Skipper genome sheds light on unique phenotypic traits and phylogeny

Background

Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the family Papilionidae (swallowtails) may be the sister to other butterflies including skippers. The moth-like features and the controversial position of skippers in Lepidoptera phylogeny make them valuable targets for comparative genomics.

Results

We obtained the 310 Mb draft genome of the Clouded Skipper (Lerema accius) from a wild-caught specimen using a cost-effective strategy that overcomes the high (1.6 %) heterozygosity problem. Comparative analysis of Lerema accius and the highly heterozygous genome of Papilio glaucus revealed differences in patterns of SNP distribution, but similarities in functions of genes that are enriched in non-synonymous SNPs. Comparison of Lepidoptera genomes revealed possible molecular bases for unique traits of skippers: a duplication of electron transport chain components could result in efficient energy supply for their rapid flight; a diversified family of predicted cellulases might allow them to feed on cellulose-enriched grasses; an expansion of pheromone-binding proteins and enzymes for pheromone synthesis implies a more efficient mate-recognition system, which compensates for the lack of clear visual cues due to the similarities in wing colors and patterns of many species of skippers. Phylogenetic analysis of several Lepidoptera genomes suggested that the position of Hesperiidae remains uncertain as the tree topology varied depending on the evolutionary model.

Conclusion

Completion of the first genome from the family Hesperiidae allowed comparative analyses with other Lepidoptera that revealed potential genetic bases for the unique phenotypic traits of skippers. This work lays the foundation for future experimental studies of skippers and provides a rich dataset for comparative genomics and phylogenetic studies of Lepidoptera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1846-0) contains supplementary material, which is available to authorized users.     

The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes

Background  

Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall structurally into three different classes, I, II, III, with class IIa being pediocin-like single entities and class IIb being two-peptide bacteriocins. Self-protective cognate immunity proteins are usually co-transcribed with these toxins. Several examples of cognates for IIa have already been solved structurally. Streptococcus pyogenes, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable.     

The effect of rainfall on population dynamics in Sahara-Sahel rodents

In arid and semi-arid regions, rainfall is scarce, limiting primary productivity and animal reproduction. As long-term population monitoring is limited in remote arid areas, indirect and remote technicals are needed. We investigated if and how populations of rodents in Sahara-Sahel responded to past events of rainfall. Using short field surveys and remotely sensed rainfall data, spanning between years 2010 to 2015, we tested if rainfall prior to field surveys affected populations of Gerbillus rodents. Generalized additive analysis showed that amount of moonlight (the effect of number of days away from full moon) negatively correlated with number of trapped animals. When controlling for moonlight and geographic and temporal variation, rainfall up to 1 year prior to surveys positively and rainfall 2 years prior to surveys negatively correlated with number of trapped gerbils. We suggest that the effect of increased number of gerbils resulted from reproduction and population density increase after bursts of primary productivity. Negative correlation with rainfall could be related to increased predation or other ecological effects (e.g., resource collapse, pathogens spread) on prey population densities and activity levels. Our results suggest multiphase delayed effect of gerbils population response to rainfall implying interactive model of population regulation in rodent communities on Sahara-Sahel. Presented indirect method and results are readily applicable to population monitoring and management of remote and understudied areas.     

Structural genomics: keeping up with expanding knowledge of the protein universe

Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space--a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a re-assessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006.     

SCEPTRANS: an online tool for analyzing periodic transcription in yeast

SUMMARY: SCEPTRANS is designed for analysis of microarray timecourse data related to periodic phenomena in the budding yeast. The server allows for easy viewing of temporal profiles of multiple genes in a number of datasets. Additional functionality includes searching for coexpressed genes, periodicity and correlation analysis, integrating functional annotation and localization data as well as advanced operations on sets of genes. AVAILABILITY: Available online at http://sceptrans.org/     

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

BACKGROUND: Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. RESULTS: We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. CONCLUSIONS: The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.     

The theory of the frequency response of ellipsoidal biological cells in rotating electrical fields

In this paper we have presented in as compact a form as possible the theoretical formalism that is needed to predict the frequency response of a biological cell of arbitrary ellipsoidal shape to a frequency dependant rotating external field. The formalism is much more complicated than that for a spherical or cylindrical cell where the radial vector is always parallel to the surface normal at each point of the surface. In addition to providing the theory we have demonstrated that the spin rate and its frequency dependance is very intimately related to the electrical properties of the cell interior and to that of the suspending fluid. It is possible to probe these properties of the cell and its environment by utilizing this technique. This aspect has been demonstrated by examining rotational changes as a function of the conductivity of both the cell interior and its suspending liquid. We also have shown, by considering a very simple model for the cell and the two dielectric constants, that the frequency spectrum is shape dependant. All our calculations have been carried out for "lossy" systems with frictional dissipation where energy minimization methods are no longer applicable. The invariant form of the Poynting vector forms the basis of the method.