Prediction of the Ligands of the CYP9e Subfamily of Ant Cytochrome P450 with the ChEBI Ontologies of Chemical and Biological Characteristics

Cytochromes P450 are involved in the metabolism of various endogenous and exogenous compounds, and their role in the detoxification of xenobiotics has been extensively studied. CYP9e, one of the subfamilies of cytochromes P450, whose functions have been poorly studied, is amplified in the black garden ant Lasius niger. We have performed molecular modeling of 23 proteins of this family belonging to L. niger and other ant species, as well as molecular docking and virtual screening of suspected ligands. The substances used as ligands have been annotated with ChEBI ontologies to predict the chemical and biological properties of molecules forming complexes with CYP9e of ants. It has been shown that, among the ligands forming energetically favorable complexes, ChEBI ontologies of mycotoxins, phytotoxins, steroids, glycosides and terpenoids are overrepresented. Nevertheless, it has been demonstrated that in carrying out a large number of inaccurate simulations, the results of function predictions can be correlated with molecular docking and the evolutionary history of a protein family.     

Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions

Background

Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes.

Results

We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns. We also sequenced the plastome of Adianthum hispidulum (Pteridaceae). Unexpectedly, we found high variability in the IR region, including duplication of rrn16 in D. blanfordii, complete loss of trnI-GAU in D. filix-mas, its pseudogenization due to the loss of an exon in D. blanfordii. Analysis of previously reported plastomes of Polypodiales demonstrated that Woodwardia unigemmata and Lepisorus clathratus have unusual insertions in the IR region. The sequence of these inserted regions has high similarity to several LSC fragments of ferns outside of Polypodiales and to spacer between tRNA-CGA and tRNA-TTT genes of mitochondrial genome of Asplenium nidus. We suggest that this reflects the ancient DNA transfer from mitochondrial to plastid genome occurred in a common ancestor of ferns. We determined the marked conservation of gene content and relative evolution rate of genes and intergenic spacers in the IRs of Polypodiales. Faster evolution of the four intergenic regions had been demonstrated (trnA- orf42, rrn16-rps12, rps7-psbA and ycf2-trnN).

Conclusions

IRs of Polypodiales plastomes are dynamic, driven by such events as gene loss, duplication and putative lateral transfer from mitochondria.

     

Genomic exaptation enables <Emphasis Type="Italic">Lasius niger</Emphasis> adaptation to urban environments

Background

The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger – the most successful urban inhabitant of all ants – and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus.

Results

Sequences from 272 M Illumina reads were assembled into 41,406 contigs with total length of 245 MB, and N50 of 16,382 bp, similar to other ant genome assemblies enabling comparative genomic analysis. Remarkably, the predicted proteome of L. niger is significantly enriched relative to other ant genomes in terms of abundance of domains involved in nucleic acid binding, DNA repair, and nucleotidyl transferase activity, reflecting transposable element proliferation and a likely genomic response. With respect to environmental stress, we note a proliferation of various detoxification genes, including glutatione-S-transferases and those in the cytochrome P450 families. Notably, the CYP9 family is highly expanded with 19 complete and 21 nearly complete members - over twice as many compared to other ants. This family exhibits the signatures of strong directional selection, with eleven positively selected positions in ligand-binding pockets of enzymes. Gene family contraction was detected for several components of the olfactory system, accompanied by instances of both directional selection and relaxation.

Conclusions

Our results suggest that the success of L. niger in urbanized areas may be the result of fortuitous coincidence of several factors, including the expansion of the CYP9 cytochrome family due to coevolution with parasitic fungi, the diversification of DNA repair systems as an answer to proliferation of retroelements, and the reduction of olfactory system and behavioral preadaptations from non-territorial subdominant life strategies found in natural environments. Diversification of cytochromes and DNA repair systems along with reduced odorant communication are the basis of L. niger pollutant resistance and polyphagy, while non-territorial and mobilization strategies allows more efficient exploitation of large but patchy food sources.

     

In situ analysis by microspectroscopy reveals triterpenoid compositional patterns within leaf cuticles of Prunus laurocerasus

The cuticular waxes on the leaves of Prunus laurocerasus are arranged in distinct layers differing in triterpenoid concentrations (Jetter et al., Plant Cell Environ 23:619–628, 2000). In addition to this transversal gradient, the lateral distribution of cuticular triterpenoids must be investigated to fully describe the spatial distribution of wax components on the leaf surfaces. In the present investigation, near infrared (NIR) Raman microspectroscopy, coherent anti-Stokes Raman scattering (CARS) microscopy, and third harmonic generation (THG) spectroscopy were employed to map the triterpenoid distribution in isolated cuticles from adaxial and abaxial sides of P. laurocerasus leaves. The relative concentrations of ursolic acid and oleanolic acid were calculated by treating the cuticle spectra as linear combinations of reference spectra from the major compounds found in the wax. Raman maps of the adaxial cuticle showed that the triterpenoids accumulate to relatively high concentrations over the periclinal regions of the pavement cells, while the very long chain aliphatic wax constituents are distributed fairly evenly across the entire adaxial cuticle. In the analysis of the abaxial cuticles, the triterpenoids were found to accumulate in greater amounts over the guard cells relative to the pavement cells. The very long chain aliphatic compounds accumulated in the cuticle above the anticlinal cell walls of the pavement cells, and were found at low concentrations above the periclinals and the guard cells.     

Genomic Signatures of Selection between Urban and Rural Populations of Black Garden Ant <Emphasis Type="Italic">Lasius niger</Emphasis>

Black garden ant L. niger is known as a dominant species of urban ant fauna in Europe. Successful propagation of L. niger in transformed ecosystems was associated with behavioral traits in many surveys; however, molecular and genetic basis of such adaptation was never studied. In the present study, genomes of populations from the city of Moscow and natural habitats of Moscow oblast are compared. Pooled samples from rural and urban habitats are collected and sequenced with Illumina HiSeq. SNP frequency, Tajima’s D, and fixation index are estimated with PoPoolation and Popoolation2 software. SNP frequencies are significantly different in 64 genes according to Fisher’s exact test. Some of these genes are detected as affected by recent selection. Out of 64 genes, 26 encode retrotransposon proteins. The genes of immune response to viral and fungal infections, fatty acid synthases, and elements of the Hippo/Fat pathway have different SNP frequencies between populations. Certain retrotransposon genes also can be under selection. It is important to note that repressors and mediators of RNA polymerase II are significantly different between urban and rural populations of L. niger. These genes can influence retrotransposon mobility.