Evolutionary conservation of amino acid composition in paralogous insect vitellogenins

Relish as a Candidate Marker for Transgenerational Immune Priming in a Dampwood Termite (Blattodae: Archeotermopsidae)

Natural selection should favor the transfer of immune competence from one generation to the next in a context-dependent manner. Transgenerational immune priming (TGIP) is expected to evolve when species exploit pathogen-rich environments and exhibit extended overlap of parent-offspring generations. Dampwood termites are hemimetabolous, eusocial insects (Blattodea: Archeotermopsidae) that possess both of these traits. We predict that offspring of pathogen-exposed queens of Zootermopsis angusticollis will show evidence of a primed immune system relative to the offspring of unexposed controls. We found that Relish transcripts, one of two immune marker loci tested, were enhanced in two-day-old embryos when laid by Serratia-injected queens. These data implicate the immune deficiency (IMD) signaling pathway in TGIP. Although an independent antibacterial assay revealed that embryos do express antibacterial properties, these do not vary as a function of parental treatment. Taken together, Z. angusticollis shows transcriptional but not translational evidence for TGIP. This apparent incongruence between the transcriptional and antimicrobial response from termites suggests that effectors are either absent in two-day-old embryos or their activity is too subtle to detect with our antibacterial assay. In total, we provide the first suggestive evidence of transgenerational immune priming in a termite.

Molecular changes in vitellogenin gene of Spodoptera exigua after long-time exposure to cadmium - Toxic side effect or microevolution?

The reproduction of pest insects is a continuously ongoing issue, especially in the environmental pollution context. Natural or artificial stressing factors enforce a kind of trade-off, most often between growth/survival and reproduction, which improves fitness of the organism. Harmful factors, such as cadmium, can affect the vitellogenesis leading to reduction of yolk synthesis and egg production. The aim of this study was to assess whether 130-generational selection to cadmium in food might have induced change in vitellogenesis of Spodoptera exigua. We analyzed the level of Vg gene expression in S. exigua from the control and the cadmium strain at regular time intervals within 48h after eclosion. The full sequence of Vg gene was also compared between strains. The vitellogenin gene expression in both strains was time-dependent. This dependence was more visible in the control strain. In the cadmium strain the vitellogenin expression was significantly lower, comparing with the control strain in the first day after eclosion but increased significantly in the second day. The sequenced CDS (5286bp long) of the control and the cadmium strains were translated into protein sequences containing both 1761 aa. The protein sequences comparison revealed that there is one amino acid change at aa position 1282. Multiple alignments of six orthologous proteins from different species showed that amino acid change is located in the conserved position. Long-lasting exposure to cadmium resulted in permanent mutation in vitellogenin gene. We do not know yet if the mutation can improve fitness of the cadmium-selected insects. However, we can suppose that the mutation is neutral or even beneficial. The mutation and most probably additional effects of cadmium exposure have an influence on the vitellogenin expression. Some modification in the expression of the vitellogenin receptor are also likely to be important.

Molecular characterization and expression of vitellogenin gene from Spodoptera exigua exposed to cadmium stress

In this study, we cloned a full-length cDNA encoding vitellogenin (Vg) in Spodoptera exigua. The complete Vg cDNA consists of 5694 nucleotides with a long open reading frame encoding 1761 amino acid residues. The deduced amino acid sequence shared high similarity with the Vgs of other lepidopteran insects, particularly in the C-terminal region including the GL/ICG motif, five cysteine residues and DGXR motif. We analyzed the spatiotemporal expression of Vg transcripts in S. exigua by RT-PCR and Real-time Quantitative PCR. The results revealed that Vg was expressed specifically in the female fat body and was detectable after 5th day female pupae. The maximum level of Vg mRNA appeared in 48-h-old female adults and started to decrease quickly. When exposed to cadmium (Cd) (25-100mg/kg), there was a significantly decreased Vg level in female adults. The information presented in this study suggested the Vg in S. exigua could be significantly affected by Cd pressure.

Dynamics of expression of two vitellogenin genes in the Chagas' disease vector Triatoma infestans: Analysis throughout pre-vitellogenesis and vitellogenesis

The reproductive success of all oviparous species depends on vitellogenin (Vg) biosynthesis and its accumulation in the developing oocytes. The expression levels of two Vg genes (Vg1 and Vg2) were analyzed by qPCR and western blot in fat body and ovaries of adult females, at different times after ecdysis (pre-vitellogenic phase) and after blood feeding of females (vitellogenic phase). Vg genes were also evaluated in fat bodies of adult males as well as in female fifth instar nymphs. No trace of Vg mRNA was detected in adult males or in nymphs. Vg1 and Vg2 were expressed in the fat bodies and ovaries of adult females. The Vg genes start to be expressed slightly in both tissues of adult females during pre-vitellogenesis. After blood feeding, Vg1 and Vg2 were up regulated and significant levels of Vg transcripts as well as protein expression were observed in fat bodies sampled throughout vitellogenesis. During this period however, the distribution patterns of Vg1 and Vg2 transcripts showed two peaks around early and advanced vitellogenesis (days 4 and 12 post-feeding, respectively). In the ovaries, levels of mRNAs increased from the day 10 post-blood feeding onwards. In addition, the immunofluorescence assays showed a strong signal for vitellin in the yolk bodies of terminal follicles of vitellogenic females. The involvement of fat body and ovary in the synthesis of Vg suggests different roles of Vgs in supporting the growth of oocytes.

Detecting false positive sequence homology: a machine learning approach

Background

Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches that are used to identify homologous genes and combine them into two fundamentally distinct classes: orthologs and paralogs. Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection.

Results

In this paper we develop biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. We demonstrate that our machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set.

Conclusions

Our process increases the quality of output from other clustering algorithms by providing a novel post-processing method that is both fast and efficient at removing low quality clusters of putative homologous genes recovered by heuristic-based approaches.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-0955-3) contains supplementary material, which is available to authorized users.

cDNA isolation and characterization of two vitellogenin genes in the Chagas' disease vector Triatoma infestans (Hemiptera, Reduviidae)

Two vitellogenin genes (Vg1 and Vg2) were identified in the Chagas' disease vector Triatoma infestans. The putative coding sequence corresponding to Vg2 was found to be 5553bp long, encoding 1851 amino acids in a single open reading frame. The comparative analysis of the deduced amino acid sequences from Vg1 and Vg2 cDNA fragments of T. infestans revealed 58.94% of identity with 76.43% of homology. The phylogenetic tree based on the complete Vg amino acid sequences of hemimetabolous insects unambiguously supported two clusters, one consisting of Vg sequences from dictyopteran and the other containing Vg sequences of hemipteran. The Vg1 and Vg2 mRNAs were detected in fat bodies and ovaries of adult females with the highest levels of both Vg transcripts in the first tissue. Quantitative PCR showed low expression of Vg2 in head and muscle of adult females, while the Vg1 transcript was not present in these organs. Neither Vg1 nor Vg2 was expressed in fifth instar nymph fat bodies or in adult male fat bodies, heads, and muscles.

Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins

The amino acid sequences of soluble, ordered proteins with stable structures have evolved due to biological and physical requirements, thus distinguishing them from random sequences. Previous analyses have focused on extracting the features that frequently appear in protein substructures, such as α-helix and β-sheet, but the universal features of protein sequences have not been addressed. To clarify the differences between native protein sequences and random sequences, we analyzed 7368 soluble, ordered protein sequences, by inspecting the observed and expected occurrences of 400 amino acid pairs in local proximity, up to 10 residues along the sequence in comparison with their expected occurrence in random sequence. We found the trend that the hydrophobic residue pairs and the polar residue pairs are significantly decreased, whereas the pairs between a hydrophobic residue and a polar residue are increased. This trend was universally observed regardless of the secondary structure content but was not observed in protein sequences that include intrinsically disordered regions, indicating that it can be a general rule of protein foldability. The possible benefits of this rule are discussed from the viewpoints of protein aggregation and disorder, which are both caused by low-complexity regions of hydrophobic or polar residues.