Project description:Phosphate (Pi) is an essential element to all living cells yet fluctuations in Pi concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton clade living in the world’s oceans adapting to and surviving long periods of sub-optimal conditions and resuming growth as soon as nutrient concentrations permit. The knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. Using high-throughput RNA sequencing we have identified the dynamics of the model diatom Phaeodactylum tricornutum global transcriptome in response to Pi fluctuations. We report genes encoding previously unidentified putative Pi transporters that, together with the alkaline phosphatases genes highly expressed under Pi depletion, are probably accountable for a very efficient Pi scavenging system. Our data also reveal the complexity of the P. tricornutum responsive sensory and signaling system that combines bacterial two-component systems with more complex pathways reminiscent of metazoans. This intricate set of membrane receptors and signal-transduction related proteins is likely responsible for the detection of environmental nutrient fluctuations, triggering a multitude of signaling cascades leading to gene regulatory events that define new adaptive physiological states. This together with the novel detection of a multitude of long non-coding intergenic RNAs specifically expressed under Pi stress, begins to provide insights into the complex molecular regulatory program involved in the resilience and ecological success of diatoms. Examination of Pi-responsive transcriptoms in diatoms.
Project description:We used microarrays to investigate the transcriptome of 6 days old male flies exposed to either 15 or 25 C development at either constant or fluctuating temperatures. Further, we investigated gene expression at benign (20C) and high (35C) temperatures With global climate change temperature means and variability are expected to increase. Thus, exposures to elevated temperatures are expected to become an increasing challenge for terrestrial ectotherm populations. While evolutionary adaptation seems to be constrained or proceed at an insufficient pace, many populations are expected to rely on phenotypic plasticity (thermal acclimation) for coping with the predicted changes. However, the effects of fluctuating temperature on the molecular mechanisms and the implications for heat tolerance are not well understood. To understand and predict consequences of climate change it is important to investigate how different components of the thermal environment, including fluctuating thermal conditions, contribute to changes in thermal acclimation. In this study we investigated the impact of mean and diurnal fluctuation of temperature on heat tolerance in Drosophila melanogaster and on the underlying molecular mechanisms in adult male flies. Flies from two constant and two ecologically relevant fluctuating temperature regimes were tested for their critical thermal maxima (CTmax) and associated global gene expression profiles at benign and thermally stressful conditions. Both temperature parameters contributed independently to the thermal acclimation, with regard to heat tolerance as well as the global gene expression profile. Although the independent transcriptional effects caused by fluctuations were relatively small, they are likely to be essential for our understanding of thermal adaptation. Thus, high temperature acclimation ability might not be measured correctly and might even be underestimated at constant temperatures. Our data suggests that the particular mechanisms affected by thermal fluctuations are related to phototransduction and environmental sensing. Thus genes and pathways involved in those processes are likely to be of major importance in a future warmer and more fluctuating climate. Eight experimental groups were analyzed in triplicate, in total 24 Affymetrix GeneChip Drosophila Genome 2.0 Arrays
Project description:Thermal exposure of sessile marine animals inhabiting estuarine intertidal regions is a matter of serious concern. The Hong Kong oyster, Crassostrea hongkongensis is one of the dominant sessile inhabitants of marine intertidal region which undergoes large seasonal temperature fluctuations every year. The oyster has developed several adaptation mechanisms to cope with acute thermal stress. However, the genetic basis of these mechanisms remain largely unclear. To better understand how acute thermal exposure affects the biology of the oyster, two cDNA libraries obtained from the gill of oysters exposed to thermal stress and ambient temperature were sequenced using the Digital Gene Expression (DGE) tag profiling strategy. In total, 5.9 and 6.2 million reads were obtained for thermal stress and control libraries respectively, with approximately 74.25% and 75.02 % of the reads mapping to the C. hongkongensis reference sequence. A total of 605 differentially expressed transcripts could be detected in the thermal stress group as compared to the control group, of which 378 are up-regulated and 227 are down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these Differentially Expressed Genes (DEGs) were enriched with a broad spectrum of biological processes and pathways, including those associated with chaperones, antioxidants, immunity, apoptosis and cytoskeletal reorganization. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum was the most affected metabolic pathway, which plays an important role in the unfolded protein response (UPR) and ER-associated degradation (ERAD) processes. Our results demonstrate the complex multi-modal cellular response to thermal stress in C. hongkongensis. Overall design: Digital gene expression tag profiling analysis of the Hong Kong oyster
Project description:This study examined differentially expressed (DE) gene transcripts and regulated pathways of two geographically distinct channel catfish (Ictalurus punctatus) strains and one hybrid catfish (I. punctatus x [blue catfish] I. furcatus) strain to test whether one particular catfish type handled thermal stress better. Following a six-week growth experiment, where fish were subjected to daily cycling temperatures of either 27-31°C or 32-36°C, mimicking pond fluctuations. We sequenced 18 cDNA libraries of liver samples to obtain 61 million reads per library. There were 5,443 DE transcripts and 41,689 regulated pathways. Northern channel catfish had the highest amount of DE transcripts (48.6%), 5 times that of southern channel catfish, and the greatest amount of transcripts with fold changes ≥ 2. The overall amount of temperature-induced DE transcripts between southern hybrid and southern channel catfish was fairly comparable in relation to that of northern channel catfish, however, there were more transcripts up- or downregulated with ≥ 2 fold changes in channel catfish strains compared to the southern hybrid catfish. Results from this study strongly suggest genetic differences between geographic catfish types affect physiological responses to thermal stress. Furthermore, a number of genes were linked to thermal stress tolerance, which may be beneficial for understanding geographic differences in thermal stress tolerance in ectotherms and for strain development of catfish. Hepatic mRNA profiles of three fingerling catfish types following a six week growth experiment of daily cycling temperatures of either 27-31°C or 32-36°C, mimicking pond fluctuations.
Project description:Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results: Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions: This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and may be used for acclimation to environmental conditions. RNA-seq study of sRNA populations in two species of diatoms using Illumina GAII high-throughput sequencing
Project description:The interplay between phenotypic plasticity and adaptive evolution has long been an important topic of evolutionary biology. This process is critical to our understanding of a species evolutionary potential in light of rapid climate changes. Despite recent theoretical work, empirical studies of natural populations, especially in marine invertebrates, are scarce. In this study, we investigated the relationship between adaptive divergence and plasticity by integrating genetic and phenotypic variation in Pacific oysters from its natural range in China. Genome resequencing of 371 oysters revealed unexpected fine-scale genetic structure that is largely consistent with phenotypic divergence in growth, physiology, thermal tolerance and gene expression across environmental gradient. These findings suggest that selection and local adaptation are pervasive and together with limited gene flow shape adaptive divergence. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and likely favored by selection in organisms facing dynamic environments such as oysters. Divergence in heat response and tolerance implies that the evolutionary potential to a warming climate differs among oyster populations. We suggest that trade-offs in energy allocation are important to adaptive divergence with acetylation playing a role in energy depression under thermal stress.
Project description:Alteration of normal ploidy (aneuploidy) is an important mechanism of evolution of species. It has been linked to a rapid response to stress and is regarded as a hallmark of cancer. While increased genomic instability of aneuploid cells can accelerate genetic diversification and facilitate adaptation, these cells also face the adverse effects of gene imbalance, resulting in fitness cost. Here, to understand the mechanisms through which cells respond to aneuploidy and develop tolerance leading to fitness restoration, we subjected disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution, forcing disomy maintenance with selection markers. We characterized mutations, karyotype alterations and gene expression changes throughout adaptive evolution, and analyzed them to dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates, and endured a diverse array of adaptive events. Despite remarkable diversity of these events, cells tended to evolve towards normal ploidy through both chromosomal DNA loss and changes in gene expression. We identified genes commonly altered during the evolution of disomic strains, and genes recurrently mutated in multiple lines. Our analyses revealed protein translation, amino acid biosynthesis, transcription regulation, stress response, and nucleotide and protein degradation as key pathways for the adaptive response to aneuploidy and identified transcription factors that mediate this response. Together, these findings define cellular strategies that underlie tolerance to aneuploidy. Overall design: We compared the transcriptome data of laboratory evolved (600 generations) and unevolved disomic yeast strains to find the signatures of aneuploidy adaptation
Project description:BbMBF1 played crucial roles in mediating response the prolonged thermal stress, a determinant to the environmental fitness of fungal entomopathogens. We characterized for the first time that disruption of BbMBF1 reduced the mycelial tolerance to the 9-h thermal stress under 40°C. The global transcriptome involved in the response to the thermal stress was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in fungal response to the themal stress. 1. Total RNA obtained from BbMBF1 disruption mutant were compared to that of wild type strain under control conditin (free of thermal stress); 2. Total RNA obtained from BbMBF1 disruption mutant were compared to that of WT strain under 9-h thermal stress at 40°C.
Project description:We isolate the cultivable microbiome of a diatom and show that different bacteria have commensal, antagonistic, or synergistic effects on the diatom. One synergistic bacterium enhances growth of the diatom by production of auxin, a phytohormone. The diatom and its synergistic bacterium appear to use auxin and tryptophan as signaling molecules that drive nutrient exchange. Detection of auxin molecules and biosynthesis gene transcripts in the Pacific Ocean suggests that these interactions are widespread in marine ecosystems. Overall design: Transcriptomes were collected for triplicate diatom cultures harvested at the mid-exponential growth phase in the defined seawater medium Aquil either without any bacteria, i.e. axenic (control), or with a Sulfitobacter sp. SA11 that was previously isolated from the diatom (Pseudo-nitzschia multiseries). In addition, transcriptomes were collected for triplicate bacterial cultures (Sulfitobacter sp. SA11) harvested at the mid-exponential phase in the defined seawater medium Aquil either without the diatom (supplemented with 1 uM glucose to allow for bacterial growth) or with the diatom (P. multiseries strain PC9). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. For the diatom transcriptome, pooled counts for the +bacterium treatment were normalized to pooled counts for the axenic “control” treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor. For the bacterial transcriptome, pooled counts for the +diatom treatment were normalized to pooled counts for the +glucose “control” treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.
Project description:Pleiotropic regulatory mutations affect diverse cellular processes, posing an explicit challenge to our multi-scale understanding of the genotype-phenotype relationships across multiple biological scales. Adaptive Laboratory Evolution (ALE) allows for such mutations to be found and characterized in the context of clear selection pressures. Here, several ALE-selected single-mutation variants in Escherichia coli’s RNA polymerase (RNAP) are detailed using an integrated multi-scale experimental and computational approach. While these mutations increase cellular growth rates in steady environments, they reduce tolerance to stress and environmental fluctuations. We detail structural changes in the RNAP that rewire the transcriptional machinery to rebalance proteome and energy allocation towards growth and away from several hedging and stress functions. SurprisinglyW, we find that while these mutations occur in diverse locations in the RNAP, they share a common adaptive mechanism. In turn, these findings highlight the resource allocation trade-offs organisms face and suggest how the structure of the regulatory network enhances evolvability. Overall design: Samples were taken from mid-log phase of batch cultures or steady state phase in chemostat cultures. RNAseq was performed by paired end libraries in a modified dUTP method (see methods in paper)