Genetic modifications of metallothionein enhance the tolerance and bioaccumulation of heavy metals in Escherichia coli

Metallothioneins (MTs) are low molecular weight cysteine-rich proteins that bind to metals. Owing to their high cysteine (Cys) content, MTs are effective mediators of heavy metal detoxification. To enhance the heavy metal binding ability of MT from the freshwater crab Sinopotamon henanense (ShMT), sequence-based multiple sequence alignment (MSA) and structure-based molecular docking simulation (MDS) were conducted in order to identify amino acid residues that could be mutated to bolster such metal-binding activity. Site-directed mutagenesis was then used to modify the primary structure of ShMT, and the recombinant proteins were further enhanced using the SUMO fusion expression system to yield SUMO-ShMT1, SUMO-ShMT2, and SUMO-ShMT3 harboring one-, two-, and three- point mutations, respectively. The resultant modified proteins were primarily expressed in a soluble form and exhibited the ability to readily bind to heavy metals. Importantly, these modified proteins exhibited significantly enhanced heavy metal binding capacities, and they improved Cd²⁺, Cu²⁺ and Zn²⁺ tolerance and bioaccumulation in Escherichia coli (E. coli) in a manner dependent upon the number of introduced point mutations (SUMO-ShMT3 > SUMO-ShMT2 > SUMO-ShMT1 > SUMO-ShMT > control). Indeed, E. coli cells harboring the pET28a-SUMO-ShMT3 expression vector exhibited maximal Cd²⁺, Cu²⁺, and Zn²⁺ bioaccumulation that was increased by 1.86 ± 0.02-, 1.71 ± 0.03-, and 2.13 ± 0.02-fold relative to that in E. coli harboring the pET28a-SUMO-ShMT vector. The present study offers a basis for the preparation of genetically engineered bacteria that are better able to bioaccumulate and tolerate heavy metals, thus providing a foundation for biological heavy metal water pollution treatment.

Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

Background

Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments.

Results

We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations.

Conclusions

Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01079-0.

Fiscal Expenditures on Science and Technology and Environmental Pollution: Evidence from China

Studying the driving factors of environmental pollution is of great importance for China. Previous literature mainly focused on the cause of national aggregate emission changes. However, research about the effect of fiscal expenditures on science and technology (FESTs) on environmental pollution is rare. Considering the large gap among cities in China, it is necessary to investigate whether and how FESTs affect environmental pollution among cities. We adopted three kinds of typical environmental pollutants including sulfur dioxide (SO₂) emissions, wastewater emission, and atmospheric particulate matter less than 2.5 micrometers in diameter (PM_2.5). Using the data of 260 prefecture-level cities over ten years in China, we found that FESTs play a significantly positive role in reducing sulfur dioxide (SO₂) emissions and PM_2.5 concentrations, but fail to alleviate wastewater emissions. Specifically, for every 1% increase in FESTs, SO₂ emissions were reduced by 5.317% and PM_2.5 concentrations were reduced by 5.329%. Furthermore, we found that FESTs reduced environmental pollution by impeding fixed asset investments and by promoting research and development activities (R&D). Moreover, the impacts of FESTs on environmental pollution varied across regions and sub-periods. Our results are robust to a series of additional checks, including alternative econometric specifications, generalized method of moments (GMM) analysis and overcoming potential endogeneity with an instrumental variable. Our findings confirm that government efforts can be effective on pollution control in China. Hence, all governments should pay more attention to FESTs for sustainable development and environmental quality improvements.

Spatial genetic and epigenetic structure of Thlaspi arvense (field pennycress) in China

Thlaspi arvense (field pennycress) is widespread in temperate regions of the northern hemisphere. We estimated the genetic and epigenetic structure of eight T. arvense populations (131 individuals) in China using amplified fragment length polymorphism and methylation-sensitive amplified polymorphism molecular-marker techniques. We detected low diversity at both genetic (mean = 0.03; total = 0.07) and epigenetic (mean = 0.04; total = 0.07) levels, while significant genetic (F_ST = 0.42, P < 0.001) and epigenetic (F_ST = 0.32, P < 0.001) divergence was found across the distribution range. Using Mantel testing, we found spatial genetic and epigenetic differentiation, consistent with isolation-by-distance models. We also identified a strong correlation between genetic and epigenetic differentiation (r = 0.7438, P < 0.001), suggesting genetic control of the epigenetic variation. Our results indicate that mating system, natural selection and gene flow events jointly structure spatial patterns of genetic and epigenetic variation. Moreover, epigenetic variation may serve as a basis of natural selection and ecological evolution to enable species to adapt to heterogeneous habitats. Our study provides novel clues for the adaptation of T. arvense.

Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense

Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (field pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in nonstressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this "stimulation effect" could be transferred partially in the form of stress memory to at least two generations of offspring in nonstressed environments. In addition, we observed a parallel change in functionally important traits, that is, phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance.

Tandem oligomeric expression of metallothionein enhance heavy metal tolerance and bioaccumulation in Escherichia coli

Metallothioneins (MTs) are a family of low molecular weight, cysteine-rich, metal-binding proteins, which play important roles in metal homeostasis and heavy metal detoxification. In our previous study, a novel full length MT cDNA was successfully cloned from the freshwater crab (Sinopotamon henanense). In the present study, tandem repeats of two and three copies of the crab MT gene were integrated by overlap extension PCR (SOE-PCR) and expressed in Escherichia coli. The SUMO fusion expression system was adopted to increase the stability and solubility of the recombinant MT proteins. The recombinant proteins were purified and their metal-binding abilities were further analyzed by the ultraviolet absorption spectral scan. Furthermore, the metal tolerance and bioaccumulation of E. coli cells expressing oligomeric MTs were determined. Results showed that the recombinant plasmids pET28a-SUMO-2MT and pET28a-SUMO-3MT were successfully constructed. SDS-PAGE analysis showed that the SUMO-2MT and SUMO-3MT were expressed mainly in the soluble forms. Oligomeric MTs expression significantly enhanced Cu, Cd or Zn tolerance and accumulation in E. coli in the order: SUMO-3MT˃SUMO-2MT˃SUMO-MT˃control. Cells harboring pET28a-SUMO -3MT exhibited the highest Cu, Cd or Zn bioaccumulation at 5.8-fold, 3.1-fold or 6.7-fold higher than that of the control cells. Our research could lay a foundation for large-scale preparation of MTs and provide a scientific basis for bioremediation of heavy metal pollution by oligomeric MTs.

Economic losses of carbon emissions from circum-Arctic permafrost regions under RCP-SSP scenarios

Under rapid Arctic warming, the vast amount of labile organic carbon stored in Arctic permafrost soils poses a potentially huge threat. Thawing permafrost will release hundreds of billion tons of soil carbon into the atmosphere in the form of CO₂ and CH₄ that would further intensify global warming and bring more challenges to human society. In this study, we use the PInc-PanTher model to estimate carbon emissions from thawing permafrost in the circum-Arctic during 2010-2100 followed by the PAGE09 integrated assessment model to evaluate the net economic losses caused by these permafrost carbon emissions. Our results show that in terms of net present value (NPV), the release of CO₂ and CH₄ from circum-Arctic permafrost will generate estimated net economic losses of US$2.5 trillion (5-95% range: 0.3-11.2 US$ trillion) under the RCP4.5-SPP1 scenario and US$12.7 trillion (5-95% range: 1.6-41.8 US$ trillion) under the RCP8.5-SPP3 scenario between 2010 and 2100, which contribute ~4.9% and ~6.4% respectively of net economic losses of global carbon emissions.

Crabbe MJ, Xu F, Wang W, Ma L, Niu R, Gao X, Li X, Zhang P, Ma X, Chen H. Seasonal variations in carbon, nitrogen and phosphorus concentrations and C:N:P stoichiometry in different organs of a Larix principis-rupprechtii Mayr. plantation in the Qinling Mountains, China

Understanding how concentrations of elements and their stoichiometry change with plant growth and age is critical for predicting plant community responses to environmental change. We used long-term field experiments to explore how the leaf, stem and root carbon (C), nitrogen (N) and phosphorous (P) concentrations and their stoichiometry changed with growth and stand age in a L. principis-rupprechtii Mayr. plantation from 2012-2015 in the Qinling Mountains, China. Our results showed that the C, N and P concentrations and stoichiometric ratios in different tissues of larch stands were affected by stand age, organ type and sampling month and displayed multiple correlations with increased stand age in different growing seasons. Generally, leaf C and N concentrations were greatest in the fast-growing season, but leaf P concentrations were greatest in the early growing season. However, no clear seasonal tendencies in the stem and root C, N and P concentrations were observed with growth. In contrast to N and P, few differences were found in organ-specific C concentrations. Leaf N:P was greatest in the fast-growing season, while C:N and C:P were greatest in the late-growing season. No clear variations were observed in stem and root C:N, C:P and N:P throughout the entire growing season, but leaf N:P was less than 14, suggesting that the growth of larch stands was limited by N in our study region. Compared to global plant element concentrations and stoichiometry, the leaves of larch stands had higher C, P, C:N and C:P but lower N and N:P, and the roots had greater P and C:N but lower N, C:P and N:P. Our study provides baseline information for describing the changes in nutritional elements with plant growth, which will facilitates plantation forest management and restoration, and makes a valuable contribution to the global data pool on leaf nutrition and stoichiometry.

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r = 0.9, P < 2.2 × 10¹⁶; IMR90 fibroblasts: r = 0.94, P < 2.2 × 10¹⁶) and also have a significant positive correlation with some remote functional DNA elements like enhancers and promoters (Enhancer: hESC: r = 0.997, P = 2.3 × 10⁻⁴; IMR90: r = 0.934, P = 2 × 10⁻²; Promoter: hESC: r = 0.995, P = 3.8 × 10⁻⁴; IMR90: r = 0.996, P = 3.2 × 10⁻⁴). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.

Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs

Background

MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate the target gene expression at post-transcriptional level. They are widely involved in biological processes, such as embryonic development, cell division, differentiation, and apoptosis. Evidence suggests that miRNAs can constrain the variation of their target to buffer the fluctuation of expression. However, whether this effect can act on the genome-wide expression remains controversial.

Results

In this study, we comprehensively explored the stably expressed genes (SE genes) and fluctuant genes (FL genes) in the human genome by a meta-analysis of large scale microarray data. We found that these genes have distinct function distributions. miRNA targets are shown to be significantly enriched in SE genes by using propensity analysis of miRNA regulation, supporting the hypothesis that miRNAs can buffer whole genome expression fluctuation. The expression-buffering effect of miRNA is independent of the target site number within the 3'-untranslated region. In addition, we found that gene expression fluctuation is positively correlated with the number of transcription factor binding sites in the promoter region, which suggests that coordination between transcription factors and miRNAs leads to balanced responses to external perturbations.

Conclusions

Our study confirmed that the genetic buffering roles of miRNAs can act on genome expression fluctuation and provides insights into how miRNAs and transcription factors coordinate to cope with external perturbation.

Computational biology approaches to plant metabolism and photosynthesis: applications for corals in times of climate change and environmental stress

Knowledge of factors that are important in reef resilience helps us to understand how reef ecosystems react following major anthropogenic and environmental disturbances. The symbiotic relationship between the photosynthetic zooxanthellae algal cells and corals is that the zooxanthellae provide the coral with carbon, while the coral provides protection and access to enough light for the zooxanthellae to photosynthesise. This article reviews some recent advances in computational biology relevant to photosynthetic organisms, including Beyesian approaches to kinetics, computational methods for flux balances in metabolic processes, and determination of clades of zooxanthallae. Application of these systems will be important in the conservation of coral reefs in times of climate change and environmental stress.

Topography and spatial arrangement of reef-building corals on the fringing reefs of North Jamaica may influence their response to disturbance from bleaching

Knowledge of factors that are important in reef resilience helps us understand how reefs react following major environmental disturbances such as hurricanes and bleaching. Here we test factors that might have influenced Jamaican reef resilience to, and subsequent recovery from, the 2005 bleaching event, and which might help inform management policy for reefs in the future: reef rugosity and contact of corals with macroalgae. In addition, we test in the field, on Dairy Bull reef, whether aggregated Porites astreoides colonies exhibit enhanced growth when exposed to superior competition from Acopora palmata, as has been found by experiment with the Indo-Pacific corals Porites lobata and the superior competitor Porites rus [Idjadi, J.A., Karlson, R.H., 2007. Spatial arrangement of competitors influences coexistence of reef-building corals. Ecology 88, 2449-2454]. There were significant linear relationships between rugosity and the increase in smallest size classes for Sidastrea siderea, Colpophyllia natans, P. astreoides and Agaricia species, and between rugosity and cover of the branching coral Acropora cervicornis. Linear extension rates of A. cervicornis and radial growth rates of P. astreoides were significantly lower (p<0.025; F>6) when in contact with macroalgae. Aggregated colonies of P. astreoides in contact with one another, one of which was in contact with the faster growing competitor A. palmata showed significantly greater growth rates than with just two aggregated P. astreoides colonies alone. These findings suggest that three dimensional topography and complexity is important for reef resilience and viability in the face of environmental stressors such as bleaching. Our findings also support the idea that aggregated spatial arrangements of corals can influence the outcome of interspecific competition and promote species coexistence, important in times of reef recovery after disturbance.

Hurricanes and coral bleaching linked to changes in coral recruitment in Tobago

Knowledge of coral recruitment patterns helps us understand how reefs react following major disturbances and provides us with an early warning system for predicting future reef health problems. We have reconstructed and interpreted historical and modern-day recruitment patterns, using a combination of growth modelling and in situ recruitment experiments, in order to understand how hurricanes, storms and bleaching events have influenced coral recruitment on the Caribbean coastline of Tobago. Whilst Tobago does not lie within the main hurricane belt results indicate that regional hurricane events negatively impact coral recruitment patterns in the Southern Caribbean. In years following hurricanes, tropical storms and bleaching events, coral recruitment was reduced when compared to normal years (p=0.016). Following Hurricane Ivan in 2004 and the 2005-2006 bleaching event, coral recruitment was markedly limited with only 2% (n=6) of colonies estimated to have recruited during 2006 and 2007. Our experimental results indicate that despite multiple large-scale disturbances corals are still recruiting on Tobago's marginal reef systems, albeit in low numbers.

Scleractinian coral population size structures and growth rates indicate coral resilience on the fringing reefs of North Jamaica

Coral reefs throughout the world are under severe challenges from many environmental factors. This paper quantifies the size structure of populations and the growth rates of corals from 2000 to 2008 to test whether the Discovery Bay coral colonies showed resilience in the face of multiple acute stressors of hurricanes and bleaching. There was a reduction in numbers of colonies in the smallest size class for all the species at all the sites in 2006, after the mass bleaching of 2005, with subsequent increases for all species at all sites in 2007 and 2008. Radial growth rates (mm yr(-1)) of non-branching corals and linear extension rates (mm yr(-1)) of branching corals calculated on an annual basis from 2000-2008 showed few significant differences either spatially or temporally. At Dairy Bull reef, live coral cover increased from 13+/-5% in 2006 to 20+/-9% in 2007 and 31+/-7% in 2008, while live Acropora species increased from 2+/-2% in 2006 to 10+/-4% in 2007 and 22+/-7% in 2008. These studies indicate good levels of coral resilience on the fringing reefs around Discovery Bay in Jamaica.

Climate change and tropical marine agriculture

The coral reef ecosystem forms part of a 'seascape' that includes land-based ecosystems such as mangroves and forests, and ideally should form a complete system for conservation and management. Aquaculture, including artisanal fishing for fish and invertebrates, shrimp farming, and seaweed farming, is a major part of the farming and gleaning practices of many tropical communities, particularly on small islands, and depends upon the integrity of the reefs. Climate change is making major impacts on these communities, not least through global warming and high CO(2) concentrations. Corals grow within very narrow limits of temperature, provide livelihoods for millions of people in tropical areas, and are under serious threat from a variety of environmental and climate extremes. Corals survive and grow through a symbiotic relationship with photosynthetic algae: zooxanthellae. Such systems apply highly co-operative regulation to minimize the fluctuation of metabolite concentration profiles in the face of transient perturbations. This review will discuss research on how climate influences reef ecosystems, and how science can lead to conservation actions, with benefits for the human populations reliant on the reefs for their survival.

Climate change, global warming and coral reefs: modelling the effects of temperature

Climate change and global warming have severe consequences for the survival of scleractinian (reef-building) corals and their associated ecosystems. This review summarizes recent literature on the influence of temperature on coral growth, coral bleaching, and modelling the effects of high temperature on corals. Satellite-based sea surface temperature (SST) and coral bleaching information available on the internet is an important tool in monitoring and modelling coral responses to temperature. Within the narrow temperature range for coral growth, corals can respond to rate of temperature change as well as to temperature per se. We need to continue to develop models of how non-steady-state processes such as global warming and climate change will affect coral reefs.

Growth modelling indicates hurricanes and severe storms are linked to low coral recruitment in the Caribbean

This study set out to test the hypothesis that hurricanes and tropical storms limit the recruitment and subsequent survival of massive non-branching corals on the barrier reef off the coast of Belize in the Gulf of Honduras. Overall, the surface areas of 523 individual coral specimens were measured, and recruitment dates were then modelled. There was no significant difference in coral cover or coral biodiversity between any of the sites studied (p > 0.1). There were significant differences in non-branching coral recruitment in years when hurricanes impacted the area (p < 0.05) compared with years when no hurricanes impacted the area. There were significantly more non-branching massive corals recruited in non-hurricane years (mean 7.7) than in hurricane years (mean 3.8; p = 0.011). When years with tropical storms are added to the years with hurricanes, there was significantly lower coral recruitment (mean 4.7) relative to non-storm or hurricane years (mean 7.4; p = 0.019). These results show that hurricanes and severe storms limited the recruitment and survival of massive non-branching corals of the Mesoamerican barrier reef and on patch reefs near the Belize coast in the Caribbean, and suggests that marine park managers may need to assist coral recruitment in years where there are hurricanes or severe storms.

Global warming and coral reefs: Modelling the effect of temperature on Acropora palmata colony growth

Data on colony growth of the branching coral Acropora palmata from fringing reefs off Discovery Bay on the north coast of Jamaica have been obtained over the period 2002-2007 using underwater photography and image analysis by both SCUBA and remotely using an ROV incorporating twin lasers. Growth modelling shows that while logarithmic growth is an approximate model for growth, a 3:3 rational polynomial function provides a significantly better fit to growth data for this coral species. Over the period 2002-2007, involving several cycles of sea surface temperature (SST) change, the rate of growth of A. palmata was largely proportional to rate of change of SST, with R(2)=0.935. These results have implications for the influence of global warming and climate change on coral reef ecosystems.

Metabolism of Maillard reaction products by the human gut microbiota--implications for health

The human colonic microbiota imparts metabolic versatility on the colon, interacts at many levels in healthy intestinal and systemic metabolism, and plays protective roles in chronic disease and acute infection. Colonic bacterial metabolism is largely dependant on dietary residues from the upper gut. Carbohydrates, resistant to digestion, drive colonic bacterial fermentation and the resulting end products are considered beneficial. Many colonic species ferment proteins but the end products are not always beneficial and include toxic compounds, such as amines and phenols. Most components of a typical Western diet are heat processed. The Maillard reaction, involving food protein and sugar, is a complex network of reactions occurring during thermal processing. The resultant modified protein resists digestion in the small intestine but is available for colonic bacterial fermentation. Little is known about the fate of the modified protein but some Maillard reaction products (MRP) are biologically active by, e. g. altering bacterial population levels within the colon or, upon absorption, interacting with human disease mechanisms by induction of inflammatory responses. This review presents current understanding of the interactions between MRP and intestinal bacteria. Recent scientific advances offering the possibility of elucidating the consequences of microbe-MRP interactions within the gut are discussed.