Unlocking the Role of sMyBP-C: A Key Player in Skeletal Muscle Development and Growth.

Skeletal muscle is the largest organ in the body, responsible for gross movement and metabolic regulation. Recently, variants in the MYBPC1 gene have been implicated in a variety of developmental muscle diseases, such as distal arthrogryposis. How MYBPC1 variants cause disease is not well understood. Here, through a collection of novel gene-edited mouse models, we define a critical role for slow myosin binding protein-C (sMyBP-C), encoded by MYBPC1, across muscle development, growth, and maintenance during prenatal, perinatal, postnatal and adult stages. Specifically, Mybpc1 knockout mice exhibited early postnatal lethality and impaired skeletal muscle formation and structure, skeletal deformity, and respiratory failure. Moreover, a conditional knockout of Mybpc1 in perinatal, postnatal and adult stages demonstrates impaired postnatal muscle growth and function secondary to disrupted actomyosin interaction and sarcomere structural integrity. These findings confirm the essential role of sMyBP-C in skeletal muscle and reveal specific functions in both prenatal embryonic musculoskeletal development and postnatal muscle growth and function.

Leptospiral imelysin (LIC_10713) is secretory, immunogenic and binds to laminin, fibronectin, and collagen IV.

Leptospirosis is a widespread zoonotic disease caused by pathogenic Leptospira. Early and accurate diagnosis is the prime step in managing the disease. Secretory proteins of Leptospira remain distinguished for diagnosis due to their availability as soluble proteins in the serum and their interaction with the host immune response due to their extracellular presence. This study presents the cloning, expression, purification, and characterization of imelysin or LruB (LIC_10713), a putative leptospiral protein. We report that the localization of imelysin showed its presence in the inner membrane and in the culture supernatant. The imelysin was upregulated under in vitro physiological conditions of infection. The LIC_10713 interacted significantly with laminin, fibronectin, collagen type I, and collagen type IV in a dose-dependent manner. Phylogenetic analysis showed that LIC_10713 is predominately found in the pathogenic species of Leptospira, and the GxHxxE motif of imelysin-like proteins is represented as the amino acid sequence GWHAIE. Also, immunoglobulins in leptospirosis-infected patients recognize recombinant-LIC_10713 with 100% specificity and 90.9% sensitivity. The secretion nature, abundance, upregulation, binding to ECM components, and immunogenicity determine LIC_10713 as an important molecule that can be used as an anti-leptospirosis measure. KEY POINTS: • The imelysin-like protein (LIC_10713) of Leptospira is a secretory protein • The protein LIC_10713 can bind ECM molecules • The LIC_10713 is mainly found in pathogenic leptospires • The anti-LIC_10713 antibody from human serum can detect the r-LIC_10713.

Marine halophyte derived polyphenols inhibit glioma cell growth through mitogen-activated protein kinase signaling pathway.

Plants that are pharmacologically significant require intensive phytochemical characterization for bioactive profiling of the compounds, which has enabled their safe use in ayurvedic medicine. The present study is focused on the phytochemical analyses, quantitative estimation and profiling of secondary metabolites of leaf extract, as well as the antioxidant and cytotoxic activity of the potent halophytes such as Avicennia marina, Ceriops tagal, Ipomoea pes-caprae, and Sonneratia apetala. The in vitro antioxidant property was investigated using DPPH, ferric reducing antioxidant capacity (FRAP) assay. Bioactive compounds such as phenols, flavonoids, saponin and alkaloids were quantitatively estimated from the extracts of A.marina, C.tagal, I.pes-capra and S.apetala, which possessed higher phenol content than the other studied halophytes. The extracts at 200 µg/ml revealed higher antioxidant activity than the standard ascorbic acid and it functions as a powerful oxygen free radical scavenger with 77.37%, 75.35% and 72.84% for S.apetala, I.pes-caprae and C.tagal respectively and with least IC50 for I.pes-caprae (11.95 µg/ml) followed by C.tagal (49.94 µg/ml). Cell viability and anti-proliferative activity of different polyphenolic fractions of C.tagal (CT1 and CT2) and I.pes-caprae fraction (IP) against LN229, SNB19 revealed Ipomoea as the promising anti-cytotoxic fraction. IP-derived polyphenols was further subjected to apoptosis, migration assay, ROS and caspase - 3 and - 7 to elucidate its potentiality as a therapeutic drug. IP-polyphenols was found to have higher percentage of inhibition than the CT1 and CT2 polyphenols of C.tagal on comparison with TMZ. All the above-mentioned in-vitro analysis further validated the ability of IP-polyphenols inducing cell death via ROS-mediated caspase dependent pathway. Further, proteomic and phospho-proteomic analysis revealed the potential role of IP-polyphenols in the regulation of cell proliferation through MMK3, p53, p70 S6 kinase and RSK1 proteins involved in mitogen-activated protein kinase signaling pathway. Our analysis confirmed the promising role of I.pes-caprae derived polyphenols as an anti-metastatic compound against GBM cells.

Mycobacterium leprae hsp18 promoter-EGFP transcriptional fusion construct: Environmental stress and strain-specific expression.

The Hsp18 protein is a major T-cell antigen of Mycobacterium leprae belonging to the family of small heat-shock proteins. The protein is specifically regulated at post-translational level during the intracellular growth of M. leprae within macrophages due to auto-phosphorylation, indicating its importance in the survival of the bacterium. The promoter and regulatory sequences that control hsp18 expression are located within a 256-bp sequence upstream of the translation start site. However, there are no studies describing either characterization of the hsp18 promoter or its genetic regulation. Therefore, we constructed an hsp18-EGFP transcriptional fusion in an E. coli-Mycobacterium shuttle vector. A 168-bp sequence comprising the hsp18 promoter was cloned upstream of the EGFP gene and transformed in M. smegmatis, and the integration of the construct was confirmed by Southern hybridization. hsp18 promoter activity was measured by analyzing EGFP expression in M. smegmatis and Escherichia coli grown under different environmental stress conditions normally encountered by M. leprae in vivo. We found that the 168-bp upstream sequence of hsp18 could function as a promoter, and the regulation of hsp18 expression was host-, environmental stress-, and temperature-dependent. Appreciable EGFP expression was detected in M. smegmatis grown under normal conditions, and theexpression was significantly increased by environmental stress. However, EGFP expression was observed in E. coli only under stress conditions. Comparative sequence analysis revealed the putative sigma factor C (SigC)-binding site within the 168-bp promoter sequence of hsp18, which might be involved in the regulation of hsp18 expression during stress conditions in M. leprae. Thus, our data demonstrated the transcriptional regulation of hsp18 expression in response to different environmental stress conditions, possibly through SigC in Mycobacterium. Further, this shuttle vector could be used for the functional characterization of M. leprae genes in heterologous systems.

Cost-Effective Transcriptome-Wide Profiling of Circular RNAs by the Improved-tdMDA-NGS Method.

Covalently closed circular RNAs are neoteric to the eukaryotic family of long non-coding RNAs emerging as a result of 5'-3' backsplicing from exonic, intronic, or intergenic regions spanning the parental gene. Owing to their unique structure and stability, circular RNAs have a multitude of functional properties such as micro-RNA and protein sponges, direct and indirect modulators of gene expression, protein translation, and many unproven activities apart from being potential biomarkers. However, due to their low abundance, most of the global circular RNA identification is carried out by high-throughput NGS-based approaches requiring millions of sequencing reads. This lag in methodological advancements demands for newer, more refined, and efficient identification techniques. Here, we aim to show an improved version of our previously reported template-dependent multiple displacement amplification (tdMDA)-NGS method by superimposing the ribosomal depletion step and use of H minus reverse transcriptase and RNase H. Implication of tdMDA using highly replicative Phi29 DNA polymerase after minimizing the linear and ribosomal RNA content further intensifies its detection limit toward even the abysmally expressing circular RNA at a low NGS depth, thereby decreasing the cost of identifying a single circular RNA. A >11-fold and >6-fold increase in total circular RNA was identified from the improved-tdMDA-NGS method over the traditional method of circRNA sequencing using DCC and CIRI2 pipelines, respectively, from Oryza sativa subsp. Indica. Furthermore, the reliability of the improved-tdMDA-NGS method was also asserted in HeLa cell lines, showing a significant fold difference in comparison with the existing traditional method of circRNA sequencing. Among the identified circular RNAs, a significant percentage from both rice (∼58%) and HeLa cell lines (∼84%) is found to be matched with the previously reported circular RNAs, suggesting that the improved-tdMDA-NGS method can be adapted to detect and characterize the circular RNAs from different biological systems.

Generation of Transgenic Rice Expressing CircRNA and Its Functional Characterization.

Circular RNA (CircRNA) is yet another vital addition to the noncoding RNA family. They are mainly derived by fusion of downstream 3' splice donor with upstream 5' splice acceptor by a noncanonical form of alternative splicing mechanism called backsplicing. An array of functional aspects of these circRNAs has been reported in animal systems. However, functional investigation of circRNA in plants is very limited. In this chapter, we described a methodological outline to study the circRNA biogenesis and to characterize its function(s). Sequence of a newly identified Oryza sativa Indica circRNA flanked by complementary repeat sequences of a rice intron was assembled to yield a circRNA expression cassette. This cassette can be cloned into any plant expression vector which has a suitable promoter (CaMV 35S or ubiquitin promoter) and terminator, and can be used for any circRNA-mediated functional studies. Subsequent agroinfection of rice calli with this cassette yielded circRNA expressing transgenic plants. These transgenic plants were used to establish a correlation between the expressing circRNA, parental gene, and interacting miRNAs. Moreover, effect of circRNA overexpression on plant phenotype under various stress conditions can be studied using these transgenic plants. Also, RNA pull-down assay can be performed to identify the circRNA interacting proteins and the expression of these RBPs can also be studied from these transgenic plants.

Identification of Circular RNAs by Multiple Displacement Amplification and Their Involvement in Plant Development.

With the innovative knowledge and bioinformatics tools in the identification and characterization of noncoding RNAs, circular RNA (circRNA) is added as a new member to the noncoding RNAs family. CircRNA enrichment by rRNA depletion/RNase R or poly-A removal/RNase R treatment followed by NGS analysis is the most frequently adopted method for circular RNA identification and characterization. In this chapter, we describe the multiple displacement amplification (MDA) as a convenient method to augment the identification of even the abysmally expressed circular RNAs at low sequencing depth. Total RNA, extracted at three different developmental stages of rice, is subjected to RiboMinus and RNase R treatment to deplete the linear RNAs. The enriched circular RNAs are reverse transcribed with random hexamers. The resulting cDNA is subjected to phi29 DNA polymerase amplification using exo-resistant random pentamers to yield high molecular weight dsDNA product, followed by Illumina sequencing at ten million paired end reads per sample. The sequence analysis yielded a promising number of circRNAs with the appreciable inclusion of differentially regulated and minimally expressed circRNAs at a comparatively reduced cost.

Circular RNAs-The Road Less Traveled.

Circular RNAs are the most recent addition in the non-coding RNA family, which has started to gain recognition after a decade of obscurity. The first couple of reports that emerged at the beginning of this decade and the amount of evidence that has accumulated thereafter has, however, encouraged RNA researchers to navigate further in the quest for the exploration of circular RNAs. The joining of 5' and 3' ends of RNA molecules through backsplicing forms circular RNAs during co-transcriptional or post-transcriptional processes. These molecules are capable of effectively sponging microRNAs, thereby regulating the cellular processes, as evidenced by numerous animal and plant systems. Preliminary studies have shown that circular RNA has an imperative role in transcriptional regulation and protein translation, and it also has significant therapeutic potential. The high stability of circular RNA is rendered by its closed ends; they are nevertheless prone to degradation by circulating endonucleases in serum or exosomes or by microRNA-mediated cleavage due to their high complementarity. However, the identification of circular RNAs involves diverse methodologies and the delineation of its possible role and mechanism in the regulation of cellular and molecular architecture has provided a new direction for the continuous research into circular RNA. In this review, we discuss the possible mechanism of circular RNA biogenesis, its structure, properties, degradation, and the growing amount of evidence regarding the detection methods and its role in animal and plant systems.

Modulation of inositol 1,4,5-trisphosphate receptor type 2 channel activity by Ca2+/calmodulin-dependent protein kinase II (CaMKII)-mediated phosphorylation.

InsP(3)-mediated calcium release through the type 2 inositol 1,4,5-trisphosphate receptor (InsP(3)R2) in cardiac myocytes results in the activation of associated CaMKII, thus enabling the kinase to act on downstream targets, such as histone deacetylases 4 and 5 (HDAC4 and HDAC5). The CaMKII activity also feedback modulates InsP(3)R2 function by direct phosphorylation and results in a dramatic decrease in the receptor-channel open probability (P(o)). We have identified S150 in the InsP(3)R2 core suppressor domain (amino acids 1-225) as the specific residue that is phosphorylated by CaMKII. Site-directed mutagenesis reveals that S150 is the CaMKII phosphorylation site responsible for modulation of channel activity. Nonphosphorylatable (S150A) and phosphomimetic (S150E) mutations were studied in planar lipid bilayers. The InsP(3)R2 S150A channel showed no decrease in activity when treated with CaMKII. Conversely, the phosphomimetic (S150E) channel displayed a very low P(o) under normal recording conditions in the absence of CaMKII (2 µM InsP(3) and 250 nM [Ca(2+)](FREE)) and mimicked a WT channel that has been phosphorylated by CaMKII. Phopho-specific antibodies demonstrate that InsP(3)R2 Ser-150 is phosphorylated in vivo by CaMKIIδ. The results of this study show that serine 150 of the InsP(3)R2 is phosphorylated by CaMKII and results in a decrease in the channel open probability.