genes only at appropriate conditions. Upon host contact, many pathogens secrete toxins in order to subvert host defense systems. We find that such a secreted toxin in enteropathogenic Yersinia pseudotuberculosis is produced only at host body temperature. This regulation depends on a temperature-responsive RNA structure, an RNA thermometer, in the 5’-untranslated region of the toxin mRNA, which prevents translation at low temperatures when the bacterium is outside the host. Preventing melting of the RNA structure at 37°C by nucleotide substitutions that stabilize base pairing resulted in avirulent Yersinia strains unable to infect mice. Given that similar RNA thermometer-like structures exist upstream of related toxin genes in various bacterial pathogens, we propose that RNA thermometer-mediated toxin production is an evolutionary conserved mechanism. Interfering with opening of such regulatory structures might thus be a promising strategy targeting a broad spectrum of bacterial pathogens.

Modeling and Exploiting Microbial Temperature Response

Temperature is an important parameter in bioprocesses, influencing the structure and functionality of almost every biomolecule, as well as affecting metabolic reaction rates. In industrial biotechnology, the temperature is usually tightly controlled at an optimum value. Smart variation of the temperature to optimize the performance of a bioprocess brings about multiple complex and interconnected metabolic changes and is so far only rarely applied. Mathematical descriptions and models facilitate a reduction in complexity, as well as an understanding, of these interconnections. Starting in the 19th century with the “primal” temperature model of Svante Arrhenius, a variety of models have evolved over time to describe growth and enzymatic reaction rates as functions of temperature. Data-driven empirical approaches, as well as complex mechanistic models based on thermodynamic knowledge of biomolecular behavior at different temperatures, have been developed. Even though underlying biological mechanisms and mathematical models have been well-described, temperature as a control variable is only scarcely applied in bioprocess engineering, and as a conclusion, an exploitation strategy merging both in context has not yet been established. In this review, the most important models for physiological, biochemical, and physical properties governed by temperature are presented and discussed, along with application perspectives. As such, this review provides a toolset for future exploitation perspectives of temperature in bioprocess engineering.

Evaluating temperature-induced regulation of a ROSE-like RNA-thermometer for heterologous rhamnolipid production in Pseudomonas putida KT2440

The microbial production of rhamnolipids has been in the focus of research for the last decades. Today, mainly heterologous production systems are targeted due to the advantage of non-pathogenic hosts as well as uncoupling from complex quorum sensing regulatory networks compared to their natural producer Pseudomonas aeruginosa. In the recent past, the presence and function of a ROSE-like RNA-thermometer located in the 5′UTR of the rhamnosyltransferase genes rhlAB has been reported in wild type P. aeruginosa. In this study, the temperature-induced regulation of this native RNA-thermometer for heterologous rhamnolipid production was evaluated and its potential application for process control is discussed. For this purpose, the non-pathogenic production host P. putida KT2440 containing the rhlAB genes with the native P. aeruginosa 5′-UTR region was used. The system was evaluated and characterized regarding the effect of temperature on growth and product formation, as represented by efficiency parameters and yields. Experimental data suggests a major effect of temperature on specific rhamnolipid production rates. With maximum values of 0.23 g/(g h) at 37 °C, this constitutes a more than 60% increase compared to the production rate of 0.14 g/(g h) at the growth optimum of 30 °C. Interestingly however, control experiments unveiled that besides the regulatory effect of the RNA-thermometer, multiple metabolic effects may contribute equally to the observed increase in production rate. As such, this work constitutes an important step towards the utilization of temperature-based process designs and enables the possibility for novel approaches for process control.

Small non-coding RNA STnc640 regulates expression of fimA fimbrial gene and virulence of Salmonella enterica serovar Enteritidis

Background

Small non-coding RNAs (sRNAs) regulate bacterial gene expression at the post-transcriptional level. STnc640 is a type of sRNA that was identified in Salmonella Typhimurium.

Results

In this study, STnc640 in Salmonella Enteritidis was confirmed to be an Hfq-dependent sRNA. TargetRNA software analysis showed that fimbrial genes fimA and bcfA were likely to be the target genes of STnc640. To investigate the target mRNAs and function of STnc640 in pathogenicity, we constructed the deletion mutant strain 50336△stnc640 and the complemented strain 50336△stnc640/pstnc640 in Salmonella Enteritidis 50336. The RT-qPCR results showed that the mRNA level of fimA was decreased, while bcfA was unchanged in 50336△stnc640 compared with that in the wild type (WT) strain. The adhesion ability of 50336△stnc640 to Caco-2 cells was increased compared to the 50336 WT strain. The virulence of 50336△stnc640 was enhanced in a one-day-old chicken model of S. Enteritidis disease as determined by quantifying the 50% lethal dose (LD₅₀) of the bacterial strains.

Conclusions

The results demonstrate that STnc640 contributes to the virulence of Salmonella Enteritidis.

Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA

The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature. The collapse is shown to be a continuous transition through a combination of statistical-mechanical modeling and all-atom implicit solvent simulations. Surprisingly, CytR binds single-site cognate DNA with negative cooperativity, described by Hill coefficients less than one, resulting in a graded binding response. We show that heterogeneity arising from varying binding-competent CytR conformations or orientations at the single-molecular level contributes to negative binding cooperativity at the level of bulk measurements due to the conflicting requirements of collapse transition, large fluctuations and folding-upon-binding. Our work reports strong evidence for functionally driven thermodynamic fluctuations in determining the extent of collapse and disorder with implications in protein search efficiency of target DNA sites and regulation.

A wastewater treatment system combining Myriophyllum aquaticum and activated sludge: Optimization of construction conditions and evaluation of wastewater treatment performance

Although Myriophyllum aquaticum exhibits efficient nitrogen and phosphorus removal from wastewater, it has poor performance on organic matter removal. Here, a wastewater treatment system combining M. aquaticum and activated sludge was developed to improve its removal of organic matter. The Box-Behnken response surface methodology was used to optimize the construction conditions of the system, and the effects of time, temperature, illumination intensity, pollutant load, and dissolved oxygen (DO) on plant mass increment (PMI) and microbial biomass (MB) of the system were investigated. The wastewater remediation potential of the system was then evaluated. The results show that temperature and illumination intensity significantly affected PMI (p < 0.01), and that time, pollutant load, and DO were the most significant factors affecting MB (p < 0.01). The optimal construction conditions were 18.77 days in length, a temperature of 20.42 °C, an illumination intensity of 5827.61 Lx, a pollutant load of 120.61 mg/g plant, and a DO of 3.21 mg/L. The inoculation of activated sludge caused MB of the system to increase by four times relative to the non-inoculated system, suggesting successful formation of biofilms on M. aquaticum. Additionally, the removal of chemical oxygen demand (COD) from wastewater was significantly enhanced by the combined approach compared with a system relying solely on M. aquaticum. This study provides a new method for improving the remediation efficiency of M. aquaticum by combining the use of this species and activated sludge.

mRNA dynamics and alternative conformations adopted under low and high arginine concentrations control polyamine biosynthesis in Salmonella

Putrescine belongs to the large group of polyamines, an essential class of metabolites that exists throughout all kingdoms of life. The Salmonella speF gene encodes an inducible ornithine decarboxylase that produces putrescine from ornithine. Putrescine can be also synthesized from arginine in a parallel metabolic pathway. Here, we show that speF expression is controlled at multiple levels through regulatory elements contained in a long leader sequence. At the heart of this regulation is a short open reading frame, orf34, which is required for speF production. Translation of orf34 interferes with Rho-dependent transcription termination and helps to unfold an inhibitory RNA structure sequestering speF ribosome-binding site. Two consecutive arginine codons in the conserved domain of orf34 provide a third level of speF regulation. Uninterrupted translation of orf34 under conditions of high arginine allows the formation of a speF mRNA structure that is degraded by RNase G, whereas ribosome pausing at the consecutive arginine codons in the absence of arginine enables the formation of an alternative structure that is resistant to RNase G. Thus, the rate of ribosome progression during translation of the upstream ORF influences the dynamics of speF mRNA folding and putrescine production. The identification of orf34 and its regulatory functions provides evidence for the evolutionary conservation of ornithine decarboxylase regulatory elements and putrescine production.

Polyamines are widely distributed in nature, they bind nucleic acids and proteins and although their exact mechanism of action is not clear, their effect on fundamental cellular functions is well documented. The canonical biosynthesis pathway of polyamines is conserved and begins with speF encoding ornithine decarboxylase, an inducible enzyme that produces putrescine from ornithine. Putrescine can also be produced from arginine in an alternative metabolic pathway. Here, we show that the rate of ribosome progression during translation of a short ORF (ORF34) upstream of speF influences the dynamics of speF mRNA folding and thus putrescine production. Uninterrupted translation of orf34 carrying two consecutive arginine codons, under conditions of high arginine, results in the formation of a speF mRNA structure that is degraded by RNase G, whereas ribosomes slow-down at the consecutive arginine codons in the absence of arginine enables the formation of an alternative structure that is unsusceptible to RNase G and thus results in putrescine production. The study of Salmonella speF regulation provides evidence that, despite variations in the mechanistic details, RNA-based regulation of putrescine biosynthesis and ornithine decarboxylase is conserved from bacteria to mammals.

Interactions within the microbiome alter microbial interactions with host chemical defences and affect disease in a marine holobiont

Our understanding of diseases has been transformed by the realisation that people are holobionts, comprised of a host and its associated microbiome(s). Disease can also have devastating effects on populations of marine organisms, including dominant habitat formers such as seaweed holobionts. However, we know very little about how interactions between microorganisms within microbiomes - of humans or marine organisms – affect host health and there is no underpinning theoretical framework for exploring this. We applied ecological models of succession to bacterial communities to understand how interactions within a seaweed microbiome affect the host. We observed succession of surface microbiomes on the red seaweed Delisea pulchra in situ, following a disturbance, with communities ‘recovering’ to resemble undisturbed states after only 12 days. Further, if this recovery was perturbed, a bleaching disease previously described for this seaweed developed. Early successional strains of bacteria protected the host from colonisation by a pathogenic, later successional strain. Host chemical defences also prevented disease, such that within-microbiome interactions were most important when the host’s chemical defences were inhibited. This is the first experimental evidence that interactions within microbiomes have important implications for host health and disease in a dominant marine habitat-forming organism.

Reverse Engineering of a Thermosensing Regulator Switch

To address the mechanism of thermosensing and its implications for molecular engineering, we previously deconstructed the functional components of the bacterial thermosensor DesK, a histidine kinase with a five-span transmembrane domain that detects temperature changes. The system was first simplified by building a sensor that consists of a single chimerical transmembrane segment that retained full sensing capacity. Genetic and biophysical analysis of this minimal sensor enabled the identification of three modular components named determinants of thermodetection (DOTs). Here we combine and tune the DOTs to determine their contribution to activity. A transmembrane zipper represents the master DOT that drives a reversible and activating dimerization through the formation of hydrogen bonds. Our findings provide the mechanism and insights to construct a synthetic transmembrane helix based on a poly-valine scaffold that harbors the DOTs and regulates the activity. The construct constitutes a modular switch that may be exploited in biotechnology and genetic circuitry.

RNA Thermometers in Bacterial Pathogens

Temperature variation is one of the multiple parameters a microbial pathogen encounters when it invades a warm-blooded host. To survive and thrive at host body temperature, human pathogens have developed various strategies to sense and respond to their ambient temperature. An instantaneous response is mounted by RNA thermometers (RNATs), which are integral sensory structures in mRNAs that modulate translation efficiency. At low temperatures outside the host, the folded RNA blocks access of the ribosome to the translation initiation region. The temperature shift upon entering the host destabilizes the RNA structure and thus permits ribosome binding. This reversible zipper-like mechanism of RNATs is ideally suited to fine-tune virulence gene expression when the pathogen enters or exits the body of its host. This review summarizes our present knowledge on virulence-related RNATs and discusses recent developments in the field.

Heat shock response in archaea

An adequate response to a sudden temperature rise is crucial for cellular fitness and survival. While heat shock response (HSR) is well described in bacteria and eukaryotes, much less information is available for archaea, of which many characterized species are extremophiles thriving in habitats typified by large temperature gradients. Here, we describe known molecular aspects of archaeal heat shock proteins (HSPs) as key components of the protein homeostasis machinery and place this in a phylogenetic perspective with respect to bacterial and eukaryotic HSPs. Particular emphasis is placed on structure–function details of the archaeal thermosome, which is a major element of the HSR and of which subunit composition is altered in response to temperature changes. In contrast with the structural response, it is largely unclear how archaeal cells sense temperature fluctuations and which molecular mechanisms underlie the corresponding regulation. We frame this gap in knowledge by discussing emerging questions related to archaeal HSR and by proposing methodologies to address them. Additionally, as has been shown in bacteria and eukaryotes, HSR is expected to be relevant for the control of physiology and growth in various stress conditions beyond temperature stress. A better understanding of this essential cellular process in archaea will not only provide insights into the evolution of HSR and of its sensing and regulation, but also inspire the development of biotechnological applications, by enabling transfer of archaeal heat shock components to other biological systems and for the engineering of archaea as robust cell factories.

Switching Protein Conformational Substates by Protonation and Mutation

Protein modules that regulate the availability and conformational status of transcription factors determine the rapidity, duration, and magnitude of cellular response to changing conditions. One such system is the single-gene product Cnu, a four-helix bundle transcription co-repressor, which acts as a molecular thermosensor regulating the expression of virulence genes in enterobacteriaceae through modulation of its native conformational ensemble. Cnu and related genes have also been implicated in pH-dependent expression of virulence genes. We hypothesize that protonation of a conserved buried histidine (H45) in Cnu promotes large electrostatic frustration, thus disturbing the H-NS, a transcription factor, binding face. Spectroscopic and calorimetric methods reveal that H45 exhibits a suppressed p K_a of ∼5.1, the protonation of which switches the conformation to an alternate native ensemble in which the fourth helix is disordered. The population redistribution can also be achieved through a mutation H45V, which does not display any switching behavior at pH values greater than 4. The Wako-Saitô-Muñoz-Eaton (WSME) statistical mechanical model predicts specific differences in the conformations and fluctuations of the fourth and first helices of Cnu determining the observed pH response. We validate these predictions through fluorescence lifetime measurements of a sole tryptophan, highlighting the presence of both native and non-native interactions in the regions adjoining the binding face of Cnu. Our combined experimental-computational study thus shows that Cnu acts both as a thermo- and pH-sensor orchestrated via a subtle but quantifiable balance between the weak packing of a structural element and protonation of a buried histidine that promotes electrostatic frustration.

Bioinspired Infrared Sensing Materials and Systems

Bioinspired engineering offers a promising alternative approach in accelerating the development of many man-made systems. Next-generation infrared (IR) sensing systems can also benefit from such nature-inspired approach. The inherent compact and uncooled operation of biological IR sensing systems provides ample inspiration for the engineering of portable and high-performance artificial IR sensing systems. This review overviews the current understanding of the biological IR sensing systems, most of which are thermal-based IR sensors that rely on either bolometer-like or photomechanic sensing mechanism. The existing efforts inspired by the biological IR sensing systems and possible future bioinspired approaches in the development of new IR sensing systems are also discussed in the review. Besides these biological IR sensing systems, other biological systems that do not have IR sensing capabilities but can help advance the development of engineered IR sensing systems are also discussed, and the related engineering efforts are overviewed as well. Further efforts in understanding the biological IR sensing systems, the learning from the integration of multifunction in biological systems, and the reduction of barriers to maximize the multidiscipline collaborations are needed to move this research field forward.

Host Sensing by Pathogenic Fungi

The ability to cause disease extends from the ability to grow within the host environment. The human host provides a dynamic environment to which fungal pathogens must adapt to in order to survive. The ability to grow under a particular condition (i.e., the ability to grow at mammalian body temperature) is considered a fitness attribute and is essential for growth within the human host. On the other hand, some environmental conditions activate signaling mechanisms resulting in the expression of virulence factors, which aid pathogenicity. Therefore, pathogenic fungi have evolved fitness and virulence attributes to enable them to colonize and infect humans. This review highlights how some of the major pathogenic fungi respond and adapt to key environmental signals within the human host.