Binding Protein Family Research Articles

Comprehensive Identification of AREB Gene Family in Populus euphratica Oliv. and Functional Analysis of PeAREB04 in Drought Tolerance.

The transcription factors in the ABA Response Element Binding (AREB) protein family were differentially regulated under multiple stress conditions; however, functional analyses of AREB in Populus euphratica Oliv. had not been conducted previously. In the present study, the comprehensive identification of the P. euphratica AREB gene family and the function of PeAREB04 in response to drought stress in P. euphratica were elucidated. A comprehensive analysis of the PeAREB family was first performed, followed by the determination of their expression patterns under drought stress. Bioinformatics analysis revealed that thirteen AREB genes were identified across the P. euphratica genome, with these genes distributed across eight chromosomes in a seemingly random pattern. Phylogenetic analysis indicated that the PeAREB genes could be categorized into four distinct branches. Cis-acting element analysis revealed that most PeAREB genes contained multiple hormone- and stress-responsive elements. Transcriptomic sequencing of P. euphratica seedlings under drought stress showed that most PeAREB genes responded rapidly to drought stress in either the leaves or roots. One gene, PeAREB04, was selected for further functional validation due to its significant upregulation in both leaves and roots under drought stress. Overexpression of PeAREB04 in Arabidopsis thaliana resulted in a high survival rate, reduced water loss in isolated leaves, and a significant reduction in stomatal aperture under natural drought conditions. Drought stress simulations using mannitol further demonstrated that overexpression of PeAREB04 significantly enhanced root elongation. These findings indicate that the identification of the PeAREB gene family and the characterization of PeAREB04's role in drought stress have been largely accomplished. Furthermore, the PeAREB04 gene demonstrates considerable potential as a key target for future genetic engineering strategies aimed at enhancing plant drought resistance.

Genome-Wide Identification and Expression Analysis of Members in the YT521-B Homology Domain-Containing RNA Binding Protein Family in Ginkgo biloba.

N6-methyladenosine (m6A) is a widespread post-transcriptional modification of RNA in eukaryotes. The conserved YTH-domain-containing RNA binding protein has been widely reported to serve as a typical m6A reader in various species. However, no studies have reported the m6A readers in Ginkgo biloba (G. biloba). In this study, a systematic analysis of the m6A reader (YTH) gene family was performed on G. biloba, identifying 10 YTH genes in its genome. Phylogenetic analysis of protein-coding sequences revealed that YTH genes from G. biloba could be classified into two subgroups: GbDC1 and GbDC2 in GbDC and GbDF1-8 in GbDF, each with similar motifs and gene structures. In G. biloba, the predicated aromatic cage pocket of the YTH domains in the YTH gene family is uniformly composed of tryptophan residues (WWW). Subcellular localization experiments verified that GbDC1 is indeed localized in the nucleus, while GbDF1 is localized in both the nucleus and the cytoplasm. The expression patterns of the identified m6A reader genes showed a wide distribution but were tissue-specific. Most genes were highly expressed in leaves, followed by the stem, while the lowest expression tendency was found in the roots. Cis-regulatory element analysis predicted the possible functions of YTH genes in G. biloba, which were mainly responsive to plant hormones such as ABA and MeJA, as well as stress responses. Furthermore, the expression levels of YTH genes indeed changed significantly after ABA, MeJA, and NaCl treatments, suggesting that they can be affected by these abiotic factors. In addition, the PLAAC prediction results indicate that prion domains exist in GbDF1, GbDF2, GbDF3, GbDF4, GbDF6, GbDF7, GbDF8, and GbDC1, and phase separation is possible. This study provides a foundation for further investigation of the effects of m6A methylation on gene expression regulation in G. biloba and other forest trees.

Low serum S100A6 levels are associated RP-ILD risk in anti-MDA5-positive dermatomyositis.

Anti-MDA5-positive dermatomyositis (anti-MDA5-DM) is a rare autoimmune disease that often leads to rapid-progressive interstitial lung disease (RP-ILD). The lack of effective prediction and treatment methods makes RP-ILD a major risk factor for death in patients with this condition. S100A6 is a member of the S100 Ca2 + - binding protein family, which plays important roles in inflammation, tumor, injury, and fibroblast reparation. This study aims to explore the correlation between serum S100A6 and RP-ILD in anti-MDA5-DM, and to determine whether S100A6 can be used as a specific biomarker to predict RP-ILD. The authors enrolled 80 participants, including 20 healthy volunteers, 20 patients with anti-synthase syndrome, and 40 patients with anti-MDA5-positive dermatomyositis. Serum samples were collected and the levels of S100A6 were measured using ELISA. Logistic regression was used to analyze the relationship between serum S100A6 levels and RP-ILD, along with other clinical and laboratory parameters. RESULTS: Serum S100A6 levels were significantly lower in anti-MDA5-DM patients with RP-ILD than those without RP-ILD (odds ratio:0.393 (95% CI, 0.164-0.943, p = 0.036)). High serum S100A6 level was found to be a protective factor for RP-ILD. This study shows that high serum S100A6 level may be a protective factor for RP-ILD in anti-MDA5-DM patients. Serum S100A6 may be used as a specific biomarker to predict whether RP-ILD occurs in anti-MDA5-DM. Key Points • This researchdiscovers and reports a biomarker (S100A6) for distinguishing potential RP-ILD in Anti-MDA5 positive dermatomyositis.

CHD6 eviction of promoter nucleosomes maintains housekeeping transcriptional program in prostate cancer

CHD6, a member of the chromodomain helicase DNA binding protein family, has been implicated in various diseases and tumors. However, its precise binding model of CHD6 on regulatory functional genes remains poorly understood. In this study, we discovered sharp peaks of CHD6, as the first member of CHD family for housekeeping process, binding only to the promoter region of genes in C4-2 cell line. These genes, with conserved sharp CHD6 peaks across tumor cells, likely represent housekeeping genes ADNP and GOLGA5. Genes with sharp CHD6 peaks exhibit stable and low expression levels, sharing epigenetic features similar with housekeeping genes. Furthermore, this regulatory model also exists in both HEK293 cells and cardiomyocytes. Overall, the results of this study demonstrate that CHD6 binds to the promoter regions of housekeeping genes, regulating their histone modifications, chromatin structure, and gene expression.

MYBBP1A‑mediated IGFBP4 promoter methylation promotes epithelial‑mesenchymal transition and metastasis through activation of NOTCH pathway in liver cancer.

Metastatic hepatocellular carcinoma (HCC) seriously threatens patients' prognosis. It was previously suggested that the insulin growth factor binding protein (IGFBP) family could serve as cancer suppressors in the development and metastasis of HCC. However, the role of IGFBP4 and its underlying molecular mechanism in HCC metastasis is elusive. In the present study, it was found that IGFBP4 is significantly downregulated in HCC, whose expression is positively correlated with the prognosis of patients with HCC. Overexpression of IGFBP4 restrained migration abilities and cancer metastasis of HCC cells both in vitro and in vivo. Furthermore, it was found that IGFBP4 represses HCC metastasis by inhibiting epithelial‑mesenchymal transition. Molecular mechanism studies showed that overexpression of IGFBP4 obviously suppresses NOTCH1 signaling in HCC. As for the upstream regulatory mechanism, it was revealed that downregulation of IGFBP4 in HCC was caused by CpG islands' hyper‑methylation‑dependent degradation mediated by MYBBP1A. Inhibition of MYBBP1A limited HCC metastatic ability and silence of IGFBP4 at the same time restored HCC metastatic potentials. Clinical data demonstrated that low expression of IGFBP4 was found in patients with HCC, especially with lymphatic metastasis. High MYBBP1A expression and low IGFBP4 expression in HCC were correlated with poor survival of patients with HCC. Summarily, in the present study, it was revealed that MYBBP1A/IGFBP4/NOTCH1 pathway could play a crucial role in the progression and metastasis of HCC, which stimulates novel therapeutic and diagnostic strategies against metastatic HCC.

Association of GhGeBP genes with fiber quality and early maturity related traits in upland cotton

Transcription Factors (TFs) are key regulators of how plants grow and develop. Among the diverse TF families, the Glabrous-enhancer binding protein (GeBP) family plays a key role in trichome initiation and leaf development. The specific roles of GeBP TFs in plants remain largely unexplored, although GeBP transcription factors play important roles in plants. This study identified 16 GhGeBP genes in Gossypium hirsutum, ranging from 534 bp (GhGeBP14) to 1560 bp (GhGeBP2). Phylogenetic analysis grouped 16 GhGeBP genes clustered into three subgroups, unevenly distributed across 14 chromosomes. Analysis of the cis-acting elements revealed 408 motifs in the 2 kb upstream regions of the promoters, including stress-responsive, phytohormone-responsive, and light-responsive elements. Tissue-specific expression analysis showed 8 GhGeBP genes were highly expressed across all tissues, while GhGeBP4 and GhGeBP12 were down-regulated under conditions of drought, salt, cold, and heat stress. A genome-wide association study (GWAS) identified GhGeBP4 was associated with fiber micronaire (FM) and fiber strength (FS), while GhGeBP9 was linked to the node of the first fruiting branch (NFFB) and flowering time (FT). Haplotype analysis revealed that GhGeBP4-HAP2 exhibited higher fiber quality traits, while GhGeBP9-HAP2 was associated with early maturity. The results of this study offer significant insights that are worthy of further investigation into the role of the GhGeBP gene family in G. hirsutum and promising targets for marker-assisted selection strategies in cotton breeding programs, particularly for improving fiber quality and early maturity traits.

A budding yeast-centric view of oxysterol binding protein family function

The Trans Golgi Network (TGN)/endosomal system is a sorting center for cargo brought via the anterograde secretory pathway and the endocytic pathway that internalizes material from the plasma membrane. As many of the cargo that transit this central trafficking hub are components of key homeostatic signaling pathways, TGN/endosomes define a critical signaling hub for cellular growth control. A particularly interesting yet incompletely understood aspect of regulation of TGN/endosome function is control of this system by two families of lipid exchange/lipid transfer proteins. The phosphatidylinositol transfer proteins promote pro-trafficking phosphoinositide (i.e. phosphatidylinositol-4-phosphate) signaling pathways whereas proteins of the oxysterol binding protein family play reciprocal roles in antagonizing those arms of phosphoinositide signaling. The precise mechanisms for how these lipid binding proteins execute their functions remain to be resolved. Moreover, information regarding the coupling of individual members of the oxysterol binding protein family to specific biological activities is particularly sparse. Herein, we review what is being learned regarding functions of the oxysterol binding protein family in the yeast model system. Focus is primarily directed at a discussion of the Kes1/Osh4 protein for which the most information is available.

Antimicrobial Functions of Galectins from Fish, Mollusks, and Crustaceans: A Review.

Galectins are a member of the β-galactoside binding protein family, which play a pivotal role in the immune defense of vertebrates as a pattern recognition receptor and occupy an important position in the innate immune system of invertebrates. The study of galectins in aquatic organisms has only recently emerged. Galectins in aquatic animals exhibit agglutination activity toward bacteria, inhibit bacterial growth, and enhance phagocytosis of immune cells. Additionally, some galectins contribute to the antiviral immune defenses of aquatic animals. This review aims to review recent advancements in the antimicrobial mechanisms, molecular structures, and evolution of galectins from fish, mollusks, and crustaceans. The antimicrobial galectins, as crucial components in the innate immune defense, pave new avenues for developing innovative disease control strategies in aquaculture.

Single-cell transcriptomics of pediatric Burkitt lymphoma reveals intra-tumor heterogeneity and markers of therapy resistance

Burkitt lymphoma (BL) is the most frequent B-cell lymphoma in pediatric patients. While most patients are cured, a fraction of them are resistant to therapy. To investigate BL heterogeneity and the features distinguishing therapy responders (R) from non-responders (NR), we analyzed by single-cell (sc)-transcriptomics diagnostic EBV-negative BL specimens. Analysis of the non-tumor component revealed a predominance of immune cells and a small representation of fibroblasts, enriched in NR. Tumors displayed patient-specific features, as well as shared subpopulations that expressed transcripts related to cell cycle, signaling pathways and cell-of-origin signatures. Several transcripts were differentially expressed in R versus NR. The top candidate, Tropomyosin 2 (TPM2), a member of the tropomyosin actin filament binding protein family, was confirmed to be significantly higher in NR both at the transcript and protein level. Stratification of patients based on TPM2 expression at diagnosis significantly correlated with prognosis, independently of TP53 mutations. These results indicate that BL displays transcriptional heterogeneity and identify candidate biomarkers of therapy resistance.

An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression

Previously, we showed that the germ cell-specific nuclear protein RBMXL2 represses cryptic splicing patterns during meiosis and is required for male fertility (Ehrmann et al., 2019). Here, we show that in somatic cells the similar yet ubiquitously expressed RBMX protein has similar functions. RBMX regulates a distinct class of exons that exceed the median human exon size. RBMX protein-RNA interactions are enriched within ultra-long exons, particularly within genes involved in genome stability, and repress the selection of cryptic splice sites that would compromise gene function. The RBMX gene is silenced during male meiosis due to sex chromosome inactivation. To test whether RBMXL2 might replace the function of RBMX during meiosis we induced expression of RBMXL2 and the more distantly related RBMY protein in somatic cells, finding each could rescue aberrant patterns of RNA processing caused by RBMX depletion. The C-terminal disordered domain of RBMXL2 is sufficient to rescue proper splicing control after RBMX depletion. Our data indicate that RBMX and RBMXL2 have parallel roles in somatic tissues and the germline that must have been conserved for at least 200 million years of mammalian evolution. We propose RBMX family proteins are particularly important for the splicing inclusion of some ultra-long exons with increased intrinsic susceptibility to cryptic splice site selection.

HnRNP A1, hnRNP A2B1, and hnRNP K are dysregulated in tauopathies, but do not colocalize with tau pathology.

Tau interacts with multiple heterogeneous nuclear ribonucleoproteins (hnRNPs)-a family of RNA binding proteins that regulate multiple known cellular functions, including mRNA splicing, mRNA transport, and translation regulation. We have previously demonstrated particularly significant interactions between phosphorylated tau and three hnRNPs (hnRNP A1, hnRNP A2B1, and hnRNP K). Although multiple hnRNPs have been previously implicated in tauopathies, knowledge of whether these hnRNPs colocalize with tau aggregates or show cellular mislocalization in disease is limited. Here, we performed a neuropathological study examining the colocalization between hnRNP A1, hnRNP A2B1, hnRNP K, and phosphorylated tau in two brain regions (hippocampus and frontal cortex) in six disease groups (Alzheimer's disease, mild cognitive impairment, progressive supranuclear palsy, corticobasal degeneration, Pick's disease, and controls). Contrary to expectations, hnRNP A1, hnRNP A2B1, and hnRNP K did not colocalize with AT8-immunoreactive phosphorylated tau pathology in any of the tauopathies examined. However, we did observe significant cellular mislocalization of hnRNP A1, hnRNP A2B1 and hnRNP K in tauopathies, with unique patterns of mislocalization observed for each hnRNP. These data point to broad dysregulation of hnRNP A1, A2B1 and K across tauopathies with implications for disease processes and RNA regulation.

Generation of ID1/3 knockout human embryonic stem cell lines (WAe009-A-2A and WAe009-A-2B) derived from H9 using CRISPR/Cas9

ID1 and ID3 are the members of the Inhibitor of DNA Binding (ID) protein family, which negatively regulates the basic helix-loop-helix (bHLH) transcription factors by forming heterodimers, are involved in neurodevelopment, cardiovascular development, and tumor metastasis. We created twoID1/3knockout cell lines from a human embryonic stem cell (hESC) line (H9) by CRISPR/Cas9-mediated gene targeting. These cell lines maintain stem cell morphology, a normal karyotype, and the expression of pluripotent marker genes. Additionally, they retain their in vivo differentiation potential. Thecell lines are valuable tools for studying the roles of ID1/3 in neurodevelopment and cardiovascular diseases.

Functional characterization of MiFTs implicated in early flowering and stress resistances of mango

Phosphatidylethanolamine binding protein (PEBP) family plays important roles in multiple developmental processes in plants. In this study, a total of 11 PEBP gene family members were identified from the mango (Mangifera indica L.) genome, and these proteins were divided into three subfamilies based on their phylogenetic relationships: TERMINAL FLOWER 1 (TFL1)-like, MOTHER OF FT AND TFL (MFT)-like, and FLOWERING LOCUS T (FT)-like. Expression analysis revealed that MiFT1a, MiFT1b and MiFT2 were expressed mainly in leaves, whereas MiFT3 and MiFT4 were expressed mainly in embryos. The overexpression of MiFTs significantly promoted early flowering under both long- and short-day conditions. Interestingly, it still significantly promoted early flowering at 16 °C and 28 °C, with MiFT1a exhibiting the most significant, followed by MiFT1b and MiFT2. Additionally, the expression level of MiFT3 is related to the embryonic development of mango. Further studies revealed that overexpression of MiFT3 inhibited seed germination in transgenic Arabidopsis lines. In addition, the MiFT1a and MiFT1b transgenic lines did not respond to abiotic stress, while MiFT2, MiFT3 and MiFT4 enhanced resistance to salt or drought stress in Arabidopsis. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that MiFTs can interact with flower related and multiple stress proteins, such as bZIP protein (MiFD), 14–3-3 protein, zinc finger protein (MiZFP4), RING zinc-finger protein (MiRZFP34), and phosphatase 2C (MiPP2C25A and MiPP2C25B). These results indicate that FT subfamily not only regulates flowering but also participates in stress response, but there are differences in the function among these genes.

The content of soluble forms of galectins -1, -3, -4, -7, -9 in patients with renal cell cancer of various morphological types

Background: Galectins are a family of β-galactoside binding proteins that regulate the vast majority of cellular functions, including proliferation, migration, adhesion, and phagocytosis in both health and disease. More and more experimental and clinical evidence indicates that galectins are involved in many stages of carcinogenesis, including patients with renal cell carcinoma (RCC). Aim: To analyze the clinical significance of soluble forms of galectins -1, -3, -4, -7, -9 in patients with various histological RCC types. Materials and methods: We performed a retrospective analysis of the clinical significance of galectins -1, -3, -4, -7, -9 in the serum of 140 RCC patients (84 with clear cell RCC (ccRCC), 38 with papillary (papRCC), 18 with chromophobe (chrRCC)) and in 73 healthy donors (control group), who were examined and treated from 2019 to 2023 in the N. N. Blokhin National Medical Research Center of Oncology. Galectin levels were measured in serum (obtained according to standard methods before the initiation of specific treatment) with an enzyme-linked immunosorbent assay. Results: There was a significant increase in serum galectin -1, -3, -9 levels in the whole RCC patient group, compared to the healthy donor control group; no increase was found for galectins -4 and -7. Serum galectin-1 levels in the ccRCC and papRCC patients were significantly higher than those in the controls (p = 0.0003 and p = 0.0135, respectively). No association between the serum galectins -1 and -7 and the clinical and morphological characteristics of RCC was found; however, serum galectin-7 levels in the papRCC patients correlated with the grade of tumor differentiation (r = -0.592; p = 0.001). The area under the ROC curve (AUC) for galectin-1 in ccRCC was 0.721 (p 0.0001), in papRCC 0.673 (p = 0.0086), and in chrRCC 0.576 (p = 0.355). For galectin-7, the ROC AUC values were 0.527 (p = 0.634) in ccRCC, 0.513 (p = 0.845) in papRCC, and 0.566 (p = 0.425) in chrRCC. In all histological types of RCC, there was a significant increase in serum galectin-3 compared to the controls (ccRCC, p = 0.0208; papRCC, p = 0.0014; chrRCC, p = 0.0041). The ROC analysis for galectin-3 in patients with RCC of various histological types showed AUC = 0.721 (p 0.0001) for ccRCC, 0.673 (p = 0.0086) for papRCC, and 0.576 (p = 0.355) for chrRCC. Galectin-9 levels was directly and significantly associated with the tumor size, as well as with regional metastases (r = 0.251, p = 0.021; r = 0.239, p = 0.028, respectively). The AUC values for galectin-4 were 0.619 (p = 0.021) in ccRCC, 0.577 (p = 0.214) in papRCC, and 0.534 (p = 0.666) for chrRCC. For galectin-9, they were 0.649 (p = 0.0075), 0.613 (p = 0.087), and 0.539 (p = 0.637), respectively. Conclusion: The study has demonstrated a certain association between serum galectin -1, -3, -4, -7, and -9 in the patients with RCC of various histological types. Although the results of the ROC analysis indicated average quality of the model, which does not allow for the use of the obtained data for diagnostic purposes, it is necessary to continue the research for better understanding of the mechanisms of galectin functioning, before galectin-based therapeutic agents would be introduced into clinical practice for the treatment of RCC.

Exploring multigene families of odorant binding proteins and cytochrome P450 monooxygenases in the stink bug pest complex through comparative transcriptomics

Exploring multigene families of odorant binding proteins and cytochrome P450 monooxygenases in the stink bug pest complex through comparative transcriptomics

Integrative analysis of the immunological significances of guanylate binding protein family genes in microsatellite stability colorectal cancer

BackgroundMicrosatellite stability (MSS) colorectal cancer (CRC) has poor sensitivity to immunotherapy and its underlying mechanisms are still unclear. Guanylate binding proteins (GBPs) are a family of GTPase involving innate immune responses by providing defense against invading microbes and pathogens. However, the immunological significances of GBPs in MSS CRC remain unknown. MethodsWe utilized bioinformatic tools to comprehensively analysis the expression pattern, clinical relevance, prognostic value, biological function, and immunoregulation effect of distinct GBP members in MSS CRC. ResultsThe expression of all seven GBPs in MSS samples are remarkably decreased compared to microsatellite instability-high (MSI-H) samples. Among them, GBP1/2/4/5 are obviously correlated with distant metastasis status. High expression of GBP1/4/5/6 was remarkably related to favorable overall survival (OS) and progression-free survival (PFS) in CRC patients with MSS tumor. Subsequent enrichment analysis revealed that Interferon-gamma (IFN-γ) and NOD-like receptor signaling are the most relevant functions. Besides, the expression patterns of GBPs are remarkably associated with several tumor infiltrated immune cells (e.g. regulatory T cells, CD4+ T cells, and macrophages) and diverse immunoregulatory molecules (e.g. immune checkpoint biomarkers (ICBs) and major histocompatibility complex (MHC) molecules). Moreover, high GBP1/2/4/5 expression predicted better immunotherapy responsiveness in immunotherapy cohorts. ConclusionThese findings might provide novel insights for the identification of therapeutic targets and potential prognostic biomarkers of GBP family in CRC with MSS samples.

Mutational signatures and their association with cancer survival and gene expression in multiple cancer types.

Different endogenous and exogenous mutational processes cause specific patterns of somatic mutations and mutational signatures. Although their biological research has been intensive, there are only rare studies assessing the possible prognostic role of mutational signatures. We used data from The Cancer Genome Atlas to study the associations between the activity of the mutational signatures and four survival endpoints in 18 types of malignancies. We further explored the prognostic differences according to, for example, the HPV status in head and neck squamous cell carcinomas and smoking status in lung cancers. The predictive power of the signatures over time was evaluated with a dynamic area under the curve model, and the links between mutational signature activities and differences in gene expression patterns were analyzed. In 12 of 18 studied cancer types, we identified at least one mutational signature whose activity predicted survival outcomes after adjusting for the established prognostic factors. For example, overall survival was associated with the activity of mutational signatures in nine cancer types and disease-specific survival in seven cancer types. The clock-like signatures SBS5 and SBS40 were most commonly associated with survival endpoints. The genes of the myosin binding protein and melanoma antigen families were among the most substantially dysregulated genes between the signatures of low and high activity. The differences in gene expression also revealed various enriched pathways. Based on these data, specific mutational signatures associate with the gene expression and have the potential to serve as strong prognostic factors in several cancer types.

Rescue of Scn5a mis-splicing does not improve the structural and functional heart defects of a DM1 heart mouse model.

Myotonic Dystrophy Type 1 (DM1) is an autosomal dominant multisystemic disorder for which cardiac features, including conduction delays and arrhythmias, are the second leading cause of disease mortality. DM1 is caused by expanded CTG repeats in the 3' untranslated region of the DMPK gene. Transcription of the expanded DMPK allele produces mRNAs containing long tracts of CUG repeats, which sequester the Muscleblind-Like family of RNA binding proteins, leading to their loss-of-function and the dysregulation of alternative splicing. A well-characterized mis-regulated splicing event in the DM1 heart is the increased inclusion of SCN5A exon 6A rather than the mutually exclusive exon 6B that normally predominates in adult heart. As previous work showed that forced inclusion of Scn5a exon 6A in mice recapitulates cardiac DM1 phenotypes, we tested whether rescue of Scn5a mis-splicing would improve the cardiac phenotypes in a DM1 heart mouse model. We generated mice lacking Scn5a exon 6A to force the expression of the adult SCN5A isoform including exon 6B and crossed these mice to our previously established CUG960 DM1 heart mouse model. We showed that correction Scn5a mis-splicing does not improve the DM1 heart conduction delays and structural changes induced by CUG repeat RNA expression. Interestingly, we found that in addition to Scn5a mis-splicing, Scn5a expression is reduced in heart tissues of CUG960 mice and DM1-affected individuals. These data indicate that Scn5a mis-splicing is not the sole driver of DM1 heart deficits and suggest a potential role for reduced Scn5a expression in DM1 cardiac disease.

Periplasmic binding proteins Bug69 and Bug27 from Bordetella pertussis are in vitro high-affinity quinolinate binders with a potential role in NAD biosynthesis.

Bordetella's genome contains a large family of periplasmic binding proteins (PBPs) known as Bugs, whose functions are mainly unassigned. Two members, Bug27 and Bug69, have previously been considered potential candidates for the uptake of small pyridine precursors, possibly linked to NAD biosynthesis. Here, we show an in vitro affinity of Bug27 and Bug69 for quinolinate in the submicromolar range, with a marked preference over other NAD precursors. A combined sequence similarity network and genome context analysis identifies a cluster of Bug69/27 homologs that are genomically associated with the NAD transcriptional regulator NadQ and the enzyme quinolinate phosphoribosyltransferase (QaPRT, gene nadC), suggesting a functional linkage to NAD metabolism. Integrating molecular docking and structure-based multiple alignments confirms that quinolinate is the preferred ligand for Bug27 and Bug69.

Bioinformatics for Inosine: Tools and Approaches to Trace This Elusive RNA Modification.

Inosine is a nucleotide resulting from the deamination of adenosine in RNA. This chemical modification process, known as RNA editing, is typically mediated by a family of double-stranded RNA binding proteins named Adenosine Deaminase Acting on dsRNA (ADAR). While the presence of ADAR orthologs has been traced throughout the evolution of metazoans, the existence and extension of RNA editing have been characterized in a more limited number of animals so far. Undoubtedly, ADAR-mediated RNA editing plays a vital role in physiology, organismal development and disease, making the understanding of the evolutionary conservation of this phenomenon pivotal to a deep characterization of relevant biological processes. However, the lack of direct high-throughput methods to reveal RNA modifications at single nucleotide resolution limited an extended investigation of RNA editing. Nowadays, these methods have been developed, and appropriate bioinformatic pipelines are required to fully exploit this data, which can complement existing approaches to detect ADAR editing. Here, we review the current literature on the "bioinformatics for inosine" subject and we discuss future research avenues in the field.