Recent duplications drive rapid diversification of trypsin genes in 12 Drosophila

The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history

The pinfish (Lagodon rhomboides) is an ecologically, economically, and culturally relevant member of the family Sparidae, playing crucial roles in the marine food webs of the western Atlantic Ocean and Gulf of Mexico. Despite their high abundance and ecological importance, there is a scarcity of genomic resources for this species. We assembled and annotated a chromosome-scale genome for the pinfish, resulting in a highly contiguous 785 Mb assembly of 24 scaffolded chromosomes. The high-quality assembly contains 98.9% complete BUSCOs and shows strong synteny to other chromosome-scale genomes of fish in the family Sparidae, with a limited number of large-scale genomic rearrangements. Leveraging this new genomic resource, we found evidence of significant expansions of dietary gene families over the evolutionary history of the pinfish, which may be associated with an ontogenetic shift from carnivory to herbivory seen in this species. Estimates of historical patterns of population demography using this new reference genome identified several periods of population growth and contraction which were associated with ancient climatic shifts and sea level changes. This genome serves as a valuable reference for future studies of population genomics and differentiation and provides a much-needed genomic resource for this western Atlantic sparid.

Characterization of the trypsin-III from Monterey sardine (Sardinops caeruleus): Insights on the cold-adaptation from the A236N mutant

Trypsins (E.C. 3.4.21.4) are digestive enzymes that catalyze the hydrolysis of peptide bonds containing arginine and lysine residues. Some trypsins from fish species are active at temperatures just above freezing, and for that are called cold-adapted enzymes, having many biotechnological applications. In this work, we characterized a recombinant trypsin-III from Monterey sardine (Sardinops caeruleus) and studied the role of a single residue on its cold-adapted features. The A236N mutant from sardine trypsin-III showed higher activation energy for the enzyme-catalyzed reaction, it was more active at higher temperatures, and exhibited a higher thermal stability than the wild-type enzyme, suggesting a key role of this residue. The thermodynamic activation parameters revealed an increase in the activation enthalpy for the A236N mutant, suggesting the existence of more intramolecular contacts during the activation step. Molecular models for both enzymes suggest that a hydrogen-bond involving N236 may contact the C-terminal α-helix to the vicinity of the active site, thus affecting the biochemical and thermodynamic properties of the enzyme.

Direct protein-protein interaction network for insecticide resistance based on subcellular localization analysis in Drosophila melanogaster

In present study, we constructed the direct protein-protein interaction network of insecticide resistance based on subcellular localization analysis. Totally 177 of 528 resistance proteins were identified and they were located in 11 subcellular localizations. We further analyzed topological properties of the network and the biological characteristics of resistance proteins, such as k-core, neighborhood connectivity, instability index and aliphatic index. They can be used to predict the key proteins and potential mechanisms from macro-perspective. The problem of resistance has not been solved fundamentally, because the development of new insecticides can't keep pace with the development speed of resistance, and the lack of understanding of molecular mechanism of resistance. As the further analysis to reduce data noise, we constructed the direct protein-protein interaction network of insecticide resistance based on subcellular localization analysis. The interaction between proteins located at the same subcellular location belongs to direct interactions, thus eliminating indirect interaction. Totally 177 of 528 resistance proteins were identified and they were located in 11 subcellular localizations. We further analyzed topological properties of the network and the biological characteristics of resistance proteins, such as k-core, neighborhood connectivity, instability index and aliphatic index. They can be used to predict the hub proteins and potential mechanisms from macro-perspective. This is the first study to explore the insecticide resistance molecular mechanism of Drosophila melanogaster based on subcellular localization analysis. It can provide the bioinformatics foundation for further understanding the mechanisms of insecticide resistance. It also provides a reference for the study of molecular mechanism of insecticide resistance of other insects.

In-depth characterization of trypsin-like serine peptidases in the midgut of the sugar fed Culex quinquefasciatus

BACKGROUND

Culex quinquefasciatus is a hematophagous insect from the Culicidae family that feeds on the blood of humans, dogs, birds and livestock. This species transmits a wide variety of pathogens between humans and animals. The midgut environment is the first location of pathogen-vector interactions for blood-feeding mosquitoes and the expression of specific peptidases in the early stages of feeding could influence the outcome of the infection. Trypsin-like serine peptidases belong to a multi-gene family that can be expressed in different isoforms under distinct physiological conditions. However, the confident assignment of the trypsin genes that are expressed under each condition is still a challenge due to the large number of trypsin-coding genes in the Culicidae family and most likely because they are low abundance proteins.

METHODS

We used zymography for the biochemical characterization of the peptidase profile of the midgut from C. quinquefasciatus females fed on sugar. Protein samples were also submitted to SDS-PAGE followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis for peptidase identification. The peptidases sequences were analyzed with bioinformatics tools to assess their distinct features.

RESULTS

Zymography revealed that trypsin-like serine peptidases were responsible for the proteolytic activity in the midgut of females fed on sugar diet. After denaturation in SDS-PAGE, eight trypsin-like serine peptidases were identified by LC-MS/MS. These peptidases have structural features typical of invertebrate digestive trypsin peptidases but exhibited singularities at the protein sequence level such as: the presence of different amino acids at the autocatalytic motif and substrate binding regions as well as different number of disulfide bounds. Data mining revealed a group of trypsin-like serine peptidases that are specific to C. quinquefasciatus when compared to the culicids genomes sequenced so far.

CONCLUSION

We demonstrated that proteomics approaches combined with bioinformatics tools and zymographic analysis can lead to the functional annotation of trypsin-like serine peptidases coding genes and aid in the understanding of the complexity of peptidase expression in mosquitoes.

Functional requirements driving the gene duplication in 12 Drosophila species

BACKGROUND

Gene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution. Most studies of young duplicates have focused on mammals, especially humans, whereas reports describing their genome-wide evolutionary patterns across the closely related Drosophila species are rare. The sequenced 12 Drosophila genomes provide the opportunity to address this issue.

RESULTS

In our study, 3,647 young duplicate gene families were identified across the 12 Drosophila species and three types of expansions, species-specific, lineage-specific and complex expansions, were detected in these gene families. Our data showed that the species-specific young duplicate genes predominated (86.6%) over the other two types. Interestingly, many independent species-specific expansions in the same gene family have been observed in many species, even including 11 or 12 Drosophila species. Our data also showed that the functional bias observed in these young duplicate genes was mainly related to responses to environmental stimuli and biotic stresses.

CONCLUSIONS

This study reveals the evolutionary patterns of young duplicates across 12 Drosophila species on a genomic scale. Our results suggest that convergent evolution acts on young duplicate genes after the species differentiation and adaptive evolution may play an important role in duplicate genes for adaption to ecological factors and environmental changes in Drosophila.