Open gaps in the evolution of the eukaryotic nucleotide excision repair.

Nucleotide excision repair (NER) is the most versatile DNA repair pathway as it removes different kinds of bulky lesions. Due to its essential role for genome integrity, it has appeared early in the evolution of species. However, most published studies are focused on humans, mice, yeast or bacteria. Considering the large amount of information on genome databases, it is currently possible to retrieve sequences from NER components in many organisms. Therefore, we have characterized the potential orthologs of 10 critical components of the human NER pathway in 12 eukaryotic species by using similarity and structural criteria through the use of bioinformatics tools. This approach has allowed us to characterize gene and protein structures comparatively, taking a glance at some evolutionary aspects of the NER pathway. We have obtained significant search results for the majority of the proteins in most of the organisms studied, mainly for factors that play a pivotal role in the pathway. However, we have revisited significant differences and found new aspects that may imply a distinct functioning of this pathway in different organisms. Through the demonstration of the heterogeneity of the gene structures and a variety in the protein architecture of the NER components evaluated, our results show important differences between human NER and evolutionarily distant eukaryotes. We highlight the lack of a canonical XPD in chicken, the divergence of XPA in plants and protozoans and the absence of XPE in the invertebrate species analyzed. In spite of this, it is remarkable the presence of this excision repair mechanism in a high number of evolutionary distant organisms, being present since the origin of eukaryotes.

Phylogenetic niche conservatism and plant diversification in South American subtropical grasslands along multiple climatic dimensions.

Phylogenetic niche conservatism can be investigated at multiple scales on an explicit geographical context. Haplotype-based comparative analyses of lineages occupying the same region, and thus subjected to similar environmental factors, allow decoupling shared evolutionary and ecological patterns, as well as multiple dimensions of adaptive diversification. Here we aimed to assess the role of environmental drivers on diversification of subtropical grassland, based on haplotypic diversity of two plant genera. We sampled two closely related and co-distributed grassland plant genera, Petunia and Calibrachoa, across their entire distribution area. Eigenvectors extracted from pairwise distances based on chloroplast DNA haplotypes were used to fit Phylogenetic Signal-Representation (PSR) curves to estimate evolutionary patterns in 19 bioclimatic variables and altitude. The PSR curves showed that altitude, precipitation, and temperature variables changed at different rates with haplotype differentiation. Altitude and temperature traits evolved under conditions closer to a neutral dynamics, whereas precipitation traits differentiated following more complex models. Our results indicated that the diversification in the two genera was more limited by precipitation conditions. Based on these novel findings, we suggest that future studies should test the possible impact of precipitation variables on the process of ecological differentiation in these genera.

Modified expression of antioxidant genes in lobster cockroach, Nauphoeta cinerea exposed to methylmercury and monosodium glutamate.

Methylmercury (MeHg) is a neurotoxicant that poses risk to human health and the environment, while glutamate homeostasis is necessary for the proper functioning of the brain. We have previously shown an increase in oxidative stress after cockroach exposure to diet containing monosodium glutamate (MSG), both separately and combined with a low dose of methylmercury. We herein seek to corroborate these findings by quantifying the expression levels of certain antioxidant genes in Nauphoeta cinerea exposed to MeHg and MSG. Cockroaches were fed with the basal diet alone, basal diet +2% NaCl, basal diet +2% MSG; basal diet +0.125 mg/g MeHg, basal diet +0.125 mg/g MeHg +2% NaCl; and basal diet +0.125 mg/g MeHg +2% MSG for 21 days and mRNA from head homogenate was used to quantify the expression of antioxidant genes such as glutathione-s-transferase (GstS, GstT, GstD), thioredoxin (Trx1, Trx2, Trx5), peroxiredoxin (prx4), superoxide dismutase (Sod), catalase (Cat). MeHg, NaCl and MSG alone downregulated mRNA levels of GstS and Trx5, in contrast, co-exposure of MeHg + MSG, upregulated these genes. MeHg + NaCl upregulated the mRNA levels of Cat and Sod but these genes were downregulated by NaCl alone. MeHg + NaCl and MeHg + MSG upregulated GstD and GstT. MeHg alone upregulated the transcription levels of Trx1, Trx2 and Prx4. The disruptions in the transcription levels of various genes by MeHg and MSG, reinforce the toxicity of these neurotoxicants. In general, the data suggest their additive effects and support the use of N. cinerea as a model for toxicological studies.

Simultaneous exposure to vinylcyclohexene and methylmercury in Drosophila melanogaster: biochemical and molecular analyses.

BACKGROUND: Exposure to vinylcyclohexene (VCH) and methylmercury (MeHg+) can induce oxidative stress and gene modulation. Several studies have been evaluating the effects of VCH and MeHg+, but little is known about interactive effects between them. This work aimed to assess the exposure and co-exposure effects of MeHg+ and VCH on oxidative stress and gene modulation in Drosophila melanogaster. METHODS: Reactive species production, glutathione S-transferase (GST) and acetylcholinesterase (AChE) activities were evaluated after exposure and co-exposure to VCH (1 mM) and MeHg+ (0.2 mM) for one or three days in the head and body (thorax and abdomen) of flies. The expression of genes related to redox state and inflammatory response was evaluated after exposure and co-exposure to VCH and MeHg+ for three days. RESULTS: Survival decreased only in flies co-exposed to VCH and MeHg+ for three days. All treatments increased total reactive species production after one day of exposure. However, no significant changes were observed in the head after three days of exposure. One day of exposure to VCH caused an increase in the head GST activity, whereas MeHg+ induced an increase after three days of exposure. Regarding the body, all treatments increased GST activity after one day of exposure, but only the flies exposed to MeHg+ presented an increase in GST activity after three days of exposure. Treatments did not alter AChE activity in the head. As for gene expression, there was a significant increase in the Relish transcription factor gene in the flies' body, but Nrf2, Keap1, Jafrac1, TrxR1, and NF-κß were not altered. CONCLUSION: The results suggest that exposure to VCH and MeHg+ induce oxidative stress and activation of an inflammatory response in fruit flies.

Enzymes of glycerol-3-phosphate pathway in triacylglycerol synthesis in plants: Function, biotechnological application and evolution.

Triacylglycerols (TAG) are the major form of energy storage in plants. TAG are primarily stored in seeds and fruits, but vegetative tissues also possess a high capacity for their synthesis and storage. These storage lipids are essential to plant development, being used in seedling growth during germination, pollen development, and sexual reproduction, for example. TAG are also an important source of edible oils for animal and human consumption, and are used for fuel and industrial feedstocks. The canonical pathway leading to TAG synthesis is the glycerol-3-phosphate, or Kennedy, pathway, which is an evolutionarily conserved process in most living organisms. The enzymatic machinery for synthesizing TAG is well known in several plant species, and the genes encoding these enzymes have been the focus of many studies. Here, we review recent progress on the understanding of evolutionary, functional and biotechnological aspects of the glycerol-3-phosphate pathway enzymes that produce TAG. We discuss current knowledge about their functional aspects, and summarize valuable insights into genetically engineered plants for enhancing TAG accumulation. Also, we highlight the evolutionary history of these genes and present a meta-analysis linking positive selection to gene family and plant diversification, and also to the domestication processes in oilseed crops.

De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae).

The use of Drosophila as a scientific model is well established, but the use of cockroaches as experimental organisms has been increasing, mainly in toxicology research. Nauphoeta cinerea is one of the species that has been studied, and among its advantages is its easy laboratory maintenance. However, a limited amount of genetic data about N. cinerea is available, impeding gene identification and expression analyses, genetic manipulation, and a deeper understanding of its functional biology. Here we describe the N. cinerea fat body and head transcriptome, in order to provide a database of genetic sequences to better understand the metabolic role of these tissues, and describe detoxification and stress response genes. After removing low-quality sequences, we obtained 62,121 transcripts, of which more than 50% had a length of 604 pb. The assembled sequences were annotated according to their genes ontology (GO). We identified 367 genes related to stress and detoxification; among these, the more frequent were p450 genes. The results presented here are the first large-scale sequencing of N. cinerea and will facilitate the genetic understanding of the species' biochemistry processes in future works.

Impacts of UVB radiation on food consumption of forest specialist tadpoles.

Solar ultraviolet radiation B (UVB) is an important environmental stressor for amphibian populations due to its genotoxicity, especially in early developmental stages. Nonetheless, there is an absence of works focused on the UVB effects on tadpoles' food consumption efficiency. In this work, we investigated the effects of the exposure to a low environmental-simulated dose of UVB radiation on food consumption of tadpoles of the forest specialist Hypsiboas curupi [Hylidae, Anura] species. After UVB treatment tadpoles were divided and exposed to a visible light source or kept in the dark, in order to indirectly evaluate the efficiency of DNA repair performed by photolyases and nucleotide excision repair (NER), respectively. The body mass and the amount of food in tadpoles' guts were verified in both conditions and these data were complemented by the micronuclei frequency in blood cells. Furthermore, the keratinized labial tooth rows were analyzed in order to check for possible UVB-induced damage in this structure. Our results clearly show that the body weight decrease induced by UVB radiation occurs due to the reduction of tadpoles' food consumption. This behavior is directly correlated with the genotoxic impact of UVB light, since the micronuclei frequency significantly increased after treatments. Surprisingly, the results indicate that photoreactivation treatment was ineffective to restore the food consumption activity and body weight values, suggesting a low efficiency of photolyases enzymes in this species. In addition, UVB treatments induced a higher number of breaks in the keratinized labial tooth rows, which could be also associated with the decrease of food consumption. This work contributes to better understand the process of weight loss observed in tadpoles exposed to UVB radiation and emphasizes the susceptibility of forest specialist amphibian species to sunlight-induced genotoxicity.

Contribution of WUSCHEL-related homeobox (WOX) genes to identify the phylogenetic relationships among Petunia species.

Developmental genes are believed to contribute to major changes during plant evolution, from infrageneric to higher levels. Due to their putative high sequence conservation, developmental genes are rarely used as molecular markers, and few studies including these sequences at low taxonomic levels exist. WUSCHEL-related homeobox genes (WOX) are transcription factors exclusively present in plants and are involved in developmental processes. In this study, we characterized the infrageneric genetic variation of Petunia WOX genes. We obtained phylogenetic relationships consistent with other phylogenies based on nuclear markers, but with higher statistical support, resolution in terminals, and compatibility with flower morphological changes.

Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia.

The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome.

Nuclear and plastid markers reveal the persistence of genetic identity: a new perspective on the evolutionary history of Petunia exserta.

Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize.