Genes — Open Access Journal

The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood. While a 7-8 bp VirB-binding site has been proposed, it was derived from studies at a single VirB-dependent promoter, icsB. Our previous in vivostudies at a different VirB-dependent promoter, icsP, found that the proposed VirB-binding site was insufficient for regulation. Instead, the required site was found to be organized as a near-perfect inverted repeat separated by a single nucleotide spacer. Thus, the proposed 7-8 bp VirB-binding site needed to be re-evaluated. Here, we engineer and validate a molecular tool to capture protein-DNA binding interactions in vivo. Our data show that a sequence organized as a near-perfect inverted repeat is required for VirB-DNA binding interactions in vivo at both the icsB and icsP promoters. Furthermore, the previously proposed VirB-binding site and multiple sites found as a result of its description (i.e., sites located at the virB, virF, spa15, and virA promoters) are not sufficient for VirB to bind in vivousing this tool. The implications of these findings are discussed. Full article

Late embryogenesis-abundant (LEA) proteins are a large and highly diverse family believed to function in normal plant growth and development, and in protecting cells from abiotic stress. This study presents a characterisation of 74 Solanum tuberosum LEA (StLEA) proteins belonging to nine groups. StLEA genes have few introns (≤2) and are distributed on all chromosomes, occurring as gene clusters on chromosomes 1, 2, and 10. All four StASR (StLEA7 group) genes were concentrated on chromosome 4, suggesting their evolutionary conservation on one chromosome. Expression profiles of StLEA genes, in different tissues and in response to hormone and stress treatments, indicated that 71 StLEA genes had differential expression levels, of which 68 StLEA genes were differentially expressed in response to hormones and stress exposure in the potato. Continuous high expression of StASR-2, StLEA3-3, StDHN-3, StLEA2-29, and StLEA2-14 in different tissues indicated their contribution to plant development processes. StLEA2-14, StLEA2-31, StLEA3-3, StASR-1, and StDHN-1 were upregulated by six abiotic stresses, showing their tolerance to a wide spectrum of environmental stresses. Expression analysis of 17 selected StLEA genes in response to drought, salt, heavy metal, heat, and cold treatments by quantitative real-time polymerase chain reaction indicated that StLEA proteins may be involved in distinct signalling pathways. Taken together, StLEA3, StDHN, and StASR subgroup genes may be excellent resources for potato defence against environmental stresses. These results provide valuable information and robust candidate genes for future functional analysis aimed at improving the stress tolerance of the potato. Full article

Although gene expression can vary extensively within and among populations, the genetic basis of this variation and the evolutionary forces that maintain it are largely unknown. In Drosophilamelanogaster, a 49-bp insertion/deletion (indel) polymorphism in the Metallothionein A (MtnA) gene is associated with variation in MtnA expression and oxidative stress tolerance. To better understand the functional and evolutionary significance of this polymorphism, we investigated it in several worldwide populations. In a German population, the deletion was present at a high and stable frequency over multiple seasons and years, and was associated with increased MtnA expression. There was, however, no evidence that the polymorphism was maintained by overdominant, seasonally fluctuating, or sexually antagonistic selection. The deletion was rare in a population from the species’ ancestral range in sub-Saharan Africa and is likely the result of non-African admixture, suggesting that it spread to high frequency following the species’ out-of-Africa expansion. Using data from a North American population, we found that the deletion was associated with MtnA expression and tolerance to oxidative stress induced by menadione sodium bisulfite. Our results are consistent with the deletion being selectively favored in temperate populations due to the increased MtnA expression and oxidative stress tolerance that it confers. Full article

Drought and salinity are major factors limiting crop productivity worldwide. DREB (dehydration-responsive element-binding) transcription factors play important roles in plant stress response and have been identified in a wide variety of plants. Studies on DREB are focused on the A-1 (DREB1) and A-2 (DREB2) groups. Studies on A-5 group DREBs, which represent a large proportion of the DREB subfamily, is limited. In this study, we characterized and analyzed the stress tolerance function of ScDREB10, an A-5c type DREB gene from the desert moss Syntrichia caninervis. Transactivation assay in yeast showed that ScDREB10 had transactivation activity. Transient expression assay revealed that ScDREB10was distributed both in the nucleus and cytosol of tobacco leafepidermal cells. Overexpression of ScDREB10 significantly increased the germination percentage of Arabidopsis seeds under osmotic and salt stresses, and improved the osmotic and salt stress tolerances of Arabidopsis at the seedling stage and is associated with the expression of downstream stress-related genes and improved reactive oxygen species (ROS) scavenging ability. Our study provides insight into the molecular mechanism of stress tolerance of A-5 type DREB proteins, as well as providing a promising candidate gene for crop salt and drought stress breeding. Full article

Interferons (IFNs) are pleiotropic cytokines that establish a first line of defense against viral infections in vertebrates. Several types of IFN have been identified; however, limited information is available in poultry, especially using live animal experimental models. IFN-lambda (IFN-λ) has recently been shown to exert a significant antiviral impact against viral pathogens in mammals. In order to investigate the in vivo potential of chicken IFN-λ (chIFN-λ) as a regulator of innate immunity, and potential antiviral therapeutics, we profiled the transcriptome of chIFN-λ-stimulated chicken immune organs (in vivo) and compared it with primary chicken embryo fibroblasts (in vitro). Employing the baculovirus expression vector system (BEVS), recombinant chIFN-λ3 (rchIFN-λ3) was produced and its biological activities were demonstrated. The rchIFNλ3 induced a great array of IFN-regulated genes in primary chicken fibroblast cells. The transcriptional profiling using RNA-seq and subsequent bioinformatics analysis (gene ontology, differential expressed genes, and KEGGs analysis) of the bursa of Fabricious and the thymus demonstrated an upregulation of crucial immune genes (viperin, IKKB, CCL5, IL1β, and AP1) as well as the antiviral signaling pathways. Interestingly, this experimental approach revealed contrasting evidence of the antiviral potential of chIFN-λ in both in vivo and in vitro models. Taken together, our data signifies the potential of chIFN-λ as a potent antiviral cytokine and highlights its future possible use as an antiviral therapeutic in poultry. Full article

The vacuolar iron transporter (VIT) proteins are involved in the storage and transport of iron. However, the evolution of this gene family in plants is unknown. In this study, I first identified 114 VIT genes in 14 plant species and classified these genes into seven groups by phylogenetic analysis. Conserved gene organization and motif distribution implied conserved function in each group. I also found that tandem duplication, segmental duplication and transposition contributed to the expansion of this gene family. Additionally, several positive selection sites were identified. Divergent expression patterns of soybean VIT genes were further investigated in different development stages and under iron stress. Functional network analysis exhibited 211 physical or functional interactions. The results will provide the basis for further functional studies of the VIT genes in plants. Full article

Network biology and medicine provide unprecedented opportunities and challenges for deciphering disease mechanisms from integrative viewpoints. The disease genes and their products perform their dysfunctions via physical and biochemical interactions in the form of a molecular network. The topological parameters of these disease genes in the interactome are of prominent interest to the understanding of their functionality from a systematic perspective. In this work, we provide a systems biology analysis of the topological features of complex disease genes in an integrated biomolecular network. Firstly, we identify the characteristics of four network parameters in the ten most frequently studied disease genes and identify several specific patterns of their topologies. Then, we confirm our findings in the other disease genes of three complex disorders (i.e., Alzheimer’s disease, diabetes mellitus, and hepatocellular carcinoma). The results reveal that the disease genes tend to have a higher betweenness centrality, a smaller average shortest path length, and a smaller clustering coefficient when compared to normal genes, whereas they have no significant degree prominence. The features highlight the importance of gene location in the integrated functional linkages. Full article

Drought stress significantly restricts plant growth and crop productivity. Cotton is the most important textile fiber and oilseed crop worldwide, and its cultivation is affected by drought stress, particularly in dry regions. Improving cotton tolerance to drought stress using the advanced genetic engineering technologies is a promising strategy to maintain crop production and fiber quality and meet the increasing worldwide fiber and oil demand. Dehydration-responsive element binding (DREB) transcription factors play a main role in regulating stresses-tolerance pathways in plant. This study investigated whether potato DREB2 (StDREB2) overexpression can improve drought tolerance in cotton. StDREB2 transcription factor was isolated and overexpressed in cotton. Plant biomass, boll number, relative water content, soluble sugars content, soluble protein content, chlorophyll content, proline content, gas-exchange parameters, and antioxidants enzymes (POD, CAT, SOD, GST) activity of the StDREB2-overexpressing cotton plants were higher than those of wild type plants. By contrast, the contents of malondialdehyde, hydrogen peroxide and superoxide anion of StDREB2-overexpressing transgenic plants were significantly lower than that of the wild type plants. Moreover, the transgenic cotton lines revealed higher expression levels of antioxidant genes (SOD, CAT, POD, GST) and stress-tolerant genes (GhERF2, GhNAC3, GhRD22, GhDREB1A, GhDREB1B, GhDREB1C) compared to wild-type plants. Taken together, these findings showed that StDREB2 overexpression augments drought stress tolerance in cotton by inducing plant biomass, gas-exchange characteristics, reactive oxygen species (ROS) scavenging, antioxidant enzymes activities, osmolytes accumulation, and expression of stress-related genes. As a result, StDREB2 could be an important candidate gene for drought-tolerant cotton breeding. Full article

Despite recent advances in N⁶-methyladenosine (m⁶A) biology, the regulation of crucial RNA processing steps by the RNA methyltransferase-like 3 (METTL3) in glioma stem-like cells (GSCs) remains obscure. An integrated analysis of m⁶A-RIP (RNA immunoprecipitation) and total RNA-Seq of METTL3-silenced GSCs identified that m⁶A modification in GSCs is principally carried out by METTL3. The m⁶A-modified transcripts showed higher abundance compared to non-modified transcripts. Further, we showed that the METTL3 is essential for the expression of GSC-specific actively transcribed genes. Silencing METTL3 resulted in the elevation of several aberrant alternative splicing events. We also found that putative m⁶A reader proteins play a key role in the RNA stabilization function of METTL3. METTL3 altered A-to-I and C-to-U RNA editing events by differentially regulating RNA editing enzymes ADAR and APOBEC3A. Similar to protein-coding genes, lincRNAs (long intergenic non-coding RNAs) with m⁶A marks showed METTL3-dependent high expression. m⁶A modification of 3′UTRs appeared to result in a conformation-dependent hindrance to miRNA binding to their targets. The integrated analysis of the m⁶A regulome in METTL3-silenced GSCs showed global disruption in tumorigenic pathways that are indispensable for GSC maintenance and glioma progression. We conclude that METTL3 plays a vital role in many steps of RNA processing and orchestrates successful execution of oncogenic pathways in GSCs. Full article

Post-traumatic stress disorder (PTSD) is an acquired psychiatric disorder with functionally impairing physiological and psychological symptoms following a traumatic exposure. Genetic, epigenetic, and environmental factors act together to determine both an individual’s susceptibility to PTSD and its clinical phenotype. In this literature review, we briefly review the candidate genes that have been implicated in the development and severity of the PTSD phenotype. We discuss the importance of the epigenetic regulation of these candidate genes. We review the general epigenetic mechanisms that are currently understood, with examples of each in the PTSD phenotype. Our focus then turns to studies that have examined PTSD in the context of comorbid psychiatric disorders or associated social and behavioral stressors. We examine the epigenetic variation in cases or models of PTSD with comorbid depressive disorders, anxiety disorders, psychotic disorders, and substance use disorders. We reviewed the literature that has explored epigenetic regulation in PTSD in adverse childhood experiences and suicide phenotypes. Finally, we review some of the information available from studies of the transgenerational transmission of epigenetic variation in maternal cases of PTSD. We discuss areas pertinent for future study to further elucidate the complex interactions between epigenetic modifications and this complex psychiatric disorder. Full article

The case for improving crop phosphorus-use-efficiency is widely recognized. Although much is known about the molecular and regulatory mechanisms, improvements have been hampered by the extreme complexity of phosphorus (P) dynamics, which involves soil chemistry; plant-soil interactions; uptake, transport, utilization and remobilization within plants; and agricultural practices. The urgency and direction of phosphate research is also dependent upon the finite sources of P, availability of stocks to farmers and reducing environmental hazards. This work introduces integrative systems approaches as a way to represent and understand this complexity, so that meaningful links can be established between genotype, environment, crop traits and yield. It aims to provide a large set of pointers to potential genes and research practice, with a view to encouraging members of the plant-phosphate research community to adopt such approaches so that, together, we can aid efforts in global food security. Full article

Long non-coding RNAs (lncRNAs) have emerged as important regulators in plant stress response. Here, we report a genome-wide lncRNA transcriptional analysis in response to drought stress using an expanded series of maize samples collected from three distinct tissues spanning four developmental stages. In total, 3488 high-confidence lncRNAs were identified, among which 1535 were characterized as drought responsive. By characterizing the genomic structure and expression pattern, we found that lncRNA structures were less complex than protein-coding genes, showing shorter transcripts and fewer exons. Moreover, drought-responsive lncRNAs exhibited higher tissue- and development-specificity than protein-coding genes. By exploring the temporal expression patterns of drought-responsive lncRNAs at different developmental stages, we discovered that the reproductive stage R1 was the most sensitive growth stage with more lncRNAs showing altered expression upon drought stress. Furthermore, lncRNA target prediction revealed 653 potential lncRNA-messenger RNA (mRNA) pairs, among which 124 pairs function in cis-acting mode and 529 in trans. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to oxidoreductase activity, water binding, and electron carrier activity. Multiple promising targets of drought-responsive lncRNAs were discovered, including the V-ATPase encoding gene, vpp4. These findings extend our knowledge of lncRNAs as important regulators in maize drought response. Full article

Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola. We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes. Although no causal association is shown, this lends support for the implication of DNA CpG methylation in regulating gene expression in invertebrates. Differential DNA methylation between populations showed a small but significant correlation with differential gene expression. This is consistent with a possible role of DNA methylation in local adaptation. Based on indirect inference of the presence and pattern of DNA methylation in chelicerate species whose genomes have been sequenced, we performed a comparative phylogenetic analysis. We found strong evidence for exon DNA methylation in the horseshoe crab Limulus polyphemus and in all spider and scorpion species, while most Parasitiformes and Acariformes species seem to have lost DNA methylation. Full article

Ehlers-Danlos syndrome (EDS) comprises clinically heterogeneous connective tissue disorders with diverse molecular etiologies. The 2017 International Classification for EDS recognized 13 distinct subtypes caused by pathogenic variants in 19 genes mainly encoding fibrillar collagens and collagen-modifying or processing proteins. Recently, a new EDS subtype, i.e., classical-like EDS type 2, was defined after the identification, in six patients with clinical findings reminiscent of EDS, of recessive alterations in AEBP1, which encodes the aortic carboxypeptidase–like protein associating with collagens in the extracellular matrix. Herein, we report on a 53-year-old patient, born from healthy second-cousins, who fitted the diagnostic criteria for classical EDS (cEDS) for the presence of hyperextensible skin with multiple atrophic scars, generalized joint hypermobility, and other minor criteria. Molecular analyses of cEDS genes did not identify any causal variant. Therefore, AEBP1 sequencing was performed that revealed homozygosity for the rare c.1925T>C p.(Leu642Pro) variant classified as likely pathogenetic (class 4) according to the American College of Medical Genetics and Genomics (ACMG) guidelines. The comparison of the patient’s features with those of the other patients reported up to now and the identification of the first missense variant likely associated with the condition offer future perspectives for EDS nosology and research in this field. Full article

Epigenetic changes are well-established contributors to cancer progression and normal developmental processes. The reversible modification of histones plays a central role in regulating the nuclear processes of gene transcription, DNA replication, and DNA repair. The KDM4 family of Jumonj domain histone demethylases specifically target di- and tri-methylated lysine 9 on histone H3 (H3K9me3), removing a modification central to defining heterochromatin and gene repression. KDM4 enzymes are generally over-expressed in cancers, making them compelling targets for study and therapeutic inhibition. One of these family members, KDM4B, is especially interesting due to its regulation by multiple cellular stimuli, including DNA damage, steroid hormones, and hypoxia. In this review, we discuss what is known about the regulation of KDM4B in response to the cellular environment, and how this context-dependent expression may be translated into specific biological consequences in cancer and reproductive biology. Full article

Mice with deletions of the Y-specific (non-PAR) region of the mouse Y chromosome long arm (NPYq) have sperm defects and fertility problems that increase proportionally to deletion size. Mice with abrogated function of NPYq-encoded gene Sly (sh367 Sly-KD) display a phenotype similar to that of NPYq deletion mutants but less severe. The milder phenotype can be due to insufficient Sly knockdown, involvement of another NPYq gene, or both. To address this question and to further elucidate the role of Sly in the infertile phenotype of mice with NPYq deletions, we developed an anti-SLY antibody specifically recognizing SLY1 and SLY2 protein isoforms and used it to characterize SLY expression in NPYq- and Sly-deficient mice. We also carried out transgene rescue by adding Sly1/2 transgenes to mice with NPYq deletions. We demonstrated that SLY1/2 expression in mutant mice decreased proportionally to deletion size, with ~12% of SLY1/2 retained in shSLY sh367 testes. The addition of Sly1/2 transgenes to mice with NPYq deletions rescued SLY1/2 expression but did not ameliorate fertility and testicular/spermiogenic defects. Together, the data suggest that Sly deficiency is not the sole underlying cause of the infertile phenotype of mice with NPYq deletions and imply the involvement of another NPYq gene. Full article

Effective prediction of protein tertiary structure from sequence is an important and challenging problem in computational structural biology. Ab initio protein structure prediction is based on amino acid sequence alone, thus, it has a wide application area. With the ab initio method, a large number of candidate protein structures called decoy set can be predicted, however, it is a difficult problem to select a good near-native structure from the predicted decoy set. In this work we propose a new method for selecting the near-native structure from the decoy set based on both contact map overlap (CMO) and graphlets. By generalizing graphlets to ordered graphs, and using a dynamic programming to select the optimal alignment with an introduced gap penalty, a GR_score is defined for calculating the similarity between the three-dimensional (3D) decoy structures. The proposed method was applied to all 54 single-domain targets in CASP11 and all 43 targets in CASP10, and ensemble clustering was used to cluster the protein decoy structures based on the computed CR_scores. The most popular centroid structure was selected as the near-native structure. The experiments showed that compared to the SPICKER method, which is used in I-TASSER, the proposed method can usually select better near-native structures in terms of the similarity between the selected structure and the true native structure. Full article

The WRKY gene family plays a unique role in plant stress tolerance. Quinoa is a cultivated crop worldwide that is known for its high stress tolerance. The WRKY gene family in quinoa has not yet been studied. Using a genome-wide search method, we identified 1226 WRKY genes in 15 plant species, seven animal species, and seven fungi species. WRKY proteins were not found in animal species and five fungi species, but were, however, widespread in land plants. A total of 92 CqWRKY genes were identified in quinoa. Based on the phylogenetic analysis, these CqWRKY genes were classified into three groups. The CqWRKY proteins have a highly conserved heptapeptide WRKYGQK with 15 conserved elements. Furthermore, a total of 25 CqWRKY genes were involved in the co-expression pathway of organ development and osmotic stress. The expression level of more than half of these CqWRKY genes showed significant variation under salt or drought stress. This study reports, for the first time, the findings of the CqWRKY gene family in quinoa at the genome-wide level. This information will be beneficial for our understanding of the molecular mechanisms of stress tolerance in crops, such as quinoa. Full article