The yeast prion [URE3] propagates as a misfolded amyloid form of the Ure2 protein. Propagation of amyloid-based yeast prions requires protein quality control (PQC) factors, and altering PQC abundance or activity can cure cells of prions. Yeast antiprion systems composed of PQC factors act at normal abundance to restrict establishment of the majority of prion variants that arise de novo While these systems are well described, how they or other PQC factors interact with prion proteins remains unclear. To gain insight into such interactions, we identified mutations outside the Ure2 prion-determining region that destabilize [URE3]. Despite residing in the functional domain, 16 of 17 mutants retained Ure2 activity. Four characterized mutations caused rapid loss of [URE3] yet allowed [URE3] to propagate under prion-selecting conditions. Two sensitized [URE3] to Btn2, Cur1, and Hsp42, but in different ways. Two others reduced amyloid formation in vitro Of these, one impaired prion replication and the other apparently impaired transmission. Thus, widely dispersed sites outside a prion's amyloid-forming region can contribute to prion character, and altering such sites can disrupt prion propagation by altering interactions with PQC factors.
Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This work is funded by Ramalingaswami Re-entry Fellowship (BT/RLF/re-entry/14/2019) from the Department of Biotechnology, Government of India Background Regulation of RNA stability and translation by RNA-binding proteins (RBPs) is a crucial process altering gene expression. Musashi family of RBPs comprising Msi1 and Msi2 are known to control RNA stability and translation with a well-characterized role in the hematopoietic system, gut and cancer. However, the functions of Musashi in the heart is not explored. Purpose Despite the expression of MSI2 in the heart, its role remains largely unknown. In our study, we endeavor to understand the cardiac function of MSI2. Methods RNA-seq analysis, adeno-associated virus (AAV), lentivirus, echocardiography, histopathology, proteomics, electron microscopy, luciferase assay, ROS measurement, TMRE red staining, seahorse assay, MSI2 pooldown, and H3K4me3 ChIP assay were used to elucidate the function of Msi2 in cardiomyocytes. Results Among the two Musashi members, the heart expresses only Msi2. We confirmed the presence of MSI2 in the adult mouse, rat heart, and neonatal rat cardiomyocytes. Furthermore, Msi2 is significantly enriched in the heart cardiomyocytee fraction. Next, using RNA-seq data and isoform-specific PCR primers, we identified Msi2 isoforms 1, 4 and 5, and two novel putative isoforms labeled as Msi2 6 and 7 to be expressed in the heart. Overexpression of Msi2 isoforms led to cardiac hypertrophy in cultured cardiomyocytes. Additionally, Msi2 exhibited a significant increase in a pressure-overload model of cardiac hypertrophy. We selected isoforms 4 and 7 to validate the hypertrophic effects due to their unique alternative splicing patterns. AAV9-mediated overexpression of Msi2 isoforms 4 and 7 in murine hearts led to cardiac hypertrophy, dilation, heart failure,and eventually early death, confirming a pathological function for Msi2. Using global proteomics, gene ontology, transmission electron microscopy, seahorse, and transmembrane potential measurement assys, increased MSI2 was found to cause mitochondrial dysfunction in the heart. Mechanistically, we identified Cluh and Smyd1 as direct downstream target of Msi2. Overexpression of Cluh and Smyd1 inhbited Msi2-induced cardiac mitochondrial dysfunction. Collectively, we show that Msi2 inducs hypertrophy, mitochondrial dysfunction, and heart failure. Conclusion We here show that Msi2 has a pro-hypertrophic function in cardiomyocytes leading to heart failure and death in mice. AAV9 mediated overexpression of Msi2 promoted degradation of Cluh and Smyd1 and thus led to mitochondrial dysfunction. Overexpression of Cluh and Smyd1 inhibits the pro-hypertrophic and mitochondrial dysfunction induced by Msi2.
The fruit fly, Drosophila melanogaster, is generally diurnal, but a few mutant strains, such as the circadian clock mutant Clk Jrk , have been described as nocturnal. We report here that increased nighttime activity of Clk mutants is mediated by high levels of the circadian photoreceptor CRYPTOCHROME (CRY) in large ventral lateral neurons (l-LN v s). We found that CRY expression is also required for nighttime activity in mutants that have high dopamine signaling. In fact, dopamine signaling is elevated in Clk Jrk mutants and acts through CRY to promote the nocturnal activity of this mutant. Notably, dopamine and CRY are required for acute arousal upon sensory stimulation. Because dopamine signaling and CRY levels are typically high at night, this may explain why a chronic increase in levels of these molecules produces sustained nighttime activity. We propose that CRY has a distinct role in acute responses to sensory stimuli: (1) circadian responses to light, as previously reported, and (2) noncircadian effects on arousal, as shown here.
In recent years, a rapid expansion in the field of RNAomics has led to a steep rise in data regarding expressed genes. This expansion in data has necessitated a consequent increase in the breadth and depth of tools which may be used for the study of RNA types. Gene fusions are considered hallmarks of many cancer types and may occur through chromosomal rearrangement or through noncanonical mechanisms in which chimeric RNA forms without rearrangement of the genome. To more effectively identify, validate, and understand the function of these novel RNA molecules, we present this chapter as a resource. In it, we discuss the role of fusion transcripts, identification of fusion transcripts, relevant software packages, and databases.
Pancreatic cancer is the fifth most aggressive malignancy and urgently requires new biomarkers to facilitate early detection. For providing impetus to the biomarker discovery, we have developed Pancreatic Cancer Methylation Database (PCMDB, http://crdd.osdd.net/raghava/pcmdb/), a comprehensive resource dedicated to methylation of genes in pancreatic cancer. Data was collected and compiled manually from published literature. PCMdb has 65907 entries for methylation status of 4342 unique genes. In PCMdb, data was compiled for both cancer cell lines (53565 entries for 88 cell lines) and cancer tissues (12342 entries for 3078 tissue samples). Among these entries, 47.22% entries reported a high level of methylation for the corresponding genes while 10.87% entries reported low level of methylation. PCMdb covers five major subtypes of pancreatic cancer; however, most of the entries were compiled for adenocarcinomas (88.38%) and mucinous neoplasms (5.76%). A user-friendly interface has been developed for data browsing, searching and analysis. We anticipate that PCMdb will be helpful for pancreatic cancer biomarker discovery.
We report the 5.8-Mb genome sequence of Rhodococcus triatomae BKS 15-14, isolated from an ant hill soil sample, collected from Bhitarkanika Mangrove Reserve Forest, Odisha, India. The draft genome of strain BKS 15-14 consists of 5,824,349 bp, with a G+C content of 69%, 5,387 protein-coding genes, and 57 RNAs.
Lipid Transfer Proteins (LTPs) play a crucial role in synthesizing lipid barrier polymers and are involved in defense signaling during pest and pathogen attacks. Although LTPs are conserved with multifaceted roles in plants, these are not yet identified and characterized in Cicer arietinum . In this study, a genome-wide analysis of LTPs was executed and their physiochemical properties, biochemical function, gene structure analysis, chromosomal localization, promoter analysis, gene duplication, and evolutionary analysis were performed using in silico tools. Furthermore, tissue-specific expression analysis and gene expression analysis during pest attack was also conducted for the LTPs. A total of 48 LTPs were identified and named as CaLTPs . They were predicted to be small unstable proteins with “Glycolipid transfer protein” and “Alpha-Amylase Inhibitors, Lipid Transfer and Seed Storage” domains, that are translocated to the extracellular region. CaLTPs were predicted to possess 3–4 introns and were located on all the eight chromosomes of chickpea with half of the CaLTPs being localized on chromosomes 4, 5, and 6, and found to be closely related to LTPs of Arabidopsis thaliana and Medicago trancatula . Gene duplication and synteny analysis revealed that most of the CaLTPs have evolved due to tandem or segmental gene duplication and were subjected to purifying selection during evolution. The promoters of CaLTPs had development-related, phytohormone-responsive, and abiotic and biotic stress-related cis-acting elements. A few CaLTP transcripts exhibited differential expression in diverse tissue types, while others showed no/very low expression. Out of 20 jasmonate-regulated CaLTPs , 14 exhibited differential expression patterns during Helicoverpa armigera –infestation, indicating their role in plant defense response. This study identified and characterized CaLTPs from an important legume, C. arietinum , and indicated their involvement in plant defense against H. armigera -infestation, which can be further utilized to explore lipid signaling during plant-pest interaction and pest management.
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