Identification and functional characterization of methyl-CpG binding domain protein from Tribolium castaneum

Association between the copy number variations of Methyl-CpG binding domain family and schizophrenia

Schizophrenia is recognized as one of the most severe psychiatric disorders, with its pathogenesis likely involving genetic, epigenetic, developmental, and environmental factors. Members of the Methyl-CpG Binding Domain (MBD) Family play a crucial role in the regulation of genomic DNA methylation, and studies have implicated the association between MBD family and neurodevelopmental disorders. Copy number variations (CNVs) are a significant genetic basis for human genomic variation, also playing a critical role in the genetic processes of schizophrenia. Therefore, we aimed to evaluate the susceptibility of MBD family CNVs to schizophrenia by exploring and validating them in two separate populations using CNVplex™ and qPCR methods, and to explore the relationship between MBD family CNVs and clinical phenotypes in the overall population using chi-square tests and Fisher's exact tests. Results suggest that an increase in MBD1 gene copy number and a deficiency in MBD2 gene copy number may be associated with the risk of schizophrenia. The deficiency in MBD2 gene copy number may increase the risk of delusion of reference and delusion of persecutory in the overall sample, as well as in males. This research provides preliminary evidence supporting the association between MBD family CNVs and schizophrenia, highlighting the potential role of the MBD family in the pathogenesis of schizophrenia.

DNA Methylation Machinery in Gastropod Mollusks

The role of DNA methylation in mollusks is just beginning to be understood. This review synthesizes current knowledge on this potent molecular hallmark of epigenetic control in gastropods-the largest class of mollusks and ubiquitous inhabitants of diverse habitats. Their DNA methylation machinery shows a high degree of conservation in CG maintenance methylation mechanisms, driven mainly by DNMT1 homologues, and the presence of MBD2 and MBD2/3 proteins as DNA methylation readers. The mosaic-like DNA methylation landscape occurs mainly in a CG context and is primarily confined to gene bodies and housekeeping genes. DNA methylation emerges as a critical regulator of reproduction, development, and adaptation, with tissue-specific patterns being observed in gonadal structures. Its dynamics also serve as an important regulatory mechanism underlying learning and memory processes. DNA methylation can be affected by various environmental stimuli, including as pathogens and abiotic stresses, potentially impacting phenotypic variation and population diversity. Overall, the features of DNA methylation in gastropods are complex, being an essential part of their epigenome. However, comprehensive studies integrating developmental stages, tissues, and environmental conditions, functional annotation of methylated regions, and integrated genomic-epigenomic analyses are lacking. Addressing these knowledge gaps will advance our understanding of gastropod biology, ecology, and evolution.

Functional characterisation of Fe (II) and 2OG-dependent dioxygenase TcALKBH4 in the red flour beetle, Tribolium castaneum

Alpha-ketoglutarate-dependent dioxygenase ALKB homologue 4 (ALKBH4) is a member of the Fe (II) and 2-oxoglutarate-dependent ALKB homologue family that plays important roles in epigenetic regulation by alkyl lesions removal in mammals. However, the roles of ALKBH4 in insects are not clear. Here, TcALKBH4 was cloned and functionally characterised in Tribolium castaneum. Temporal expression revealed that TcALKBH4 was highly expressed in early embryos and early pupae. Spatial expression showed that TcALKBH4 was highly expressed in the adult testis, and followed by the ovary. RNA interference targeting TcALKBH4 at different developmental stages in T. castaneum led to apparent phenotypes including the failure of development in larvae, the reduction of food intake and the deficiency of fertility in adult. However, further dot blot analyses showed that TcALKBH4 RNAi does not seem to influence 6 mA levels in vivo. qRT-PCR was used to further explore the underlying molecular mechanisms; the result showed that TcALKBH4 mediates the development of larvae possibly through 20E signalling pathway, and the fertility of female and male adult might be regulated by the expression of vitellogenesis and JH signalling pathway, respectively. Altogether, these findings will provide new insights into the potential function of ALKBH4 in insects.

Methyl-CpG binding domain (MBD)2/3 specifically recognizes and binds to the genomic mCpG site with a β-sheet in the MBD to affect embryonic development in Bombyx mori

Methyl-CpG (mCpG) binding domain (MBD) proteins especially bind with methylated DNA, and are involved in many important biological processes; however, the binding mechanism between insect MBD2/3 and mCpG remains unclear. In this study, we identified 2 isoforms of the MBD2/3 gene in Bombyx mori, MBD2/3-S and MBD2/3-L. Binding analysis of MBD2/3-L, MBD2/3-S, and 7 mutant MBD2/3-L proteins deficient in β1-β6 or α1 in the MBD showed that β2-β3-turns in the β-sheet of the MBD are necessary for the formation of the MBD2/3-mCpG complex; furthermore, other secondary structures, namely, β4-β6 and an α-helix, play a role in stabilizing the β-sheet structure to ensure that the MBD is able to bind mCpG. In addition, sequence alignment and binding analyses of different insect MBD2/3s indicated that insect MBD2/3s have an intact and conserved MBD that binds to the mCpG of target genes. Furthermore, MBD2/3 RNA interference results showed that MBD2/3-L plays a role in regulating B. mori embryonic development, similar to that of DNA methylation; however, MBD2/3-S without β4-β6 and α-helix does not alter embryonic development. These results suggest that MBD2/3-L recognizes and binds to mCpG through the intact β-sheet structure in its MBD, thus ensuring silkworm embryonic development.

Molecular and functional analysis of eclosion hormone-like gene involved in post-eclosion behavior in a beetle

Eclosion hormone (EH) is a neurohormone that plays a key role in the regulation of insect pre-ecdysis behavior at the end of each molt. Previous research has reported more than one EH gene was found in certain insects, with their functions and mechanisms still unclear. Here, aside from the classical EH gene orthologous group, we characterized another novel orthologous cluster of eclosion hormone-like (EHL) genes in Arthropoda and investigated the roles of EHL during development in Tribolium castaneum. T. castaneum EHL (TcEHL) shows high expression levels during pupal - adult development, which also positively responded to 20-hydroxyecdysone (20E) treatment as well as RNA interference (RNAi) of ECR (20E nuclear receptor). Knockdown of TcEHL prevented the tanning of the adult cuticle and caused lethal phenotypes. Further analysis indicated that knockdown of TcEHL could upregulate expression levels of the classical TcEH, and downregulate the ecdysis behavior cascade genes, as well as tanning pathway enzymes. This suggests a critical role for TcEHL in adult eclosion and cuticle tanning. In addition, our data indicated that TcEHL is responsible for the female reproduction process. Taken together, these results suggest that TcEHL has specific roles in adult cuticle tanning during the post-eclosion process and female reproduction. They also suggest that EHL gene is the ancestral copy for the EH family and it is functionally shuffled by synfunctionalization.

MiR-3017b contributes to metamorphosis by targeting sarco/endoplasmic reticulum Ca2+ ATPase in Tribolium castaneum

In recent years, increasing numbers of microRNAs (miRNAs) have been reported to regulate insect metamorphosis. One thousand, one hundred fifty-four miRNAs have been previously identified from Tribolium castaneum by high-throughput sequencing; however, little is known about which miRNAs can participate in metamorphosis, leaving the role of miRNAs in regulating the underlying mechanism elusive. Here, we report the participation of miR-3017b in the metamorphosis of T. castaneum. Temporal profiles revealed that miR-3017b was highly expressed at the late larval stage, but significantly decreased at the early pupal stage. Overexpression of miR-3017b caused larval to pupal to adult metamorphosis arrested. Dual-luciferase reporter assay and miRNA-mRNA interaction assay illustrated that miR-3017b interacts with the coding sequence of sarco/endoplasmic reticulum Ca²⁺ ATPase (SERCA) and suppresses its expression. Knockdown of SERCA caused metamorphosis arrested, similar to that observed in miR-3017b overexpression beetles. Further functional mechanism analyses revealed that 20-hydroxyecdysone application downregulates miR-3017b and up-regulates SERCA expression. The expression level of downstream genes in the 20E pathway was disrupted after overexpressing miR-3017 and the knockdown of SERCA. These results provided evidence miR-3017b-SERCA contributes to metamorphosis by regulating the 20E pathway in T. castaneum. It could advance our understanding of the coordination of 20E and miRNA regulation in insect metamorphosis.

Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses

Cytosine-5 DNA methyltransferases (C5-MTases) and methyl-CpG-binding-domain (MBD) genes can be co-expressed. They directly control target gene expression by enhancing their DNA methylation levels in humans; however, the presence of this kind of cooperative relationship in plants has not been determined. A popular garden plant worldwide, petunia (Petunia hybrida) is also a model plant in molecular biology. In this study, 9 PhC5-MTase and 11 PhMBD proteins were identified in petunia, and they were categorized into four and six subgroups, respectively, on the basis of phylogenetic analyses. An expression correlation analysis was performed to explore the co-expression relationships between PhC5-MTases and PhMBDs using RNA-seq data, and 11 PhC5-MTase/PhMBD pairs preferentially expressed in anthers were identified as having the most significant correlations (Pearson’s correlation coefficients > 0.9). Remarkably, the stability levels of the PhC5-MTase and PhMBD pairs significantly decreased in different tissues and organs compared with that in anthers, and most of the selected PhC5-MTases and PhMBDs responded to the abiotic and hormonal stresses. However, highly correlated expression relationships between most pairs were not observed under different stress conditions, indicating that anther developmental processes are preferentially influenced by the co-expression of PhC5-MTases and PhMBDs. Interestingly, the nuclear localization genes PhDRM2 and PhMBD2 still had higher correlations under GA treatment conditions, implying that they play important roles in the GA-mediated development of petunia. Collectively, our study suggests a regulatory role for DNA methylation by C5-MTase and MBD genes in petunia anther maturation processes and multi-stress responses, and it provides a framework for the functional characterization of C5-MTases and MBDs in the future.

Characterization of a sigma class GST (GSTS6) required for cellular detoxification and embryogenesis in Tribolium castaneum

The sigma glutathione S-transferases (GSTSs) are a class of cytosolic glutathione S transferases (GSTs) that play important roles in antioxidant defense in insects, but the mechanisms by which GSTSs contribute to antioxidant activity remain unclear. Here, we isolated a GSTS (GSTS6) from Tribolium castaneum and explored its function. Homology and phylogenetic analysis revealed that TcGSTS6 shared high identity with other evolutionarily conserved GSTSs. The recombinant TcGSTS6 protein had strong activity toward cumene hydroperoxide and 4-hydroxynonenal but low activity toward the universal substrate 1-chloro-2,4-dinitrobenzene. Exposure to various types of oxidative stress, including heat, cold, UV and pathogenic microbes, significantly induced TcGSTs6 expression, which indicates that it is involved in antioxidant defense. Knockdown TcGSTs6 by using RNA interference (RNAi) caused reduced antioxidant capacity, which was accomplished by cooperating with other antioxidant genes. Moreover, treatment with various insecticides such as phoxim, lambda-cyhalothrin, dichlorvos and carbofuran revealed that TcGSTS6 plays an important role in insecticide detoxification. The RNAi results showed that TcGSTS6 is essential for embryogenesis in T. castaneum. Our study elucidates the mechanism by which a GSTS contributes to antioxidant activity and enhances our understanding of the functional diversity of GSTSs in insects.

In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants

Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their growth and development. We emphasize the molecular process underlying changes in DNA methylation, differential variation for different species, the roles of non-coding RNAs in epigenetic modification, techniques for studying DNA methylation, and its role in crop improvement in tolerance to abiotic stress (drought, salinity, and heat). We summarize DNA methylation as a significant future research priority for tailoring crops according to various challenging environmental issues.

NADPH-cytochrome P450 reductase mediates the susceptibility of Asian citrus psyllid Diaphorina citri to imidacloprid and thiamethoxam

BACKGROUND

The Asian citrus psyllid Diaphorina citri has developed high levels of resistance to many insecticides, and understanding its resistance mechanism will aid in the chemical control of this species. Nicotinamide adenine dinucleotide phosphate (NADPH)-cytochrome P450 reductase (CPR) is crucial in cytochrome P450 function, and in some insects CPR knockdown has increased their susceptibility to insecticides. However, the CPR from D. citri has not been characterized and its function is undescribed.

RESULTS

The CPR gene of D. citri (DcCPR) was cloned and sequenced. The expression level of DcCPR, determined by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) analysis, was highest in the midgut and in nymphs. After feeding on double-stranded RNA for 72 h, the DcCPR messenger RNA level in D. citri adults decreased by 68.4%, and the susceptibility of D. citri to imidacloprid and thiamethoxam significantly increased. Meanwhile, after DcCPR silencing, the specific activities of DcCPR protein and P450s were significantly reduced by 41.6% and 44.7%, respectively. The subsequent western blot analysis and quantification of band intensity also showed that DcCPR content significantly decreased, consistent with the results of the specific activity test. In a eukaryotic expression assay, the viability of cells expressing DcCPR was significantly higher than the viability of cells expressing green fluorescent protein (GFP) when cells were exposed to imidacloprid or thiamethoxam.

CONCLUSION

These results indicate that DcCPR contributes to D. citri susceptibility to imidacloprid and thiamethoxam.

Functional characterization of a special dicistronic transcription unit encoding histone methyltransferase su(var)3-9 and translation regulator eIF2γ in Tribolium castaneum

Operons are rare in eukaryotes, where they often allow concerted expression of functionally related genes. While a dicistronic transcription unit encoding two unrelated genes, the suppressor of position-effect variegation su(var)3-9 and the gamma subunit of eukaryotic translation initiation factor 2 (eIF2γ) has been found in insecta, and its significance is not well understood. Here, we analyzed the evolutionary history of this transcription unit in arthropods and its functions by using model Coleoptera insect Tribolium castaneum. In T. castaneum, Tcsu(var)3-9 fused into the 80 N-terminal amino acids of TceIF2γ, the transcription of these two genes are resolved by alternative splicing. Phylogenetic analysis supports the natural gene fusion of su(var)3-9 and eIF2γ occurred in the ancestral line of winged insects and silverfish, but with frequent re-fission during the evolution of insects. Functional analysis by using RNAi for these two genes revealed that gene fusion did not invoke novel functions for the gene products. As a histone methyltransferase, Tcsu(var)3-9 is primarily responsible for H3K9 di-, and tri-methylation and plays important roles in metamorphosis and embryogenesis in T. castaneum. While TceIF2γ plays essential roles in T. castaneum by positively regulating protein translation mediated ecdysteroid biosynthesis. The vulnerability of the gene fusion and totally different role of su(var)3-9 and eIF2γ in T. castaneum confirm this gene fusion is a non-selected, constructive neutral evolution event in insect. Moreover, the positive relationship between protein translation and ecdysteroid biosynthesis gives new insights into correlations between translation regulation and hormonal signaling.

Functions of a C-type lectin with a single carbohydrate-recognition domain in the innate immunity and movement of the red flour beetle, Tribolium castaneum

C-type lectins (CTLs) are a superfamily of proteins found in almost all vertebrates and invertebrates. They play an important role in innate immune defences, development and epidermal structure. Here, a CTL with one carbohydrate-recognition domain containing a highly conserved Gln-Pro-Asp (QPD) motif was identified in Tribolium castaneum and given the name TcCTL5. Spatiotemporal analyses showed that Tcctl5 was highly expressed in the late pupa stage and mainly existed in the central nervous system and haemolymph. The transcript level of Tcctl5 was prominently induced after bacterial infection. Recombinant TcCTL5 proteins (rTcCTL5) were found to bind to lipopolysaccharide, peptidoglycan and tested bacteria and induce microbial agglutination in the presence of Ca²⁺ . Interestingly, when Tcctl5 was knocked down, the transcript level of antimicrobial peptides (AMPs) (attacin1, defensins3, coleoptericin1 and cecropins3) was prominently downregulated after induction with Gram-negative Escherichia coli. More interestingly, Tcctl5 was knocked down, leading to increased mortality and loss of locomotor activity, which exhibited less travel distances among early adults. These results demonstrate that Tcctl5 plays an important role in the innate immune reaction and the movement of T. castaneum. Thus, it may represent an alternative molecular target for pest control and thus reduce the use of pesticides in agricultural production.

BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis

Background Bioinformatics tools are of great significance and are used in different spheres of life sciences. There are wide variety of tools available to perform primary analysis of DNA and protein but most of them are available on different platforms and many remain undetected. Accessing these tools separately to perform individual task is uneconomical and inefficient. Objective Our aim is to bring different bioinformatics models on a single platform to ameliorate scientific research. Hence, our objective is to make a tool for comprehensive DNA and protein analysis. Methods To develop a reliable, straight-forward and standalone desktop application we used state of the art python packages and libraries. Bioinformatics Mini Toolbox (BMT) is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment. Results FastqTrimmer assists in quality assurance of NGS data. Gene prediction predicts the genes by homology from novel genome on the basis of reference sequence. Protein analysis and DNA analysis calculates physiochemical properties of nucleotide and protein sequences, respectively. Translation translates the DNA sequence into six open reading frames. Pairwise alignment performs pairwise global and local alignment of DNA and protein sequences on the basis or multiple matrices. Multiple alignment aligns multiple sequences and generates a phylogenetic tree. Conclusion We developed a tool for comprehensive DNA and protein analysis. The link to download BMT is https://github.com/nasiriqbal012/BMT_SETUP.git.