Comprehensive Functional Analysis of Mycobacterium tuberculosis Toxin-Antitoxin Systems: Implications for Pathogenesis, Stress Responses, and Evolution

Toxin-antitoxin (TA) systems, stress-responsive genetic elements ubiquitous in microbial genomes, are unusually abundant in the major human pathogen Mycobacterium tuberculosis. Why M. tuberculosis has so many TA systems and what role they play in the unique biology of the pathogen is unknown. To address these questions, we have taken a comprehensive approach to identify and functionally characterize all the TA systems encoded in the M. tuberculosis genome. Here we show that 88 putative TA system candidates are present in M. tuberculosis, considerably more than previously thought. Comparative genomic analysis revealed that the vast majority of these systems are conserved in the M. tuberculosis complex (MTBC), but largely absent from other mycobacteria, including close relatives of M. tuberculosis. We found that many of the M. tuberculosis TA systems are located within discernable genomic islands and were thus likely acquired recently via horizontal gene transfer. We discovered a novel TA system located in the core genome that is conserved across the genus, suggesting that it may fulfill a role common to all mycobacteria. By expressing each of the putative TA systems in M. smegmatis, we demonstrate that 30 encode a functional toxin and its cognate antitoxin. We show that the toxins of the largest family of TA systems, VapBC, act by inhibiting translation via mRNA cleavage. Expression profiling demonstrated that four systems are specifically activated during stresses likely encountered in vivo, including hypoxia and phagocytosis by macrophages. The expansion and maintenance of TA genes in the MTBC, coupled with the finding that a subset is transcriptionally activated by stress, suggests that TA systems are important for M. tuberculosis pathogenesis

Ecological commonalities among pelagic fishes: comparison of freshwater ciscoes and marine herring and sprat

Systematic comparisons of the ecology between functionally similar fish species from freshwater and marine aquatic systems are surprisingly rare. Here, we discuss commonalities and differences in evolutionary history, population genetics, reproduction and life history, ecological interactions, behavioural ecology and physiological ecology of temperate and Arctic freshwater coregonids (vendace and ciscoes, Coregonus spp.) and marine clupeids (herring, Clupea harengus, and sprat, Sprattus sprattus). We further elucidate potential effects of climate warming on these groups of fish based on the ecological features of coregonids and clupeids documented in the previous parts of the review. These freshwater and marine fishes share a surprisingly high number of similarities. Both groups are relatively short-lived, pelagic planktivorous fishes. The genetic differentiation of local populations is weak and seems to be in part correlated to an astonishing variability of spawning times. The discrete thermal window of each species influences habitat use, diel vertical migrations and supposedly also life history variations. Complex life cycles and preference for cool or cold water make all species vulnerable to the effects of global warming. It is suggested that future research on the functional interdependence between spawning time, life history characteristics, thermal windows and genetic differentiation may profit from a systematic comparison of the patterns found in either coregonids or clupeids

Capzimin is a potent and specific inhibitor of proteasome isopeptidase Rpn11

The proteasome is a vital cellular machine that maintains protein homeostasis, which is of particular importance in multiple myeloma and possibly other cancers. Targeting of proteasome 20S peptidase activity with bortezomib and carfilzomib has been widely used to treat myeloma. However, not all patients respond to these compounds, and those who do eventually suffer relapse. Therefore, there is an urgent and unmet need to develop new drugs that target proteostasis through different mechanisms. We identified quinoline-8-thiol (8TQ) as a first-in-class inhibitor of the proteasome 19S subunit Rpn11. A derivative of 8TQ, capzimin, shows >5-fold selectivity for Rpn11 over the related JAMM proteases and >2 logs selectivity over several other metalloenzymes. Capzimin stabilized proteasome substrates, induced an unfolded protein response, and blocked proliferation of cancer cells, including those resistant to bortezomib. Proteomic analysis revealed that capzimin stabilized a subset of polyubiquitinated substrates. Identification of capzimin offers an alternative path to develop proteasome inhibitors for cancer therapy

Global lake responses to climate change

Climate change is one of the most severe threats to global lake ecosystems. Lake surface conditions, such as ice cover, surface temperature, evaporation and water level, respond dramatically to this threat, as observed in recent decades. In this Review, we discuss physical lake variables and their responses to climate change. Decreases in winter ice cover and increases in lake surface temperature modify lake mixing regimes and accelerate lake evaporation. Where not balanced by increased mean precipitation or inflow, higher evaporation rates will favour a decrease in lake level and surface water extent. Together with increases in extreme-precipitation events, these lake responses will impact lake ecosystems, changing water quantity and quality, food provisioning, recreational opportunities and transportation. Future research opportunities, including enhanced observation of lake variables from space (particularly for small water bodies), improved in situ lake monitoring and the development of advanced modelling techniques to predict lake processes, will improve our global understanding of lake responses to a changing climate

Engineering organisms for industrial fuel production

Volatile fuel costs, the need to reduce greenhouse gas emissions and fuel security concerns are driving efforts to produce sustainable renewable fuels and chemicals. Petroleum comes from sunlight, CO2 and water converted via a biological intermediate into fuel over a several million year timescale. It stands to reason that using biology to short-circuit this time cycle offers an attractive alternative—but only with relevant products at or below market prices. The state of the art of biological engineering over the past five years has progressed to allow for market needs to drive innovation rather than trying to adapt existing approaches to the market. This report describes two innovations using synthetic biology to dis-intermediate fuel production. LS9 is developing a means to convert biological intermediates such as cellulosic hydrolysates into drop-in hydrocarbon product replacements such as diesel. Joule Unlimited is pioneering approaches to eliminate feedstock dependency by efficiently capturing sunlight, CO2 and water to produce fuels and chemicals. The innovations behind these companies are built with the market in mind, focused on low cost biosynthesis of existing products of the petroleum industry. Through successful deployment of technologies such as those behind LS9 and Joule Unlimited, alternative sources of petroleum products will mitigate many of the issues faced with our petroleum-based economy

Development of a fish-based index to assess the eutrophication status of European lakes

The use of the CEN (European Committee for Standardization) standard method for sampling fish in lakes using multi-mesh gillnets allowed the collection of fish assemblages of 445 European lakes in 12 countries. The lakes were additionally characterised by environmental drivers and eutrophication proxies. Following a site-specific approach including a validation procedure, a fish index including two abundance metrics (catch per unit effort expressed as fish number and biomass) and one functional metric of composition (abundance of omnivorous fish) was developed. Correlated with the proxy of eutrophication, this index discriminates between heavily and moderately impacted lakes. Additional analyses on a subset of data from Nordic lakes revealed a stronger correlation between the new fish index and the pressure data. Despite an uneven geographical distribution of the lakes and certain shortcomings in the environmental and pressure data, the fish index proved to be useful for ecological status assessment of lakes applying standardised protocols and thus supports the development of national lake fish assessment tools in line with the European Water Framework Directive