Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

Defense systems of soil microorganisms in response to compound contamination by arsenic and polycyclic aromatic hydrocarbons

Arsenic and PAHs impose environmental stress on soil microorganisms, yet their compound effects remain poorly understood. While soil microorganisms possess the ability to metabolize As and PAHs, the mechanisms of microbial response are not fully elucidated. In our study, we established two simulated soil systems using soil collected from Xixi Wetland Park grassland, Hangzhou, China. The As-600 Group was contaminated with 600 mg/kg sodium arsenite, while the As-600-PAHs-30 Group received both 600 mg/kg sodium arsenite and 30 mg/kg PAHs (phenanthrene:fluoranthene:benzo[a]pyrene = 1:1:1). These systems were operated continuously for 270 days, and microbial responses were assessed using high-throughput sequencing and metagenomic analysis. Our findings revealed that compound contamination significantly promoted the abundance of microbial defense-related genes, with general defense genes increasing by 11.07 % ∼ 74.23 % and specific defense genes increasing by 44.13 % ∼ 55.74 %. The dominate species Rhodococcus adopts these general and specific defense mechanisms to resist compound pollution stress and gain ecological niche advantages, making it a candidate strain for soil remediation. Our study contributes to the assessment of ecological damage caused by As and PAHs from a microbial perspective and provides valuable insights for soil remediation.

Anaerobic benzene oxidation in Geotalea daltonii involves activation by methylation and is regulated by the transition state regulator AbrB

Benzene is a widespread groundwater contaminant that persists under anoxic conditions. The aim of this study was to more accurately investigate anaerobic microbial degradation pathways to predict benzene fate and transport. Preliminary genomic analysis of Geotalea daltonii strain FRC-32, isolated from contaminated groundwater, revealed the presence of putative aromatic-degrading genes. G. daltonii was subsequently shown to conserve energy for growth on benzene as the sole electron donor and fumarate or nitrate as the electron acceptor. The hbs gene, encoding for 3-hydroxybenzylsuccinate synthase (Hbs), a homolog of the radical-forming, toluene-activating benzylsuccinate synthase (Bss), was upregulated during benzene oxidation in G. daltonii, while the bss gene was upregulated during toluene oxidation. Addition of benzene to the G. daltonii whole-cell lysate resulted in toluene formation, indicating that methylation of benzene was occurring. Complementation of σ54- (deficient) E. coli transformed with the bss operon restored its ability to grow in the presence of toluene, revealing bss to be regulated by σ54. Binding sites for σ70 and the transition state regulator AbrB were identified in the promoter region of the σ54-encoding gene rpoN, and binding was confirmed. Induced expression of abrB during benzene and toluene degradation caused G. daltonii cultures to transition to the death phase. Our results suggested that G. daltonii can anaerobically oxidize benzene by methylation, which is regulated by σ54 and AbrB. Our findings further indicated that the benzene, toluene, and benzoate degradation pathways converge into a single metabolic pathway, representing a uniquely efficient approach to anaerobic aromatic degradation in G. daltonii.

IMPORTANCE

The contamination of anaerobic subsurface environments including groundwater with toxic aromatic hydrocarbons, specifically benzene, toluene, ethylbenzene, and xylene, has become a global issue. Subsurface groundwater is largely anoxic, and further study is needed to understand the natural attenuation of these compounds. This study elucidated a metabolic pathway utilized by the bacterium Geotalea daltonii capable of anaerobically degrading the recalcitrant molecule benzene using a unique activation mechanism involving methylation. The identification of aromatic-degrading genes and AbrB as a regulator of the anaerobic benzene and toluene degradation pathways provides insights into the mechanisms employed by G. daltonii to modulate metabolic pathways as necessary to thrive in anoxic contaminated groundwater. Our findings contribute to the understanding of novel anaerobic benzene degradation pathways that could potentially be harnessed to develop improved strategies for bioremediation of groundwater contaminants.

Screening of functional genes for hypoxia adaptation in Tibetan pigs by combined genome resequencing and transcriptome analysis

The high-altitude, low-oxygen environment of the Qinghai-Tibet Plateau poses significant challenges for the introduction of superior livestock breeds. However, local plateau species have adapted to thrive and reproduce under these harsh conditions. Understanding the molecular mechanisms behind plateau animals' adaptation to low-oxygen environments is essential for breeding livestock suited to high-altitude regions. Tibetan pigs, which have undergone long-term natural selection and artificial breeding, have developed the ability to survive and reproduce in hypoxic environments. In this study, we conducted whole-genome resequencing of 30 Tibetan pigs from high-altitude regions and 30 Diannan small-ear pigs from low-altitude areas, to identify candidate genes that support Tibetan pigs' adaptation to hypoxic conditions through selection signal analysis. Additionally, we performed transcriptome sequencing on five tissues (heart, liver, spleen, lung, and bone marrow) from both Tibetan pigs and Diannan small-ear pigs to identify genes with significant differential expression between the two breeds. We then integrated the genomic and transcriptomic data by examining the expression of candidate genes identified in selection signal analysis across different tissues. The selection signal analysis identified 10 genes-HES4, ANGPT1, HIF3A, SPHK2, PCK2, RCN3, HIGD2A, DNM2, IRF9, and SRF-that were under positive selection in the Tibetan pig population and are associated with hypoxia adaptation. When combined with transcriptome data, we found that five of these genes-HIF3A, RCN3, HIGD2A, PCK2, and IRF9-exhibited differential expression. Through an integrated approach of selection signal and transcriptome analysis, we identified five key functional genes that contribute to the adaptation of Tibetan pigs to hypoxic environments. These findings offer new insights into the adaptability of plateau animals.

Insights into trait-association of selection signatures and adaptive eQTL in indigenous African cattle

BACKGROUND

African cattle represent a unique resource of genetic diversity in response to adaptation to numerous environmental challenges. Characterising the genetic landscape of indigenous African cattle and identifying genomic regions and genes of functional importance can contribute to targeted breeding and tackle the loss of genetic diversity. However, pinpointing the adaptive variant and determining underlying functional mechanisms of adaptation remains challenging.

RESULTS

In this study, we use selection signatures from whole-genome sequence data of eight indigenous African cattle breeds in combination with gene expression and quantitative trait loci (QTL) databases to characterise genomic targets of artificial selection and environmental adaptation and to identify the underlying functional candidate genes. In general, the trait-association analyses of selection signatures suggest the innate and adaptive immune system and production traits as important selection targets. For example, a large genomic region, with selection signatures identified for all breeds except N'Dama, was located on BTA27, including multiple defensin DEFB coding-genes. Out of 22 analysed tissues, genes under putative selection were significantly enriched for those overexpressed in adipose tissue, blood, lung, testis and uterus. Our results further suggest that cis-eQTL are themselves selection targets; for most tissues, we found a positive correlation between allele frequency differences and cis-eQTL effect size, suggesting that positive selection acts directly on regulatory variants.

CONCLUSIONS

By combining selection signatures with information on gene expression and QTL, we were able to reveal compelling candidate selection targets that did not stand out from selection signature results alone (e.g. GIMAP8 for tick resistance and NDUFS3 for heat adaptation). Insights from this study will help to inform breeding and maintain diversity of locally adapted, and hence important, breeds.

Gene Expression Shifts in Emperor Penguin Adaptation to the Extreme Antarctic Environment

Gene expression can accelerate ecological divergence by rapidly tweaking the response of an organism to novel environments, with more divergent environments exerting stronger selection and supposedly, requiring faster adaptive responses. Organisms adapted to extreme environments provide ideal systems to test this hypothesis, particularly when compared to related species with milder ecological niches. The Emperor penguin (Aptenodytes forsteri) is the only endothermic vertebrate breeding in the harsh Antarctic winter, in stark contrast with the less cold-adapted sister species, the King penguin (A. patagonicus). Assembling the first de novo transcriptomes and analysing multi-tissue (brain, kidney, liver, muscle, skin) RNA-Seq data from natural populations of both species, we quantified the shifts in tissue-enhanced genes, co-expression gene networks, and differentially expressed genes characterising Emperor penguin adaptation to the extreme Antarctic. Our analyses revealed the crucial role played by muscle and liver in temperature homeostasis, fasting, and whole-body energy metabolism (glucose/insulin regulation, lipid metabolism, fatty acid beta-oxidation, and blood coagulation). Repatterning at the regulatory level appears as more important in the brain of the Emperor penguin, showing the lowest signature of differential gene expression, but the largest co-expression gene network shift. Nevertheless, over-expressed genes related to mTOR signalling in the brain and the liver support their central role in cold and fasting responses. Besides contributing to understanding the genetics underlying complex traits, like body energy reservoir management, our results provide a first insight into the role of gene expression in adaptation to one of the most extreme environmental conditions endured by an endotherm.

Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.

Emerging Orchestrator of Ecological Adaptation: m6A Regulation of Post-Transcriptional Mechanisms

Genetic mechanisms have been at the forefront of our exploration into the substrate of adaptive evolution and phenotypic diversification. However, genetic variation only accounts for a fraction of phenotypic variation. In the last decade, the significance of RNA modification mechanisms has become more apparent in the context of organismal adaptation to rapidly changing environments. RNA m6A methylation, the most abundant form of RNA modification, is emerging as a potentially significant player in various biological processes. Despite its fundamental function to regulate other major post-transcriptional mechanisms such as microRNA and alternative splicing, its role in ecology and evolution has been understudied. This review highlights the potential importance of m6A RNA methylation in ecological adaptation, emphasising the need for further research, especially in natural systems. We focus on how m6A not only affects mRNA fate but also influences miRNA-mediated gene regulation and alternative splicing, potentially contributing to organismal adaptation. The aim of this review is to synthesise key background information to enhance our understanding of m6A mechanisms driving species survival in dynamic environments and motivate future research into the dynamics of adaptive RNA methylation.

Differential gene expression and chromatin accessibility in the medial prefrontal cortex associated with individual differences in rat behavioral models of opioid use disorder

Opioid use disorder (OUD) is a neuropsychological disease that has a devastating impact on public health. Substantial individual differences in vulnerability exist, the neurobiological substrates of which remain unclear. To address this question, we investigated genome-wide gene transcription (RNA-seq) and chromatin accessibility (ATAC-seq) in the medial prefrontal cortex (mPFC) of male and female rats exhibiting differential vulnerability in behavioral paradigms modeling different phases of OUD: Withdrawal-Induced Anhedonia (WIA), Demand, and Reinstatement. Ingenuity Pathway Analysis (IPA) of RNA-seq revealed greater changes in canonical pathways in Resilient (vs. Saline) rats in comparison to Vulnerable (vs. Saline) rats across 3 paradigms, suggesting brain adaptations that might contribute to resilience to OUD across its trajectory. Analyses of gene networks and upstream regulators implicated processes involved in oligodendrocyte maturation and myelination in WIA, neuroinflammation in Demand, and metabolism in Reinstatement. Motif analysis of ATAC-seq showed changes in chromatin accessibility to a small set of transcription factor (TF) binding sites as a function either of opioid exposure (i.e., morphine versus saline) generally or of individual vulnerability specifically. Some of these were shared across the 3 paradigms and others were unique to each. In conclusion, we have identified changes in biological pathways, TFs, and their binding motifs that vary with paradigm and OUD vulnerability. These findings point to the involvement of distinct transcriptional and epigenetic mechanisms in response to opioid exposure, vulnerability to OUD, and different stages of the disorder.

Calcineurin promotes adaptation to chronic stress through two distinct mechanisms

Adaptation to environmental stress requires coordination between stress-defense programs and cell cycle progression. The immediate response to many stressors has been well characterized, but how cells survive in challenging environments long term is unknown. Here, we investigate the role of the stress-activated phosphatase calcineurin (CN) in adaptation to chronic CaCl2 stress in Saccharomyces cerevisiae. We find that prolonged exposure to CaCl2 impairs mitochondrial function and demonstrate that cells respond to this stressor using two CN-dependent mechanisms-one that requires the downstream transcription factor Crz1 and another that is Crz1 independent. Our data indicate that CN maintains cellular fitness by promoting cell cycle progression and preventing CaCl2-induced cell death. When Crz1 is present, transient CN activation suppresses cell death and promotes adaptation despite high levels of mitochondrial loss. However, in the absence of Crz1, prolonged activation of CN prevents mitochondrial loss and further cell death by upregulating glutathione biosynthesis genes thereby mitigating damage from reactive oxygen species. These findings illustrate how cells maintain long-term fitness during chronic stress and suggest that CN promotes adaptation in challenging environments by multiple mechanisms.

Genetic Mechanisms Involved in Microbial Stress Responses

The ability of living beings to deal with abrupt environmental changes is paramount for survival, and organisms have evolved a large variety of molecular mechanisms (known globally as stress responses) to buffer the harmful effects of stressors on cellular homeostasis [...].

Comparative Transcriptomic Reveals Greater Similarities in Response to Temperature Than to Invasive Alien Predator in the Damselfly Ischnura elegans Across Different Geographic Scales

The impact of global changes on populations may not be necessarily uniform across a species' range. Here, we aim at comparing the phenotypic and transcriptomic response to warming and an invasive predator cue in populations across different geographic scales in the damselfly Ischnura elegans. We collected adult females in two ponds in southern Poland (central latitude) and two ponds in southern Sweden (high latitude). We raised their larvae in growth chambers and exposed them to combination of temperature and a predator cue released by the crayfish Orconectes limosus. When larvae reached the prefinal larval stage, they were phenotyped for traits related to growth and size and collected for a gene expression analysis. High-latitude populations exhibited greater phenotypic and transcriptomic variation than central-latitude populations. Across latitudes and ponds, temperature generally increased growth rate and the predator cue decreased mass, but the effects of temperature were also pond-specific. Comparison of the transcriptomic profiles revealed a greater overlap in the response to temperature across latitudes and ponds, especially for pathway-related oxidative stress and sugar and lipid metabolism. The transcriptomic response to a predator cue and to the interaction temperature × predator cue was more pond-specific and overlapped only for few genes and pathways related to cuticle, development and signal transduction. We demonstrated that central- and high-latitude populations may partially respond through similar mechanisms to warming and, to a lower extent to a predator cue and to the interaction temperature × predator cue. For the predator cue and the interaction, the large fraction of ponds-specific genes suggests local adaptation. We show that high-latitude populations were generally more plastic at the phenotypic and transcriptomic level and may be more capable to cope with environmental changes than their central-latitude counterparts.

Integrated Dual-Channel Retrograde Signaling Directs Stress Responses by Degrading the HAT1/TPL/IMPα-9 Suppressor Complex and Activating CAMTA3

The intricate communication between plastids and the nucleus, shaping stress-responsive gene expression, has long intrigued researchers. This study combines genetics, biochemical analysis, cellular biology, and protein modeling to uncover how the plastidial metabolite MEcPP activates the stress-response regulatory hub known as the Rapid Stress Response Element (RSRE). Specifically, we identify the HAT1/TPL/IMPα- 9 suppressor complex, where HAT1 directly binds to RSRE and its activator, CAMTA3, masking RSRE and sequestering the activator. Stress-induced MEcPP disrupts this complex, exposing RSRE and releasing CAMTA3, while enhancing Ca 2+ influx and raising nuclear Ca 2+ levels crucial for CAMTA3 activation and the initiation of RSRE- containing gene transcription. This coordinated breakdown of the suppressor complex and activation of the activator highlights the dual-channel role of MEcPP in plastid-to- nucleus signaling. It further signifies how this metabolite transcends its expected biochemical role, emerging as a crucial initiator of harmonious signaling cascades essential for maintaining cellular homeostasis under stress.

Summary

This study uncovers how the stress-induced signaling metabolite MEcPP disrupts the HAT1/TPL/IMPα-9 suppressor complex, liberating the activator CAMTA3 and enabling Ca 2+ influx essential for CAMTA3 activation, thus orchestrating stress responses via repressor degradation and activator induction.

Sensing volatiles throughout the body: geographic- and tissue-specific olfactory receptor expression in the fig wasp

An essential adaptive strategy in insects is the evolution of olfactory receptors (ORs) to recognize important volatile environmental chemical cues. Our model species, Ceratosolen fusciceps, a specialist wasp pollinator of Ficus racemosa, likely possesses an OR repertoire that allows it to distinguish fig-specific volatiles in highly variable environments. Using a newly assembled genome-guided transcriptome, we annotated 63 ORs in the species and reconstructed the phylogeny of Ceratosolen ORs in conjunction with other hymenopteran species. Expression analysis showed that though ORs were mainly expressed in the female antennae, 20% were also expressed in nonantennal tissues such as the head, thorax, abdomen, legs, wings, and ovipositor. Specific upregulated expression was observed in OR30C in the head and OR60C in the wings. We identified OR expression from all major body parts of female C. fusciceps, suggesting novel roles of ORs throughout the body. Further examination of the OR expression of C. fusciceps in widely separated geographical locations, that is, South (urban) and Northeast (rural) India, revealed distinct OR expression levels in different locations. This discrepancy likely parallels the observed variation in fig volatiles between these regions and provides new insights into the evolution of insect ORs and their expression across geographical locations and tissues.

The role of heterochronic gene expression and regulatory architecture in early developmental divergence

New developmental programs can evolve through adaptive changes to gene expression. The annelid Streblospio benedicti has a developmental dimorphism, which provides a unique intraspecific framework for understanding the earliest genetic changes that take place during developmental divergence. Using comparative RNAseq through ontogeny, we find that only a small proportion of genes are differentially expressed at any time, despite major differences in larval development and life history. These genes shift expression profiles across morphs by either turning off any expression in one morph or changing the timing or amount of gene expression. We directly connect the contributions of these mechanisms to differences in developmental processes. We examine F1 offspring - using reciprocal crosses - to determine maternal mRNA inheritance and the regulatory architecture of gene expression. These results highlight the importance of both novel gene expression and heterochronic shifts in developmental evolution, as well as the trans-acting regulatory factors in initiating divergence.

Gene body methylation evolves during the sustained loss of parental care in the burying beetle

Epigenetic modifications, such as 5-methylcytosine (5mC), can sometimes be transmitted between generations, provoking speculation that epigenetic changes could play a role in adaptation and evolution. Here, we use experimental evolution to investigate how 5mC levels evolve in populations of biparental insect (Nicrophorus vespilloides) derived from a wild source population and maintained independently under different regimes of parental care in the lab. We show that 5mC levels in the transcribed regions of genes (gene bodies) diverge between populations that have been exposed to different levels of care for 30 generations. These changes in 5mC do not reflect changes in the levels of gene expression. However, the accumulation of 5mC within genes between populations is associated with reduced variability in gene expression within populations. Our results suggest that evolved change in 5mC could contribute to phenotypic evolution by influencing variability in gene expression in invertebrates.

Comparative Genomics and the Salivary Transcriptome of the Redbanded Stink Bug Shed Light on Its High Damage Potential to Soybean

The redbanded stink bug, Piezodorus guildinii (Westwood) (Hemiptera: Pentatomidae), is a significant soybean pest in the Americas, which inflicts more physical damage on soybean than other native stink bugs. Studies suggest that its heightened impact is attributed to the aggressive digestive properties of its saliva. Despite its agricultural importance, the factors driving its greater ability to degrade plant tissues have remained unexplored in a genomic evolutionary context. In this study, we hypothesized that lineage-specific gene family expansions have increased the copy number of digestive genes expressed in the salivary glands. To investigate this, we annotated a previously published genome assembly of the redbanded stink bug, performed a comparative genomic analysis on 11 hemipteran species, and reconstructed patterns of gene duplication, gain, and loss in the redbanded stink bug. We also performed RNA-seq on the redbanded stink bug's salivary tissues, along with the rest of the body without salivary glands. We identified hundreds of differentially expressed salivary genes, including a subset lost in other stink bug lineages, but retained and expressed in the redbanded stink bug's salivary glands. These genes were significantly enriched with protein families involved in proteolysis, potentially explaining the redbanded stink bug's heightened damage to soybeans. Contrary to our hypothesis, we found no support for an enrichment of duplicated digestive genes that are also differentially expressed in the salivary glands of the redbanded stink bug. Nonetheless, these results provide insight into the evolution of this important crop pest, establishing a link between its genomic history and its agriculturally important physiology.

Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral

Phenotypic plasticity can buffer organisms against short-term environmental fluctuations. For example, previous exposure to increased temperatures can increase thermal tolerance in many species. Prior studies have found that acclimation to higher temperature can influence the magnitude of transcriptional response to subsequent acute thermal stress (hereafter, "transcriptional response modulation"). However, mechanisms mediating this gene expression response and, ultimately, phenotypic plasticity remain largely unknown. Epigenetic modifications are good candidates for modulating transcriptional response, as they broadly correlate with gene expression. Here, we investigate changes in DNA methylation as a possible mechanism controlling shifts in gene expression plasticity and thermal acclimation in the reef-building coral Acropora nana. We find that gene expression response to acute stress is altered in corals acclimated to different temperatures, with many genes exhibiting a dampened response to heat stress in corals pre-conditioned to higher temperatures. At the same time, we observe shifts in methylation during both acclimation (11 days) and acute heat stress (24 h). We observed that the acute heat stress results in shifts in gene-level methylation and elicits an acute transcriptional response in distinct gene sets. Further, acclimation-induced shifts in gene expression plasticity and differential methylation also largely occur in separate sets of genes. Counter to our initial hypothesis no overall correlation between the magnitude of differential methylation and the change in gene expression plasticity. We do find a small but statistically significant overlap in genes exhibiting both dampened expression response and shifts in methylation (14 genes), which could be candidates for further inquiry. Overall, our results suggest transcriptional response modulation occurs independently from methylation changes induced by thermal acclimation.

Characterization of Escherichia coli pathogenicity and drug resistance in yolk peritonitis

Yolk Peritonitis can lead to a rapid decline in egg production, which seriously affects the health of laying hens and the profitability of chicken farms. Escherichia coli (E. coli) is the most common cause of yolk peritonitis in laying hens. In this study, bacterial samples were collected from the ovaries and fallopian tubes of laying hens with suspected yolk peritonitis from a laying farm in Jiangsu Province, and their pathogenicity and drug resistance were investigated. Initially, morphological and biochemical detection methods were employed to isolate and identify the pathogenic bacteria. The results showed that a total of 16 strains of E. coli were isolated from laying hens with yolk peritonitis. Subsequently, the drug resistance and pathogenicity of a randomly selected E. coli strain were analyzed and predicted by genome sequencing technology, and the drug resistance of E. coli was verified by drug sensitivity test and PCR. Finally, the virulence was verified by infection experiment in mice. The study revealed that the egg-yolk peritonitis in laying hens was caused by E. coli infection, and the genome sequencing analysis revealed that the bacteria had multidrug resistance and high virulence. The drug susceptibility testing indicates that E. coli exhibited resistance to aminoglycosides, β-lactam, macrolides, fluoroquinolones, and sulfonamides. In this study, resistance genes including KdpE, aadA5, APH(3 ")-ID, APH(6)-ID, and TEM-1 were identified, and their expression levels varied across different stages of bacterial growth. The results of virulence analysis indicated a mortality rate of 50% in mice infected with E. coli at a concentration of 2.985 × 107 CFU/mL. E. coli infection resulted in damage to various tissues and organs in mice, with the intestinal tissue structure being the most severely affected. This study provides a reference for the study of drug resistance mechanisms in E. coli and provides valuable insights into the selection of drugs for the treatment of vitelline peritonitis.

Ecological transcriptomics reveals stress response pathways of a ground-herb species in a waterlogging gradient of Amazonian riparian forests

Environmental stress is a fundamental facet of life and a significant driver of natural selection in the wild. Gene expression diversity may facilitate adaptation to environmental changes, without necessary genetic change, but its role in adaptive divergence remains largely understudied in Neotropical systems. In Amazonian riparian forests, species distribution is predominantly influenced by species' waterlogging tolerance. The flooding gradient delineates distinct wetland forest types, shaping habitats and species characteristics. Here we investigated the molecular basis of environmental stress response in a tropical ground-herb species (Ischnosiphon puberulus) to environmental variation in Amazonian riparian forests. We compared environmental variables and gene expression profiles from individuals collected in two forest types: Igapó and Terra firme in the Amazonian riparian forests. Predictable seasonal flooding poses a significant challenge in Igapó compared to Terra firme environments, with the former presenting higher water column height and longer flooding duration. Our findings suggest that contrasting environmental conditions related to flooding regimes are important drivers of population genetic differentiation and differential gene expression in I. puberulus. Enriched gene ontology terms highlight associations with environmental stresses, such as defence response, water transport, phosphorylation, root development, response to auxin, salicylic acid and oxidative stress. By uncovering key environmental stress response pathways conserved across populations, I. puberulus offers novel genetic insights into the molecular basis of plant reactions to environmental constraints found in flooded areas of this highly biodiverse neotropical ecosystem.

Intraspecific variation in antibiotic resistance potential within E. coli

Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms.

OsJAZ10 negatively modulates the drought tolerance by integrating hormone signaling with systemic electrical activity in rice

Jasmonic acid (JA) plays crucial functions in plant stress response, and the synergistic interaction between JA and abscisic acid (ABA) signaling is implicated to help plants adapt to environmental challenges, whereas the underlying molecular mechanism still needs to be revealed. Here, we report that OsJAZ10, a repressor in the JA signaling, represses rice drought tolerance via inhibition of JA and ABA biosynthesis. Function loss of OsJAZ10 markedly enhances, while overexpression of OsJAZ10ΔJas reduces rice drought tolerance. The osjaz10 mutant is more sensitive to exogenous ABA and MeJA, and produces higher levels of ABA and JA after drought treatment, indicating OsJAZ10 represses the biosynthesis of these two hormones. Mechanistic study demonstrated that OsJAZ10 physically interacts with OsMYC2. Transient transcriptional regulation assays showed that OsMYC2 activates the expression of ABA-biosynthetic gene OsNCED2, JA-biosynthetic gene OsAOC, and drought-responsive genes OsRAB21 and OsLEA3, while OsJAZ10 prevents OsMYC2 transactivation of these genes. Further, the electrophoretic mobility shift assay (EMSA) confirmed that OsMYC2 directly binds to the promoters of OsNCED2 and OsRAB21. Electrical activity has been proposed to activate JA biosynthesis. Interestingly, OsJAZ10 inhibits the propagation of osmotic stress-elicited systemic electrical signals, indicated by the significantly increased PEG-elicited slow wave potentials (SWPs) in osjaz10 mutant, which is in accordance with the elevated JA levels. Collectively, our findings establish that OsJAZ10 functions as a negative regulator in rice drought tolerance by repressing JA and ABA biosynthesis, and reveal an important mechanism that plants integrate electrical events with hormone signaling to enhance the adaption to environmental stress.

Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough

Stop codon readthrough events give rise to longer proteins, which may alter the protein's function, thereby generating short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon readthrough events, we designed a library of reporters. We introduced premature stop codons into mScarlet, which enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon readthrough may occur at rates as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon readthrough events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon readthrough. The RNA polymerase was more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon readthrough by mass spectrometry revealed that temperature regulated the expression of cryptic sequences generated by stop codon readthrough in E. coli. Overall, our findings suggest that the environment affects the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.

Blue-light irradiation induced partial nitrification

The role of ray radiation from the sunlight acting on organisms has long-term been investigated. However, how the light with different wavelengths affects nitrification and the involved nitrifiers are still elusive. Here, we found more than 60 % of differentially expressed genes (DEGs) in nitrifiers were observed under irradiation of blue light with wavelengths of 440-480 nm, which were 13.4 % and 20.3 % under red light and white light irradiation respectively. Blue light was more helpful to achieve partial nitrification rather than white light or red light, where ammonium oxidization by ammonia-oxidizing archaea (AOA) with the increased relative abundance from 8.6 % to 14.2 % played a vital role. This was further evidenced by the enhanced TCA cycle, reactive oxygen species (ROS) scavenge and DNA repair capacity in AOA under blue-light irradiation. In contrast, nitrite-oxidizing bacteria (NOB) was inhibited severely to achieve partial nitrification, and the newly discovered encoded blue light photoreceptor proteins made them more sensitive to blue light and hindered cell activity. Ammonia-oxidizing bacteria (AOB) expressed genes for DNA repair capacity under blue-light irradiation, which ensured their tiny impact by light irradiation. This study provided valuable insights into the photosensitivity mechanism of nitrifiers and shed light on the diverse regulatory by light with different radiation wavelengths in artificial systems, broadening our comprehension of the nitrogen cycle on earth.

Importance of the ECM-receptor interaction for adaptive response to hypoxia based on integrated transcription and translation analysis

Low dissolved oxygen (LO) conditions represent a major environmental challenge to marine life, especially benthic animals. For these organisms, drastic declines in oxygen availability (hypoxic events) can trigger mass mortality events and thus, act as agents of selection influencing the evolution of adaptations. In sea cucumbers, one of the most successful groups of benthic invertebrates, the exposure to hypoxic conditions triggers adaptive adjustments in metabolic rates and behaviour. It is unclear, however, how these adaptive responses are regulated and the genetic mechanisms underpinning them. Here, we addressed this knowledge gap by assessing the genetic regulation (transcription and translation) of hypoxia exposure in the sea cucumber Apostichopus japonicus. Transcriptional and translational gene expression profiles under short- and long-term exposure to low oxygen conditions are tightly associated with extracellular matrix (ECM)-receptor interaction in which laminin and collagen likely have important functions. Finding revealed that genes with a high translational efficiency (TE) had a relatively short upstream open reading frame (uORF) and a high uORF normalized minimal free energy, suggesting that sea cucumbers may respond to hypoxic stress via altered TE. These results provide valuable insights into the regulatory mechanisms that confer adaptive capacity to holothurians to survive oxygen deficiency conditions and may also be used to inform the development of strategies for mitigating the harmful effects of hypoxia on other marine invertebrates facing similar challenges.

Single-Molecule-Resolution Approaches in Synaptic Biology

Synapses between neurons are the primary loci for information transfer and storage in the brain. An individual neuron, alone, can make over 10000 synaptic contacts. It is, however, not easy to investigate what goes on locally within a synapse because many synaptic compartments are only a few hundred nanometers wide in size─close to the diffraction limit of light. To observe the biomolecular machinery and processes within synapses, in situ single-molecule techniques are emerging as powerful tools. Guided by important biological questions, this Perspective will highlight recent advances in using these techniques to obtain in situ measurements of synaptic molecules in three aspects: the cell-biological machinery within synapses, the synaptic architecture, and the synaptic neurotransmitter receptors. These advances showcase the increasing importance of single-molecule-resolution techniques for accessing subcellular biophysical and biomolecular information related to the brain.

Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression

As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.

Calcineurin promotes adaptation to chronic stress through two distinct mechanisms

Adaptation to environmental stress requires coordination between stress-defense programs and cell cycle progression. The immediate response to many stressors has been well characterized, but how cells survive in challenging environments long-term is unknown. Here, we investigate the role of the stress-activated phosphatase calcineurin (CN) in adaptation to chronic CaCl2 stress in Saccharomyces cerevisiae. We find that prolonged exposure to CaCl2 impairs mitochondrial function and demonstrate that cells respond to this stressor using two CN-dependent mechanisms - one that requires the downstream transcription factor Crz1 and another that is Crz1-independent. Our data indicate that CN maintains cellular fitness by promoting cell cycle progression and preventing CaCl2-induced cell death. When Crz1 is present, transient CN activation suppresses cell death and promotes adaptation despite high levels of mitochondrial loss. However, in the absence of Crz1, prolonged activation of CN prevents mitochondrial loss and further cell death by upregulating glutathione (GSH) biosynthesis genes thereby mitigating damage from reactive oxygen species. These findings illustrate how cells maintain long-term fitness during chronic stress and suggest that CN promotes adaptation in challenging environments by multiple mechanisms.

Computational dissection of genetic variation modulating the response of multiple photosynthetic phenotypes to the light environment

BACKGROUND

The expression of biological traits is modulated by genetics as well as the environment, and the level of influence exerted by the latter may vary across characteristics. Photosynthetic traits in plants are complex quantitative traits that are regulated by both endogenous genetic factors and external environmental factors such as light intensity and CO2 concentration. The specific processes impacted occur dynamically and continuously as the growth of plants changes. Although studies have been conducted to explore the genetic regulatory mechanisms of individual photosynthetic traits or to evaluate the effects of certain environmental variables on photosynthetic traits, the systematic impact of environmental variables on the dynamic process of integrated plant growth and development has not been fully elucidated.

RESULTS

In this paper, we proposed a research framework to investigate the genetic mechanism of high-dimensional complex photosynthetic traits in response to the light environment at the genome level. We established a set of high-dimensional equations incorporating environmental regulators to integrate functional mapping and dynamic screening of gene‒environment complex systems to elucidate the process and pattern of intrinsic genetic regulatory mechanisms of three types of photosynthetic phenotypes of Populus simonii that varied with light intensity. Furthermore, a network structure was established to elucidate the crosstalk among significant QTLs that regulate photosynthetic phenotypic systems. Additionally, the detection of key QTLs governing the response of multiple phenotypes to the light environment, coupled with the intrinsic differences in genotype expression, provides valuable insights into the regulatory mechanisms that drive the transition of photosynthetic activity and photoprotection in the face of varying light intensity gradients.

CONCLUSIONS

This paper offers a comprehensive approach to unraveling the genetic architecture of multidimensional variations in photosynthetic phenotypes, considering the combined impact of integrated environmental factors from multiple perspectives.

Engineering the Soil Bacterium Pseudomonas synxantha 2-79 into a Ratiometric Bioreporter for Phosphorus Limitation

Microbial bioreporters hold promise for addressing challenges in medical and environmental applications. However, the difficulty in ensuring their stable persistence and function within the target environment remains a challenge. One strategy is to integrate information about the host strain and target environment into the design-build-test cycle of the bioreporter itself. Here, we present a case study for such an environmentally motivated design process by engineering the wheat commensal bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation. Comparative analysis showed that an exogenous P-responsive promoter outperformed its native counterparts. This reporter can selectively sense and report phosphorus limitation at plant-relevant concentrations of 25-100 μM without cross-activation from carbon or nitrogen limitation or high cell densities. Its performance is robust over a field-relevant pH range (5.8-8), and it responds only to inorganic phosphorus, even in the presence of common soil organic P. Finally, we used fluorescein-calibrated flow cytometry to assess whether the reporter's performance in shaken liquid culture predicts its performance in soil, finding that although the reporter is still functional at the bulk level, its variability in performance increases when grown in a soil slurry as compared to planktonic culture, with a fraction of the population not expressing the reporter proteins. Together, our environmentally aware design process provides an example of how laboratory bioengineering efforts can generate microbes with a greater promise to function reliably in their applied contexts.

Development-Associated Genes of the Epidermal Differentiation Complex (EDC)

The epidermal differentiation complex (EDC) is a cluster of genes that encode protein components of the outermost layers of the epidermis in mammals, reptiles and birds. The development of the stratified epidermis from a single-layered ectoderm involves an embryo-specific superficial cell layer, the periderm. An additional layer, the subperiderm, develops in crocodilians and over scutate scales of birds. Here, we review the expression of EDC genes during embryonic development. Several EDC genes are expressed predominantly or exclusively in embryo-specific cell layers, whereas others are confined to the epidermal layers that are maintained in postnatal skin. The S100 fused-type proteins scaffoldin and trichohyalin are expressed in the avian and mammalian periderm, respectively. Scaffoldin forms the so-called periderm granules, which are histological markers of the periderm in birds. Epidermal differentiation cysteine-rich protein (EDCRP) and epidermal differentiation protein containing DPCC motifs (EDDM) are expressed in the avian subperiderm where they are supposed to undergo cross-linking via disulfide bonds. Furthermore, a histidine-rich epidermal differentiation protein and feather-type corneous beta-proteins, also known as beta-keratins, are expressed in the subperiderm. The accumulating evidence for roles of EDC genes in the development of the epidermis has implications on the evolutionary diversification of the skin in amniotes.

The role of ion homeostasis in adaptation and tolerance to acetic acid stress in yeasts

Maintenance of asymmetric ion concentrations across cellular membranes is crucial for proper yeast cellular function. Disruptions of these ionic gradients can significantly impact membrane electrochemical potential and the balance of other ions, particularly under stressful conditions such as exposure to acetic acid. This weak acid, ubiquitous to both yeast metabolism and industrial processes, is a major inhibitor of yeast cell growth in industrial settings and a key determinant of host colonization by pathogenic yeast. Acetic acid toxicity depends on medium composition, especially on the pH (H+ concentration), but also on other ions' concentrations. Regulation of ion fluxes is essential for effective yeast response and adaptation to acetic acid stress. However, the intricate interplay among ion balancing systems and stress response mechanisms still presents significant knowledge gaps. This review offers a comprehensive overview of the mechanisms governing ion homeostasis, including H+, K+, Zn2+, Fe2+/3+, and acetate, in the context of acetic acid toxicity, adaptation, and tolerance. While focus is given on Saccharomyces cerevisiae due to its extensive physiological characterization, insights are also provided for biotechnologically and clinically relevant yeast species whenever available.

The beneficial effect of nanomethionine supplementation on growth performance, gene expression profile, and histopathology of heat-stressed broiler chicken

This study investigated the effects of nanomethionine (nano-meth) on performance, antioxidants, and gene expression of HSP70, HSP90 and Heat Shock factor-1 (HSF-1) from the liver, and TLR4 from the jejunum, of broiler chickens reared under normal temperatures or under heat stress. Three hundred 1-day-old chicks were randomly assigned to 5 treatment groups. Group 1 served as control. Under normal temperature, birds in group 2 received nano-meth (10 mL/L of drinking water) from d1 until the experiment ended. Group 3 birds were heat-stressed (HS) and did not receive any supplementation. Group 4 received nano-meth in the same dose from d1 old until experiment ended, and the birds were exposed to HS. Group 5 birds were HS and received supplementation of nano-meth during the HS period only. Nano-meth improved (P < 0.0001) final body weight, weight gain, feed conversion ratio, and also decreased (P < 0.0001) the effect of HS on growth performance. Reduction (P < 0.0001) in malondialdehyde and changes in antioxidant enzymes GPX and CAT activity indicated the antioxidant effect of nano-meth. Nano-meth supplementation caused an increase in the expression of HSP70 , HSP90 and HSF1, and a downregulation of TLR4 gene expression. Additionally, nano-meth-supplemented groups showed marked improvement in the histological liver structure, intestinal morphology and villus height compared to control or HS groups.

tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis

A class of noncoding RNAs, referred to as tsRNAs, is emerging with a potential to exert a new layer in gene regulation. These RNAs are breakdown products of tRNAs, either through active processing or passive cleavage or both. Since tRNAs are part of the general machinery for translation, their expression levels and activities are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize that Drosophila pupation, being a special developmental stage during which there is a global limitation of nutrients, represents a system in which such a link may readily reveal itself. We show that specific tsRNAs indeed show a dynamic accumulation upon entering the pupal stage. We describe experiments to characterize the mode of tsRNA action and, through the use of such gained knowledge, conduct a genome-wide analysis to assess the functions of dynamically expressed tsRNAs. Our results show that the predicted target genes are highly enriched in biological processes specific to this stage of development including metamorphosis. We further show that tsRNA action is required for successful pupation, providing direct support to the hypothesis that tsRNAs accumulated during this stage are critical to the gene expression program at this stage of development.

Nutrient deprivation alters the rate of COPII subunit recruitment at ER subdomains to tune secretory protein transport

Co-assembly of the multilayered coat protein complex II (COPII) with the Sar1 GTPase at subdomains of the endoplasmic reticulum (ER) enables secretory cargoes to be concentrated efficiently within nascent transport intermediates, which subsequently deliver their contents to ER-Golgi intermediate compartments. Here, we define the spatiotemporal accumulation of native COPII subunits and secretory cargoes at ER subdomains under differing nutrient availability conditions using a combination of CRISPR/Cas9-mediated genome editing and live cell imaging. Our findings demonstrate that the rate of inner COPII coat recruitment serves as a determinant for the pace of cargo export, irrespective of COPII subunit expression levels. Moreover, increasing inner COPII coat recruitment kinetics is sufficient to rescue cargo trafficking deficits caused by acute nutrient limitation. Our findings are consistent with a model in which the rate of inner COPII coat addition acts as an important control point to regulate cargo export from the ER.

Performance of Orbicella faveolata larval cohorts does not align with previously observed thermal tolerance of adult source populations

Orbicella faveolata, commonly known as the mountainous star coral, is a dominant reef-building species in the Caribbean, but populations have suffered sharp declines since the 1980s due to repeated bleaching and disease-driven mortality. Prior research has shown that inshore adult O. faveolata populations in the Florida Keys are able to maintain high coral cover and recover from bleaching faster than their offshore counterparts. However, whether this origin-specific variation in thermal resistance is heritable remains unclear. To address this knowledge gap, we produced purebred and hybrid larval crosses from O. faveolata gametes collected at two distinct reefs in the Upper Florida Keys, a nearshore site (Cheeca Rocks, CR) and an offshore site (Horseshoe Reef, HR), in two different years (2019, 2021). We then subjected these aposymbiotic larvae to severe (36°C) and moderate (32°C) heat challenges to quantify their thermal tolerance. Contrary to our expectation based on patterns of adult thermal tolerance, HR purebred larvae survived better and exhibited gene expression profiles that were less driven by stress response under elevated temperature compared to purebred CR and hybrid larvae. One potential explanation could be the compromised reproductive output of CR adult colonies due to repeated summer bleaching events in 2018 and 2019, as gametes originating from CR in 2019 contained less storage lipids than those from HR. These findings provide an important counter-example to the current selective breeding paradigm, that more tolerant parents will yield more tolerant offspring, and highlight the importance of adopting a holistic approach when evaluating larval quality for conservation and restoration purposes.

Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases

Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.

Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis

Regulatory variants in gene expression serve as bridges linking genetic variation and phenotypic plasticity. Environmental conditions typically influence the effects of regulatory variants on phenotypic plasticity; however, such genotype-by-environment interactions (G × E) are poorly understood. This study aimed to investigate the genetic basis of G × E in estuarine oyster (Crassostrea ariakensis), which is an important model animal for studying environmental adaption owing to its high plasticity and large intraspecific divergence. Genome-wide mapping of expression quantitative trait loci (eQTLs) for 23 environmental adaptive genes was performed for 256 estuarine oysters. We identified 1194 eQTL single nucleotide polymorphisms (eSNPs), including 433 cis-eSNPs in four genes and 722 trans-eSNPs in eight genes. The expression variation explanation of cis-eSNPs (9.95%) was significantly higher than that of trans-eSNPs (9.15%). We specifically showed cis- and trans-eSNPs with high linkage disequilibrium (LD) for Traf7, Slc6a5, Ggt, and Dap3. For example, we identified a cis-regulatory LD block containing 68 cis-eSNP and a trans-regulatory LD block, including 20 trans-eSNPs in Traf7. A high proportion (85%) of 40 vital eSNPs exhibited significant G × E effects. We identified crossing and nonparallel interactions of G × E, with the tag cis-eSNPs of Baat and Slc6a5 as representatives. Our results indicated that cis-eQTLs are highly conserved. This study provides insights into the understanding of adaptive evolutionary mechanisms and phenotypic response prediction to variable environments, as well as the genetic improvement for superior adaptive traits for genetic resource conservation and aquaculture.

Advances in Algomics technology: Application in wastewater treatment and biofuel production

Advanced sustainable bioremediation is gaining importance with rising global pollution. This review examines microalgae's potential for sustainable bioremediation and process enhancement using multi-omics approaches. Recently, microalgae-bacterial consortia have emerged for synergistic nutrient removal, allowing complex metabolite exchanges. Advanced bioremediation requires effective consortium design or pure culture based on the treatment stage and specific roles. The strain potential must be screened using modern omics approaches aligning wastewater composition. The review highlights crucial research gaps in microalgal bioremediation. It discusses multi-omics advantages for understanding microalgal fitness concerning wastewater composition and facilitating the design of microalgal consortia based on bioremediation skills. Metagenomics enables strain identification, thereby monitoring microbial dynamics during the treatment process. Transcriptomics and metabolomics encourage the algal cell response toward nutrients and pollutants in wastewater. Multi-omics role is also summarized for product enhancement to make algal treatment sustainable and fit for sustainable development goals and growing circular bioeconomy scenario.

Enhancing sludge methanogenesis with changed micro-environment of anaerobic microorganisms by Fenton iron mud

Conductive materials have been demonstrated to enhance sludge methanogenesis, but few researches have concentrated on the interaction among conductive materials, microorganisms and their immediate living environment. In this study, Fenton iron mud with a high abundance of Fe(III) was recycled and applied in anaerobic reactors to promote anaerobic digestion (AD) process. The results show that the primary content of extracellular polymeric substances (EPS) such as polysaccharides and proteins increased significantly, possibly promoting microbial aggregation. Furthermore, with the increment of redox mediators including humic substances in EPS and Fe(III) introduced by Fenton iron mud, the direct interspecies electron transfer (DIET) between methanogens and interacting bacteria could be accelerated, which enhanced the rate of methanogenesis in anaerobic digestion (35.21 ± 4.53% increase compared to the control). The further analysis of the anaerobic microbial community confirmed the fact that Fenton iron mud enriched functional microorganisms, such as the abundance of CO2-reducing (e.g. Chloroflexi) and Fe(III)-reducing bacteria (e.g., Tepidimicrobium), thereby expediting the electron transfer reaction in the AD process via microbial DIET and dissimilatory iron reduction (DIR). This work will make it possible for using the recycled hazardous material - Fenton iron mud to improve the performance of anaerobic granular sludge during methanogenesis.

Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins

AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).

Urbanization drives adaptive evolution in a Neotropical bird

Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.

Resurrecting urban sunflowers: Phenotypic and molecular changes between antecedent and modern populations separated by 36 years

Resurrection experiments provide a unique opportunity to evaluate phenotypic and molecular evolution in response to environmental challenges. To understand the evolution of urban populations of Helianthus annuus, we compared plants from 36-year-old antecedent seed collections to modern seed collections from the same area using molecular and quantitative genetic approaches. We found 200 differentially expressed transcripts between antecedent and modern groups, and transcript expression was generally higher in modern samples as compared to antecedent samples. Admixture analysis indicated gene flow from domesticated to modern populations over time. After a greenhouse refresher generation, one antecedent-modern population pair was grown under two water availability (well-watered and drought) and temperature (ambient and elevated by 2.8°C) conditions reflecting historical and contemporary climates. Overall, 78% (7 out of 9) of traits differed between the antecedent and modern populations, with modern individuals displaying some trait changes that are coherent with climate changes expectations and some trait changes in the direction of crop varieties. Phenotypic selection analysis showed that modern trait values were often favoured by selection, especially in environmental treatments resembling modern conditions. Trait heritability in the antecedent population was five times as high as in the modern population, on average. In addition, phenotypic plasticity for some traits, such as flowering phenology, was present in the antecedent population but absent in the modern population. The combination of phenotypic and molecular information suggests that evolution has been influenced by crop-wild introgression, adaptive processes and drift. We discuss these results in the context of continued evolution in response to anthropogenic factors.

Phenotypic variance partitioning by transcriptomic gene expression levels and environmental variables for anthropometric traits using GTEx data

Phenotypic variation in human is the results of genetic variation and environmental influences. Understanding the contribution of genetic and environmental components to phenotypic variation is of great interest. The variance explained by genome-wide single nucleotide polymorphisms (SNPs) typically represents a small proportion of the phenotypic variance for complex traits, which may be because the genome is only a part of the whole biological process to shape the phenotypes. In this study, we propose to partition the phenotypic variance of three anthropometric traits, using gene expression levels and environmental variables from GTEx data. We use the gene expression of four tissues that are deemed relevant for the anthropometric traits (two adipose tissues, skeletal muscle tissue and blood tissue). Additionally, we estimate the transcriptome-environment correlation that partly underlies the phenotypes of the anthropometric traits. We found that genetic factors play a significant role in determining body mass index (BMI), with the proportion of phenotypic variance explained by gene expression levels of visceral adipose tissue being 0.68 (SE = 0.06). However, we also observed that environmental factors such as age, sex, ancestry, smoking status, and drinking alcohol status have a small but significant impact (0.005, SE = 0.001). Interestingly, we found a significant negative correlation between the transcriptomic and environmental effects on BMI (transcriptome-environment correlation = -0.54, SE = 0.14), suggesting an antagonistic relationship. This implies that individuals with lower genetic profiles may be more susceptible to the effects of environmental factors on BMI, while those with higher genetic profiles may be less susceptible. We also show that the estimated transcriptomic variance varies across tissues, e.g., the gene expression levels of whole blood tissue and environmental variables explain a lower proportion of BMI phenotypic variance (0.16, SE = 0.05 and 0.04, SE = 0.004 respectively). We observed a significant positive correlation between transcriptomic and environmental effects (1.21, SE = 0.23) for this tissue. In conclusion, phenotypic variance partitioning can be done using gene expression and environmental data even with a small sample size (n = 838 from GTEx data), which can provide insights into how the transcriptomic and environmental effects contribute to the phenotypes of the anthropometric traits.

Transcriptomic analysis reveals the rareness of genetic assimilation of gene expression in environmental adaptations

Genetic assimilation is the evolutionary process by which an environmentally induced phenotype becomes genetically encoded and constitutive. Genetic assimilation has been proposed as a concluding step in environmental adaptation, but its prevalence has not been systematically investigated. Analyzing transcriptomic data collected upon reciprocal transplant, we address this question in the experimental evolution, domestication, or natural evolution of seven diverse species. We find that genetic assimilation of environment-induced gene expression is the exception rather than the rule and that substantially more genes retain than lose their expression plasticity upon organismal adaptations to new environments. The probability of genetic assimilation of gene expression decreases with the expression level and number of transcription factors controlling the gene, suggesting that genetic assimilation results primarily from passive losses of gene regulations that are not mutationally robust. Hence, for gene expression, our findings argue against the purported generality or importance of genetic assimilation to environmental adaptation.

Timed Pulses in DNA Strand Displacement Reactions

Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays, we demonstrate here a strategy to achieve temporally programmed pulse output signals in DNA-based strand displacement reactions (SDRs). To achieve this, we rationally designed input strands that, once bound to their target duplex, can be gradually degraded, resulting in a pulse output signal. We also designed blocker strands that suppress strand displacement and determine the time at which the pulse reaction is generated. We show that by controlling the degradation rate of blocker and input strands, we can finely control the delayed pulse output over a range of 10 h. We also prove that it is possible to orthogonally delay two different pulse reactions in the same solution by taking advantage of the specificity of the degradation reactions for the input and blocker strands. Finally, we show here two possible applications of such delayed pulse SDRs: the time-programmed pulse decoration of DNA nanostructures and the sequentially appearing and self-erasing formation of DNA-based patterns.

Environmentally robust cis-regulatory changes underlie rapid climatic adaptation

Changes in gene expression are thought to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene expression differences in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5 to 10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis-regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans-effects, which showed greater sensitivity to temperature. Nonetheless, we found a small subset of temperature-dependent cis-regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis-regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis-regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans, may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis, illustrating the genetic and nongenetic mechanisms underlying the establishment of populations in new environments.

A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes

Coarse-grained resource allocation models (C-GRAMs) are simple mathematical models of cell physiology, where large components of the macromolecular composition are abstracted into single entities. The dynamics and steady-state behaviour of such models provides insights on optimal allocation of cellular resources and have explained experimentally observed cellular growth laws, but current models do not account for the uptake of compound sources of carbon and nitrogen. Here, we formulate a C-GRAM with nitrogen and carbon pathways converging on biomass production, with parametrizations accounting for respirofermentative and purely respiratory growth. The model describes the effects of the uptake of sugars, ammonium and/or compound nutrients such as amino acids on the translational resource allocation towards proteome sectors that maximized the growth rate. It robustly recovers cellular growth laws including the Monod law and the ribosomal growth law. Furthermore, we show how the growth-maximizing balance between carbon uptake, recycling, and excretion depends on the nutrient environment. Lastly, we find a robust linear correlation between the ribosome fraction and the abundance of amino acid equivalents in the optimal cell, which supports the view that simple regulation of translational gene expression can enable cells to achieve an approximately optimal growth state.

Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases

The most highly expressed genes in microbial genomes tend to use a limited set of synonymous codons, often referred to as "preferred codons." The existence of preferred codons is commonly attributed to selection pressures on various aspects of protein translation including accuracy and/or speed. However, gene expression is condition-dependent and even within single-celled organisms transcript and protein abundances can vary depending on a variety of environmental and other factors. Here, we show that growth rate-dependent expression variation is an important constraint that significantly influences the evolution of gene sequences. Using large-scale transcriptomic and proteomic data sets in Escherichia coli and Saccharomyces cerevisiae, we confirm that codon usage biases are strongly associated with gene expression but highlight that this relationship is most pronounced when gene expression measurements are taken during rapid growth conditions. Specifically, genes whose relative expression increases during periods of rapid growth have stronger codon usage biases than comparably expressed genes whose expression decreases during rapid growth conditions. These findings highlight that gene expression measured in any particular condition tells only part of the story regarding the forces shaping the evolution of microbial gene sequences. More generally, our results imply that microbial physiology during rapid growth is critical for explaining long-term translational constraints.

MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance

The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability to physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. Analysis of EGRIN 2.0 shows how modulation of the MtrAB two-component signaling system tunes Mtb growth in response to related host microenvironmental cues. Disruption of MtrAB by tunable CRISPR interference confirms that the signaling system regulates multiple peptidoglycan hydrolases, among other targets, that are important for cell division. Further, MtrA decreases the effectiveness of antibiotics by mechanisms of both intrinsic resistance and drug tolerance. Together, the model-enabled dissection of complex MtrA regulation highlights its importance as a drug target and illustrates how EGRIN 2.0 facilitates discovery and mechanistic characterization of Mtb adaptation to specific host microenvironments within the host.

Understanding and applying biological resilience, from genes to ecosystems

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand 'biological resilience', or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience.