Ecological nitrogen limitation shapes the DNA composition of plant genomes

GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences

The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Diptera, Coleoptera and Lepidoptera. Two species of Diptera, Bombylius major and B. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Diptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.

Genome-material costs and functional trade-offs in the autopolyploid Solidago gigantea (giant goldenrod) series

PREMISE

Increased genome-material costs of N and P atoms inherent to organisms with larger genomes have been proposed to limit growth under nutrient scarcities and to promote growth under nutrient enrichments. Such responsiveness may reflect a nutrient-dependent diploid versus polyploid advantage that could have vast ecological and evolutionary implications, but direct evidence that material costs increase with ploidy level and/or influence cytotype-dependent growth, metabolic, and/or resource-use trade-offs is limited.

METHODS

We grew diploid, autotetraploid, and autohexaploid Solidago gigantea plants with one of four ambient or enriched N:P ratios and measured traits related to material costs, primary and secondary metabolism, and resource-use.

RESULTS

Relative to diploids, polyploids invested more N and P into cells, and tetraploids grew more with N enrichments, suggesting that material costs increase with ploidy level. Polyploids also generally exhibited strategies that could minimize material-cost constraints over both long (reduced monoploid genome size) and short (more extreme transcriptome downsizing, reduced photosynthesis rates and terpene concentrations, enhanced N-use efficiencies) evolutionary time periods. Furthermore, polyploids had lower transpiration rates but higher water-use efficiencies than diploids, both of which were more pronounced under nutrient-limiting conditions.

CONCLUSIONS

N and P material costs increase with ploidy level, but material-cost constraints might be lessened by resource allocation/investment mechanisms that can also alter ecological dynamics and selection. Our results enhance mechanistic understanding of how global increases in nutrients might provide a release from material-cost constraints in polyploids that could impact ploidy (or genome-size)-specific performances, cytogeographic patterning, and multispecies community structuring.

Adaptation to a limiting element involves mitigation of multiple elemental imbalances

About 20 elements underlie biology and thus constrain biomass production. Recent systems-level observations indicate that altered supply of one element impacts the processing of most elements encompassing an organism (i.e. ionome). Little is known about the evolutionary tendencies of ionomes as populations adapt to distinct biogeochemical environments. We evolved the bacterium Serratia marcescens under five conditions (i.e. low carbon, nitrogen, phosphorus, iron or manganese) that limited the yield of the ancestor compared with replete medium, and measured the concentrations and use efficiency of these five, and five other elements. Both physiological responses of the ancestor, as well as evolutionary responses of descendants to experimental environments involved changes in the content and use efficiencies of the limiting element, and several others. Differences in coefficients of variation in elemental contents based on biological functions were evident, with those involved in biochemical building (C, N, P, S) varying least, followed by biochemical balance (Ca, K, Mg, Na), and biochemical catalysis (Fe, Mn). Finally, descendants evolved to mitigate elemental imbalances evident in the ancestor in response to limiting conditions. Understanding the tendencies of such ionomic responses will be useful to better forecast biological responses to geochemical changes.

Impact of beaver ponds on biogeochemistry of organic carbon and nitrogen along a fire-impacted stream

Wildfires, which are increasing in frequency and severity in the western U.S., impact water quality through increases in erosion, and transport of nutrients and metals. Meanwhile, beaver populations have been increasing since the early 1900s, and the ponds they create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). However, it remains unknown how the presence of beaver ponds in burned watersheds may impact retention and transformation of chemical constituents originating in burned uplands (e.g., pyrogenic dissolved organic matter; pyDOM) and the consequences for downstream water quality. Here, we investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments. The chemistry and microbiology of surface water and sediment changed along a stream sequence starting upstream of fire and flowing through multiple beaver ponds and interconnecting stream reaches within a burned high-elevation forest watershed. The relative abundance of N-containing compounds increased in surface water of the burned beaver ponds, which corresponded to lower C/N and O/C, and higher aromaticity as characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The resident microbial communities lack the capacity to process such aromatic pyDOM, though genomic analyses demonstrate their potential to metabolize various compounds in the anaerobic sediments of the beaver ponds. Collectively, this work highlights the role of beaver ponds as biological "hotspots" with unique biogeochemistry in fire-impacted systems.

Stoichiometry versus ecology: the relationships between genome size and guanine-cytosine content, and tissue nitrogen and phosphorus in grassland herbs

BACKGROUND AND AIMS

Plant tissue nitrogen (N) and phosphorus (P) and genome traits, such as genome size and guanine-cytosine (GC) content, scale with growth or metabolic rates and are linked to plant ecological strategy spectra. Tissue NP stoichiometry and genome traits are reported to affect plant growth, metabolic rates or ecological strategies in contrasting ways, although the elemental costs for building and maintaining DNA are typically overlooked.

METHODS

We formulated stoichiometry- and ecology-based predictions on the relationship between genome size and GC content to tissue N, P and N : P and tested them on a set of 130 herbaceous species from a temperate grassland using ordinary, phylogenetic and quantile regression.

KEY RESULTS

Genome size was only negatively linked to plant N and N : P in species with very small genomes. We found no link between genome size and plant P. GC content was negatively linked to plant N and P but we found these significant links consistently in both GC-rich and GC-poor species. Finally, GC content correlated positively with plant N : P but only in species with GC-rich genomes.

CONCLUSIONS

Our results provide stronger support for the ecology-based predictions than the stoichiometry-based predictions, and for the links between GC content and plant N and P stoichiometry than for genome size. We argue that the theories of plant metabolic rates and ecological strategies (resource-acquisitive vs. conservative or ruderal vs. stress-tolerator spectra) better explain interspecific genome-NP stoichiometry relationships at the tissue level (although relatively weakly) than the stoichiometric theory based on the elemental costs for building and maintaining DNA.

Enhanced Speciation of Pyrogenic Organic Matter from Wildfires Enabled by 21 T FT-ICR Mass Spectrometry

Wildfires affect soils through the formation of pyrogenic organic matter (pyOM) (e.g., char and soot). While many studies examine the connection between pyOM persistence and carbon (C) composition, nitrogen (N) transformation in wildfire-impacted systems remains poorly understood. Thermal reactions in wildfires transform biomass into a highly complex, polyfunctional, and polydisperse organic mixture that challenges most mass analyzers. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that achieves resolving powers sufficient to separate species that differ in mass by the mass of an electron across a wide molecular weight range (m/z 150-1500). We report enhanced speciation of organic N by positive-ion electrospray ionization (ESI) that leverages ultrahigh resolving power (m/Δm_50% = 1 800 000 at m/z 400) and mass accuracy (<10-100 ppb) achieved by FT-ICR MS at 21 T. Isobaric overlaps, roughly the mass of an electron (M_e^- = 548 μDa), are resolved across a wide molecular weight range and are more prevalent in positive ESI than negative ESI. The custom-built 21 T FT-ICR MS instrument identifies previously unresolved mass differences in C_cH_hN_nO_oS_s formulas and assigns more than 30 000 peaks in a pyOM sample. This is the first molecular catalogue of pyOM by positive-ion ESI 21 T FT-ICR MS and presents a method to provide new insight into terrestrial cycling of organic carbon and nitrogen in wildfire impacted ecosystems.

Genome downsizing after polyploidy: mechanisms, rates and selection pressures

An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO₂ uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

BACKGROUND

Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts.

RESULTS

We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.

CONCLUSIONS

These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.

Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in glioma

Background

The five-year survival rate and therapeutic effect of malignant glioma is low. Identification of key/associated proteins and pathways in glioma is necessary for developing effective diagnosis and targeted therapy of glioma. In addition, Glioma involves hypoxia-specific microenvironment, whether hypoxia restriction influences the stoichioproteomic characteristics of expressed proteins is unknown.

Methods

In this study, we analyzed the most comprehensive immunohistochemical data from 12 human glioma samples and 4 normal cell types of cerebral cortex, identified differentially expressed proteins (DEPs), and researched the oxygen contents of DEPs, highly and lowly expressed proteins. Further we located key genes on human genome to determine their locations and enriched them for key functional pathways.

Results

Our results showed that although no difference was detected on whole proteome, the average oxygen content of highly expressed proteins is 6.65% higher than that of lowly expressed proteins in glioma. A total of 1480 differentially expressed proteins were identified in glioma, including 226 up regulated proteins and 1254 down regulated proteins. The average oxygen content of up regulated proteins is 2.56% higher than that of down regulated proteins in glioma. The localization of differentially expressed genes on human genome showed that most genes were on chromosome 1 and least on Y. The up regulated proteins were significantly enriched in pathways including cell cycle, pathways in cancer, oocyte meiosis, DNA replication etc. Functional dissection of the up regulated proteins with high oxygen contents showed that 51.28% of the proteins were involved in cell cycle and cyclins.

Conclusions

Element signature of oxygen limitation could not be detected in glioma, just as what happened in plants and microbes. Unsaved use of oxygen by the highly expressed proteins and DEPs were adapted to the fast division of glioma cells. This study can help to reveal the molecular mechanism of glioma, and provide a new approach for studies of cancer-related biomacromolecules. In addition, this study lays a foundation for application of stoichioproteomics in precision medicine.

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0571-y) contains supplementary material, which is available to authorized users.

Stoichiogenomics reveal oxygen usage bias, key proteins and pathways associated with stomach cancer

Stomach cancer involves hypoxia-specific microenvironments. Stoichiogenomics explores environmental resource limitation on biological macromolecules in terms of element usages. However, the patterns of oxygen usage by proteins and the ways that proteins adapt to a cancer hypoxia microenvironment are still unknown. Here we compared the oxygen and carbon contents ([C]) between proteomes of stomach cancer (hypoxia) and two stomach glandular cells (normal). Key proteins, genome locations, pathways, and functional dissection associated with stomach cancer were also studied. An association of oxygen content ([O]) and protein expression level was revealed in stomach cancer and stomach glandular cells. For differentially expressed proteins (DEPs), oxygen contents in the up regulated proteins were3.2%higherthan that in the down regulated proteins in stomach cancer. A total of 1,062 DEPs were identified; interestingly none of these proteins were coded on Y chromosome. The up regulated proteins were significantly enriched in pathways including regulation of actin cytoskeleton, cardiac muscle contraction, pathway of progesterone-mediated oocyte maturation, etc. Functional dissection of the up regulated proteins with high oxygen contents showed that most of them were cytoskeleton, cytoskeleton associated proteins, cyclins and signaling proteins in cell cycle progression. Element signature of resource limitation could not be detected in stomach cancer for oxygen, just as what happened in plants and microbes. Unsaved use of oxygen by the highly expressed proteins was adapted to the rapid growth and fast division of the stomach cancer cells. In addition, oxygen usage bias, key proteins and pathways identified in this paper laid a foundation for application of stoichiogenomics in precision medicine.

Impacts of soil nitrogen and phosphorus levels on cytotype performance of the circumboreal herb Chamerion angustifolium: implications for polyploid establishment

PREMISE

Although polyploidy commonly occurs in angiosperms, not all polyploidization events lead to successful lineages, and environmental conditions could influence cytotype dynamics and polyploid success. Low soil nitrogen and/or phosphorus concentrations often limit ecosystem primary productivity, and changes in these nutrients might differentially favor some cytotypes over others, thereby influencing polyploid establishment.

METHODS

We grew diploid, established tetraploid, and neotetraploid Chamerion angustifolium (fireweed) in a greenhouse under low and high soil nitrogen and phosphorus conditions and different competition treatments and measured plant performance (height, biomass, flower production, and root bud production) and insect damage responses. By comparing neotetraploids to established tetraploids, we were able to examine traits and responses that might directly arise from polyploidization before they are modified by natural selection and/or genetic drift.

RESULTS

We found that (1) neopolyploids were the least likely to survive and flower and experienced the most herbivore damage, regardless of nutrient conditions; (2) both neo- and established tetraploids had greater biomass and root bud production under nutrient-enriched conditions, whereas diploid biomass and root bud production was not significantly affected by nutrients; and (3) intra-cytotype competition more negatively affected diploids and established tetraploids than it did neotetraploids.

CONCLUSIONS

Following polyploidization, biomass and clonal growth might be more immediately affected by environmental nutrient availabilities than plant survival, flowering, and/or responses to herbivory, which could influence competitive dynamics. Specifically, polyploids might have competitive and colonizing advantages over diploids under nutrient-enriched conditions favoring their establishment, although establishment may also depend upon the density and occurrences of other related cytotypes in a population.

Effects of soil nitrogen on diploid advantage in fireweed, Chamerion angustifolium (Onagraceae)

In many ecosystems, plant growth and reproduction are nitrogen limited. Current and predicted increases of global reactive nitrogen could alter the ecological and evolutionary trajectories of plant populations. Nitrogen is a major component of nucleic acids and cell structures, and it has been predicted that organisms with larger genomes should require more nitrogen for growth and reproduction and be more negatively affected by nitrogen scarcities than organisms with smaller genomes. In a greenhouse experiment, we tested this hypothesis by examining whether the amount of soil nitrogen supplied differentially influenced the performance (fitness, growth, and resource allocation strategies) of diploid and autotetraploid fireweed (Chamerion angustifolium). We found that soil nitrogen levels differentially impacted cytotype performance, and in general, diploids were favored under low nitrogen conditions, but this diploid advantage disappeared under nitrogen enrichment. Specifically, when nitrogen was scarce, diploids produced more seeds and allocated more biomass toward seed production relative to investment in plant biomass or total plant nitrogen than did tetraploids. As nitrogen supplied increased, such discrepancies between cytotypes disappeared. We also found that cytotype resource allocation strategies were differentially dependent on soil nitrogen, and that whereas diploids adopted resource allocation strategies that favored current season reproduction when nitrogen was limiting and future reproduction when nitrogen was more plentiful, tetraploids adopted resource allocation strategies that favored current season reproduction under nitrogen enrichment. Together these results suggest nitrogen enrichment could differentially affect cytotype performance, which could have implications for cytotypes' ecological and evolutionary dynamics under a globally changing climate.

We Are What We Eat: A Stoichiometric and Ecometabolomic Study of Caterpillars Feeding on Two Pine Subspecies of Pinus sylvestris

Many studies have addressed several plant-insect interaction topics at nutritional, molecular, physiological, and evolutionary levels. However, it is still unknown how flexible the metabolism and the nutritional content of specialist insect herbivores feeding on different closely related plants can be. We performed elemental, stoichiometric, and metabolomics analyses on leaves of two coexisting Pinus sylvestris subspecies and on their main insect herbivore; the caterpillar of the processionary moth (Thaumetopoea pityocampa). Caterpillars feeding on different pine subspecies had distinct overall metabolome structure, accounting for over 10% of the total variability. Although plants and insects have very divergent metabolomes, caterpillars showed certain resemblance to their plant-host metabolome. In addition, few plant-related secondary metabolites were found accumulated in caterpillar tissues which could potentially be used for self-defense. Caterpillars feeding on N and P richer needles had lower N and P tissue concentration and higher C:N and C:P ratios, suggesting that nutrient transfer is not necessarily linear through trophic levels and other plant-metabolic factors could be interfering. This exploratory study showed that little chemical differences between plant food sources can impact the overall metabolome of specialist insect herbivores. Significant nutritional shifts in herbivore tissues could lead to larger changes of the trophic web structure.

Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities

Nitrogen is crucially limiting in ocean surface waters, and its availability varies substantially with coastal regions typically richer in nutrients than open oceans. In a biological stoichiometry framework, a parsimonious strategy of nitrogen allocation predicts nitrogen content of proteins to be lower in communities adapted to open ocean than to coastal regions. To test this hypothesis we have directly interrogated marine microbial communities, using a series of metagenomics datasets with a broad geographical distribution from the Global Ocean Sampling Expedition. Analyzing over 20 million proteins, we document a ubiquitous signal of nitrogen conservation in open ocean communities, both in membrane and non-membrane proteins. Efficient nitrogen allocation is expected to specifically target proteins that are expressed at high rate in response to nitrogen starvation. Furthermore, in order to preserve protein functional efficiency, economic nitrogen allocation is predicted to target primarily the least functionally constrained regions of proteins. Contrasting the NtcA-induced pathway, typically up-regulated in response to nitrogen starvation, with the arginine anabolic pathway, which is instead up-regulated in response to nitrogen abundance, we show how both these predictions are fulfilled. Using evolutionary rates as an informative proxy of functional constraints, we show that variation in nitrogen allocation between open ocean and coastal communities is primarily localized in the least functionally constrained regions of the genes triggered by NtcA. As expected, such a pattern is not detectable in the genes involved in the arginine anabolic pathway. These results directly link environmental nitrogen availability to different adaptive strategies of genome evolution, and emphasize the relevance of the material costs of evolutionary change in natural ecosystems.

The Amount of Nitrogen Used for Photosynthesis Modulates Molecular Evolution in Plants

Genome and transcript sequences are composed of long strings of nucleotide monomers (A, C, G, and T/U) that require different quantities of nitrogen atoms for biosynthesis. Here, it is shown that the strength of selection acting on transcript nitrogen content is influenced by the amount of nitrogen plants require to conduct photosynthesis. Specifically, plants that require more nitrogen to conduct photosynthesis experience stronger selection on transcript sequences to use synonymous codons that cost less nitrogen to biosynthesize. It is further shown that the strength of selection acting on transcript nitrogen cost constrains molecular sequence evolution such that genes experiencing stronger selection evolve at a slower rate. Together these findings reveal that the plant molecular clock is set by photosynthetic efficiency, and provide a mechanistic explanation for changes in plant speciation rates that occur concomitant with improvements in photosynthetic efficiency and changes in the environment such as light, temperature, and atmospheric CO2 concentration.

Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides

Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing cancer cells.

Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli

Organismal stoichiometry refers to the relative proportion of chemical elements in the biomass of organisms, and it can have important effects on ecological interactions from population to ecosystem scales. Although stoichiometry has been studied extensively from an ecological perspective, much less is known about the rates and directions of evolutionary changes in elemental composition. We measured carbon, nitrogen and phosphorus content of 12 Escherichia coli populations that evolved under controlled carbon-limited, serial-transfer conditions for 50 000 generations. The bacteria evolved higher relative nitrogen and phosphorus content, consistent with selection for increased use of the more abundant elements. Total carbon assimilated also increased, indicating more efficient use of the limiting element. We also measured stoichiometry in one population repeatedly through time. Stoichiometry changed more rapidly in early generations than later on, similar to the trajectory seen for competitive fitness. Altogether, our study shows that stoichiometry evolved over long time periods, and that it did so in a predictable direction, given the carbon-limited environment.

Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

BACKGROUND

Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism's environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood.

RESULTS

Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes.

CONCLUSIONS

Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.

Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin Sandy Land, northeast China

Caragana microphylla (Leguminosae) is a dominant climax semishrub species in northern China. We evaluated genetic variation within and among populations sampled from three different environmental gradients in Horqin Sandy Land in northern China using intersimple sequence repeats markers and investigated the possible existence of relationships between genetic diversity and environmental factors. The results showed that C. microphylla have high genetic diversity, and environmental gradients affected genetic diversity of C. microphylla populations. Genetic diversity of all populations was affected by many environmental factors and as well correlated with warm index and soil Olsen phosphorus (SOP) concentration. These results have important implications for restoration and management of these degraded ecosystems in arid and semi‐arid areas.

Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii

Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans.

Genome size and ploidy influence angiosperm species' biomass under nitrogen and phosphorus limitation

Angiosperm genome sizes (GS) range c. 2400-fold, and as nucleic acids are amongst the most phosphorus- (P) and nitrogen (N)-demanding cellular biomolecules, we test the hypothesis that a key influence on plant biomass and species composition is the interaction between N and P availability and plant GS. We analysed the impact of different nutrient regimes on above-ground biomass of angiosperm species with different GS, ploidy level and Grime's C-S-R (competitive, stress-tolerant, ruderal) plant strategies growing at the Park Grass Experiment (Rothamsted, UK), established in 1856. The biomass-weighted mean GS of species growing on plots with the addition of both N and P fertilizer were significantly higher than that of plants growing on control plots and plots with either N or P. The plants on these N + P plots are dominated by polyploids with large GS and a competitive plant strategy. The results are consistent with our hypothesis that large genomes are costly to build and maintain under N and P limitation. Hence GS and ploidy are significant traits affecting biomass growth under different nutrient regimes, influencing plant community composition and ecosystem dynamics. We propose that GS is a critical factor needed in models that bridge the knowledge gap between biodiversity and ecosystem functioning.

Life-history evolution in the anthropocene: effects of increasing nutrients on traits and trade-offs

Variation in life-history traits can have major impacts on the ecological and evolutionary responses of populations to environmental change. Life-history variation often results from trade-offs that arise because individuals have a limited pool of resources to allocate among traits. However, human activities are increasing the availability of many once-limited resources, such as nitrogen and phosphorus, with potentially major implications for the expression and evolution of life-history trade-offs. In this review, we synthesize contemporary life history and sexual selection literature with current research on ecosystem nutrient cycling to highlight novel opportunities presented by anthropogenic environmental change for investigating life-history trait development and evolution. Specifically, we review four areas where nutrition plays a pivotal role in life-history evolution and explore possible implications in the face of rapid, human-induced change in nutrient availability. For example, increases in the availability of nutrients may relax historical life-history trade-offs and reduce the honesty of signaling systems. We argue that ecosystems experiencing anthropogenic nutrient inputs present a powerful yet underexplored arena for testing novel and longstanding questions in organismal life-history evolution.

Nitrogen limitation as a driver of genome size evolution in a group of karst plants

Genome size is of fundamental biological importance with significance in predicting structural and functional attributes of organisms. Although abundant evidence has shown that the genome size can be largely explained by differential proliferation and removal of non-coding DNA of the genome, the evolutionary and ecological basis of genome size variation remains poorly understood. Nitrogen (N) and phosphorus (P) are essential elements of DNA and protein building blocks, yet often subject to environmental limitation in natural ecosystems. Using phylogenetic comparative methods, we test this hypothesis by determining whether leaf N and P availability affects genome sizes in 99 species of Primulina (Gesneriaceae), a group of soil specialists adapted to limestone karst environment in south China. We find that genome sizes in Primulina are strongly positively correlated with plant N content, but the correlation with plant P content is not significant when phylogeny history was taken into account. This study shows for the first time that N limitation might have been a plausible driver of genome size variation in a group of plants. We propose that competition for nitrogen nutrient between DNA synthesis and cellular functions is a possible mechanism for genome size evolution in Primulina under N-limitation.

Global biodiversity, stoichiometry and ecosystem function responses to human-induced C-N-P imbalances

Global change analyses usually consider biodiversity as a global asset that needs to be preserved. Biodiversity is frequently analysed mainly as a response variable affected by diverse environmental drivers. However, recent studies highlight that gradients of biodiversity are associated with gradual changes in the distribution of key dominant functional groups characterized by distinctive traits and stoichiometry, which in turn often define the rates of ecosystem processes and nutrient cycling. Moreover, pervasive links have been reported between biodiversity, food web structure, ecosystem function and species stoichiometry. Here we review current global stoichiometric gradients and how future distributional shifts in key functional groups may in turn influence basic ecosystem functions (production, nutrient cycling, decomposition) and therefore could exert a feedback effect on stoichiometric gradients. The C-N-P stoichiometry of most primary producers (phytoplankton, algae, plants) has been linked to functional trait continua (i.e. to major axes of phenotypic variation observed in inter-specific analyses of multiple traits). In contrast, the C-N-P stoichiometry of higher-level consumers remains less precisely quantified in many taxonomic groups. We show that significant links are observed between trait continua across trophic levels. In spite of recent advances, the future reciprocal feedbacks between key functional groups, biodiversity and ecosystem functions remain largely uncertain. The reported evidence, however, highlights the key role of stoichiometric traits and suggests the need of a progressive shift towards an ecosystemic and stoichiometric perspective in global biodiversity analyses.

Vulnerability of coastal ecosystems to changes in harmful algal bloom distribution in response to climate change: projections based on model analysis

Harmful algal blooms (HABs), those proliferations of algae that can cause fish kills, contaminate seafood with toxins, form unsightly scums, or detrimentally alter ecosystem function have been increasing in frequency, magnitude, and duration worldwide. Here, using a global modeling approach, we show, for three regions of the globe, the potential effects of nutrient loading and climate change for two HAB genera, pelagic Prorocentrum and Karenia, each with differing physiological characteristics for growth. The projections (end of century, 2090-2100) are based on climate change resulting from the A1B scenario of the Intergovernmental Panel on Climate Change Institut Pierre Simon Laplace Climate Model (IPCC, IPSL-CM4), applied in a coupled oceanographic-biogeochemical model, combined with a suite of assumed physiological 'rules' for genera-specific bloom development. Based on these models, an expansion in area and/or number of months annually conducive to development of these HABs along the NW European Shelf-Baltic Sea system and NE Asia was projected for both HAB genera, but no expansion (Prorocentrum spp.), or actual contraction in area and months conducive for blooms (Karenia spp.), was projected in the SE Asian domain. The implications of these projections, especially for Northern Europe, are shifts in vulnerability of coastal systems to HAB events, increased regional HAB impacts to aquaculture, increased risks to human health and ecosystems, and economic consequences of these events due to losses to fisheries and ecosystem services.

Functional characterization of the rice UDP-glucose 4-epimerase 1, OsUGE1: a potential role in cell wall carbohydrate partitioning during limiting nitrogen conditions

Plants grown under inadequate mineralized nitrogen (N) levels undergo N and carbon (C) metabolic re-programming which leads to significant changes in both soluble and insoluble carbohydrate profiles. However, relatively little information is available on the genetic factors controlling carbohydrate partitioning during adaptation to N-limitation conditions in plants. A gene encoding a uridine-diphospho-(UDP)-glucose 4-epimerase (OsUGE-1) from rice (Oryza sativa) was found to be N-responsive. We developed transgenic rice plants to constitutively over-express the OsUGE-1 gene (OsUGE1-OX1-2). The transgenic rice lines were similar in size to wild-type plants at the vegetative stage and at maturity regardless of the N-level tested. However, OsUGE1-OX lines maintained 18-24% more sucrose and 12-22% less cellulose in shoots compared to wild-type when subjected to sub-optimal N-levels. Interestingly, OsUGE1-OX lines maintained proportionally more galactose and glucose in the hemicellulosic polysaccharide profile of plants compared to wild-type plants when grown under low N. The altered cell wall C-partitioning during N-limitation in the OsUGE1-OX lines appears to be mediated by OsUGE1 via the repression of the cellulose synthesis associated genes, OsSus1, OsCesA4, 7, and 9. This relationship may implicate a novel control point for the deposition of UDP-glucose to the complex polysaccharide profiles of rice cell walls. However, a direct relationship between OsUGE1 and cell wall C-partitioning during N-limitation requires further investigation.

Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins

To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution.

GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes

BACKGROUND

"Stoichioproteomics" relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels.

RESULTS

Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline.

CONCLUSIONS

The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.

Mutational bias and gene conversion affect the intraspecific nitrogen stoichiometry of the Arabidopsis thaliana transcriptome

The transcriptome and proteome of Arabidopsis thaliana are reduced in nitrogen content when compared with other taxa, which may result from ecological nitrogen limitation. We hypothesized that if the A. thaliana transcriptome is selected for a low nitrogen content, nitrogen-reducing derived alleles of single nucleotide polymorphisms (SNPs) should segregate at higher frequencies than nitrogen-increasing alleles. This pattern should be stronger in populations with a larger effective population size (N(e)) if natural selection is more efficient in large than in small populations. We analyzed variation in the nitrogen content in the transcriptome of 80 natural accessions of A. thaliana. In contrast to our expectations, derived alleles increase the nitrogen content in all accessions, and there is a positive correlation between nitrogen difference and derived allele frequency, which is strongest with nonsynonymous SNPs (nsSNPs). Also, there is a positive correlation between nitrogen difference and N(e) that was mainly caused by nsSNPs. These observations led us to reject the hypothesis that the transcriptome of A. thaliana is currently under selection to reduce nitrogen content. Instead, we show that a change in nitrogen content is a side effect of interacting evolutionary factors that influence base composition and include mutational bias, purifying selection of functionally deleterious alleles, and GC-biased gene conversion. We provide strong evidence that GC-biased gene conversion may play an important role for base composition in the highly selfing plant A. thaliana.

A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

Background

The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach.

Results

The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs.

Conclusions

This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides.

Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition

The new field of 'stoichiogenomics' integrates evolution, ecology and bioinformatics to reveal surprising patterns of the differential usage of key elements [e.g. nitrogen (N)] in proteins and nucleic acids. Because the canonical amino acids as well as nucleotides differ in element counts, natural selection owing to limited element supplies might bias monomer usage to reduce element costs. For example, proteins that respond to N limitation in microbes use a lower proportion of N-rich amino acids, whereas proteome- and transcriptome-wide element contents differ significantly for plants as compared with animals, probably because of the differential severity of element limitations. In this review, we show that with these findings, new directions for future investigations are emerging, particularly via the increasing availability of diverse metagenomic and metatranscriptomic data sets.

Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus

Nitrogen (N) is a fundamental component of nucleotides and amino acids and is often a limiting nutrient in natural ecosystems. Thus, study of the N content of biomolecules may establish important connections between ecology and genomics. However, while significant differences in the elemental composition of whole organisms are well documented, how the flux of nutrients in the cell has shaped the evolution of different cellular processes remains poorly understood. By examining the elemental composition of major functional classes of proteins in four multicellular eukaryotic model organisms, we find that the catabolic machinery shows substantially lower N content than the anabolic machinery and the rest of the proteome. This pattern suggests that ecological selection for N conservation specifically targets cellular components that are highly expressed in response to nutrient limitation. We propose that the RNA component of the anabolic machineries is the mechanistic force driving the elemental imbalance we found, and that RNA functions as an intracellular nutrient reservoir that is degraded and recycled during starvation periods. A comparison of the elemental composition of the anabolic and catabolic machineries in species that have experienced different levels of N limitation in their evolutionary history (animals versus plants) suggests that selection for N conservation has preferentially targeted the catabolic machineries of plants, resulting in a lower N content of the proteins involved in their catabolic processes. These findings link the composition of major cellular components to the environmental factors that trigger the activation of those components, suggesting that resource availability has constrained the atomic composition and the molecular architecture of the biotic processes that enable cells to respond to reduced nutrient availability.