Research progress on non-coding small RNA in oral submucosal fibrosis / 口腔疾病防治

@#Oral submucous fibrosis (OSF) is one of the most common precancerous lesions of the oral mucosa, and its pathogenesis has not been fully elucidated. Small noncoding RNAs (SncRNAs), a class of RNA molecules that do not code for proteins, have been widely reported to be involved in the regulation of a variety of human diseases. An increasing number of studies have shown that a variety of SncRNAs play important roles in the pathogenesis of OSF. Current studies have shown that microRNAs (miRNAs) are involved in OSF disease progression by regulating the expression of related transcription factors and genes or epithelial mesenchymal transformation to regulate the activation of fibroblasts (FBs). Long noncoding RNAs (lncRNAs) that transform growth factor-β/suppressor of mothers against decapentaplegic (TGF-β/Smad) signaling pathways or interact with miRNAs are involved in the development of OSF. Circular RNAs (circRNAs) play a role in OSF by interacting with miRNAs. tRNA-derived small RNAs (tsRNAs) are involved in the progression of various fibrotic diseases, but their specific mechanism of action in OSF still needs to be further explored. In the future, it is still necessary to focus on the targets of SncRNAs mediating OSF progression and explore their function and molecular mechanism in OSF to provide new ideas for the diagnosis and treatment of OSF.

Significance of anti-Jo-1 antibody's clinical stratification in idiopathic inflammatory myopathy and disease spectrum / 北京大学学报(医学版)

OBJECTIVE@#To investigate the significance of anti-histidyl tRNA synthetase (Jo-1) antibody in idiopathic inflammatory myopathies (IIM) and its diseases spectrum.@*METHODS@#We enrolled all the patients who were tested positive for anti-Jo-1 antibody by immunoblotting in Peking University People's Hospital between 2016 and 2022. And the patients diagnosed with anti-synthetase antibody syndrome (ASS) with negative serum anti-Jo-1 antibody were enrolled as controls. We analyzed the basic information, clinical characteristics, and various inflammatory and immunological indicators of the patients at the onset of illness.@*RESULTS@#A total of 165 patients with positive anti-Jo-1 antibody were enrolled in this study. Among them, 80.5% were diagnosed with connective tissue disease. And 57.6% (95/165) were diagnosed with IIM, including ASS (84/165, 50.9%), immune-mediated necrotizing myopathy (7/165, 4.2%) and dermatomyositis (4/165, 2.4%). There were 23.0% (38/165) diagnosed with other connective tissue disease, mainly including rheumatoid arthritis (11/165, 6.7%), undifferentiated connective tissue disease (5/165, 3.0%), interstitial pneumonia with autoimmune features (5/165, 3.0%), undifferentiated arthritis (4/165, 2.4%), Sjögren's syndrome (3/165, 1.8%), systemic lupus erythematosus (3/165, 1.8%), systemic vasculitis (3/165, 1.8%), and so on. Other cases included 3 (1.8%) malignant tumor patients, 4 (2.4%) infectious cases and so on. The diagnoses were not clear in 9.1% (15 /165) of the cohort. In the analysis of ASS subgroups, the group with positive serum anti-Jo-1 antibody had a younger age of onset than those with negative serum anti-Jo-1 antibody (49.9 years vs. 55.0 years, P=0.026). Clinical manifestations of arthritis (60.7% vs. 33.3%, P=0.002) and myalgia (47.1% vs. 22.2%, P=0.004) were more common in the ASS patients with positive anti-Jo-1 antibody. With the increase of anti-Jo-1 antibody titer, the incidence of the manifestations of arthritis, mechanic hands, Gottron sign and Raynaud phenomenon increased, and the proportion of abnormal creatine kinase and α-hydroxybutyric dehydrogenase index increased in the ASS patients. The incidence of myalgia and myasthenia were significantly more common in this cohort when anti-Jo-1 antibody-positive ASS patients were positive for one and more myositis specific antibodies/myositis associated autoantibodies (P < 0.05).@*CONCLUSION@#The disease spectrum in patients with positive serum anti-Jo-1 antibody includes a variety of diseases, mainly ASS. And anti-Jo-1 antibody can also be found in many connective tissue diseases, malignant tumor, infection and so on.

Research progress of tRNA-derived fragments as biomarkers for diagnostic and prognostic assessment of tumors / 国际生物医学工程杂志

Cancer is the second-leading cause of death worldwide. Cancer mortality is largely caused by the absence of recognizable early signs and a poor prognosis. Therefore, developing efficient diagnostic and prognostic biomarkers is crucial to reducing the incidence of cancer and improving its prognostic accuracy. tRNA-derived fragments are a new class of non-coding RNAs with important regulatory roles in cancer biology. In this paper, the research progress of tRNA-derived fragments as biomarkers in tumorigenesis, development, and prognosis was reviewed to provide a theoretical basis for cancer diagnosis and prognostic assessment.

5'-tiRNA-Gln inhibits hepatocellular carcinoma progression by repressing translation through the interaction with eukaryotic initiation factor 4A-I / 医学前沿

tRNA-derived small RNAs (tsRNAs) are novel non-coding RNAs that are involved in the occurrence and progression of diverse diseases. However, their exact presence and function in hepatocellular carcinoma (HCC) remain unclear. Here, differentially expressed tsRNAs in HCC were profiled. A novel tsRNA, tRNAGln-TTG derived 5'-tiRNA-Gln, is significantly downregulated, and its expression level is correlated with progression in patients. In HCC cells, 5'-tiRNA-Gln overexpression impaired the proliferation, migration, and invasion in vitro and in vivo, while 5'-tiRNA-Gln knockdown yielded opposite results. 5'-tiRNA-Gln exerted its function by binding eukaryotic initiation factor 4A-I (EIF4A1), which unwinds complex RNA secondary structures during translation initiation, causing the partial inhibition of translation. The suppressed downregulated proteins include ARAF, MEK1/2 and STAT3, causing the impaired signaling pathway related to HCC progression. Furthermore, based on the construction of a mutant 5'-tiRNA-Gln, the sequence of forming intramolecular G-quadruplex structure is crucial for 5'-tiRNA-Gln to strongly bind EIF4A1 and repress translation. Clinically, 5'-tiRNA-Gln expression level is negatively correlated with ARAF, MEK1/2, and STAT3 in HCC tissues. Collectively, these findings reveal that 5'-tiRJNA-Gln interacts with EIF4A1 to reduce related mRNA binding through the intramolecular G-quadruplex structure, and this process partially inhibits translation and HCC progression.

The Roles of the Canonical Members of Ribonuclease A Family in Tumorigenesis / 中国生物化学与分子生物学报

In human, the ribonuclease A (RNase A) family contains 8 canonical members (RNase 1-RNase 8). Research evidence indicated that all the canonical members of this family, except RNase 8, are involved in the occurrence and development of a variety of tumors, including pancreatic cancer, colorectal cancer, bladder cancer, breast cancer, and skin cancer, etc. During tumorigenesis, the expression of specific RNase increased and glycosylation modifications changed, which are potential markers for tumor diagnosis; They also participate in tumor initiation, growth, and metastasis with a variety of mechanisms, and are potential targets for tumor therapy; Meanwhile, some members have the function of killing tumor cells and inhibiting tumor development, and it is possible to develop into tumor therapeutic drugs. Concretely, RNase 1 suppresses tumor growth by directly killing tumor cells or reducing local inflammation through its ribonuclease activity-dependent cytotoxicity and extracellular RNA degradation functions; however, its binding and activation of ephrin A4 signaling pathway promotes breast cancer initiation. RNase 2 and RNase 3 are important components of eosinophil granule proteins that play an important role in anti-tumor immune defense, and their function of killing tumor cells depends on both cationic nature and ribonuclease activity. RNase 4 and RNase 5 can promote tumorigenesis by inducing angiogenesis, promoting tumor cell proliferation, and inhibiting tumor cell apoptosis. The molecular mechanisms of RNase 5 action include promoting the transcription of 47 S precursor rRNA, activating signaling pro-tumor growth signaling pathways, and generating tRNA-derived stress-induced RNA (tiRNA). Besides, RNase 6 and RNase 7 are related to the occurrence of tumors thought their specific role and mechanism are still unclear. In this review, we summarized the relevance and mechanism of RNase A family members on promoting or inhibiting tumors and analyzed their clinical application potentials.

Targeting TRMT5 suppresses hepatocellular carcinoma progression via inhibiting the HIF-1α pathways / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Accumulating evidence has confirmed the links between transfer RNA (tRNA) modifications and tumor progression. The present study is the first to explore the role of tRNA methyltransferase 5 (TRMT5), which catalyzes the m1G37 modification of mitochondrial tRNAs in hepatocellular carcinoma (HCC) progression. Here, based on bioinformatics and clinical analyses, we identified that TRMT5 expression was upregulated in HCC, which correlated with poor prognosis. Silencing TRMT5 attenuated HCC proliferation and metastasis both in vivo and in vitro, which may be partially explained by declined extracellular acidification rate (ECAR) and oxygen consumption rate (OCR). Mechanistically, we discovered that knockdown of TRMT5 inactivated the hypoxia-inducible factor-1 (HIF-1) signaling pathway by preventing HIF-1α stability through the enhancement of cellular oxygen content. Moreover, our data indicated that inhibition of TRMT5 sensitized HCC to doxorubicin by adjusting HIF-‍1α. In conclusion, our study revealed that targeting TRMT5 could inhibit HCC progression and increase the susceptibility of tumor cells to chemotherapy drugs. Thus, TRMT5 might be a carcinogenesis candidate gene that could serve as a potential target for HCC therapy.

Mutación heterocigota, autosómica recesiva del gen RARS2 en una paciente colombiana de padres no consanguíneos / Autosomal recessive heterocygote mutation of the RARS2 gene in a colombian patient with non- consanguineous parents

Las nuevas metodologías de secuenciación masiva han permitido caracterizar e identificar variantes genéticas asociadas a diferentes patologías. En este trabajo se presenta el caso de una paciente con una mutación del gen RARS2 que codifica la enzima arginino-ARNt ligasa para la codificación de proteínas. Esta alteración genética se manifiesta en hipoplasia pontocerebelosa tipo 6, con una prevalencia de <1/1 000 0000, caracterizada por un cerebelo y un puente de menor tamaño asociados a un retraso grave en el neurodesarrollo. El análisis de caso permite un mejor conocimiento de enfermedades de origen genético, específicamente, de aquellas con patrones de herencia autosómicos recesivos de padres no consanguíneos. Su estudio sobre todo en lo relacionado con el ámbito familiar y socioeconómico, y su base genética, ayuda a una mejor calidad de vida de los pacientes y su familia.

The latest method of next-generation sequencing has allowed the characterization and identification of genetic variants associated to diverse pathologies. In this article, we present the case of female patient with a mutation of the RARS2 gene that encodes the enzyme for arginyl tRNA synthetase for coding of proteins. This genetic alteration manifests in pontocerebellar hypoplasia type 6, with a prevalence of <1/1,000,0000, characterized by a cerebellum and pons that are smaller in size and are associated with severe neurodevelopmental delay. The analysis of the case of this patient provides better knowledge of diseases of genetic origin; specifically, regarding genetic diseases of autosomal recessive patterns of inheritance from non-consanguineous parents. The impact of these studies; specially within the family, social, economic and genetic aspects helps provide a better quality of life for these patients and their family.

MELAS syndrome caused by A3252G mutation in MT-TL1 gene: One case report and literature review / 中华内分泌代谢杂志

Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes(MELAS) is one of the most common inherited mitochondrial diseases. This paper reports a rare mutation associated with MELAS syndrome, the m. 3252 A>G mutation in the MT-TL1 gene encoding the mitochondrial tRNALeu(UUR). The 6-year-old girl suffered from recurrent convulsion and lactic acidemia. The mtDNA sequencing detected a variant m. 3252A>G(MT-TL1 gene) in the proband and her maternal relatives. The heteroplasmic levels in peripheral blood and urine sediment were 66.53% and 97.42%, respectively, which were obviously higher than those of her maternal relatives. Together with 3 previously reported cases, the variant m. 3252A>G could be classified pathogenic. All the reported pathogenic variants in MT-TL1 gene were reviewed to explore the genotype-phenotype correlations of pathogenic variants in MT-TL1 gene.

The expression of the recombinant human phenylalanine-tRNA ligase beta subunit gene in hepatocellular carcinoma and its prognostic value / 中华老年医学杂志

Objective:To analyze the expression of the recombinant human phenylalanine-tRNA ligase beta subunit(FARSB)gene in hepatocellular carcinoma(HCC)and explore its association with clinicopathologic characteristics and prognosis.Methods:Data sets of hepatocellular carcinoma and paracancerous tissues were downloaded from the Cancer Genome Atlas(TCGA), and the data were analyzed using the R and Perl programming languages.Cox regression and the Kaplan-Meier method were used to analyze the relationship between clinicopathological characteristics and overall survival.Gene set enrichment analysis(GSEA)was used to predict the signal pathways involved in the regulation of FARSB.qPCR and Western blot were used to verify the expression level of FARSB in hepatocellular carcinoma and adjacent tissues.Results:FARSB was highly expressed in HCC and the prognosis of HCC patients with high FARSB expression was poor.The clinical stage, T stage, M stage and FARSB were significantly correlated with overall survival, while only high FARSB expression was an independent prognostic factor in HCC patients.Conclusions:High expression of FARSB indicates a poor prognosis in HCC patients and FARSB can be used as a marker for poor prognosis in HCC.

Effects of RARS2 on cell proliferation, invasion, migration and chemotherapy resistance of pancreatic cancer / 中华肝胆外科杂志

Objective:To investigate the effects of mitochondrial arginyl-tRNA synthase (RARS2) on cell proliferation, invasion, migration and chemotherapy resistance of pancreatic cancer.Methods:Human pancreatic cancer cell lines AsPC-1 and PANC-1 were divided into negative control group, RARS2 interference group-1, RARS2 interference group-2, RARS2 overexpression control group and RARS2 overexpression group. Cell proliferation and sensitivity to gemcitabine were detected by CCK-8 assay, and cell invasion and migration were detected by Transwell assay. Western blot was used to detect the expression of RARS2 under different concentrations and different times of gemcitabine treatment. Western blot and PCR were used to detect the expression of RARS2 in gemcitabine-resistant AsPC cell.Results:Inhibition of RARS2 expression in AsPC-1 and PANC-1 cells significantly inhibited cell proliferation and enhanced sensitivity of gemcitabine to chemotherapy. Overexpression of RARS2 enhanced cell proliferation and decreased sensitivity to gemcitabine. In AsPC-1 cells, the number of migrated cells (100×) in negative control group, RARS2 interference group-1, RARS2 interference group-2, RARS2 overexpression control group and RARS2 overexpression group were (586.7±37.4) cells/field, (195.7±18.6) cells/field, (237.0±17.1) cells/field, (157.7±19.1) cells/field, (456.0±23.1) cells/field, the number of invasive cells were (87.7±13.2) cells/field, (24.7±6.5) cells/field, (31.7±6.1) cells/field, (29.3±4.5) cells/field, (94.3±9.3) cells/field, respectively. The migration and invasion ability of cells were decreased after the expression of RARS2 was decreased, and the migration and invasion ability of cells were enhanced after the expression of RARS2 was increased. PCR and Western blot assay showed that RARS2 expression in the gemcitabine-resistant AsPC-1 was higher than that in the common cell line. In AsPC-1 cells, the expression of RARS2 increased with increasing gemcitabine concentration and treatment time.Conclusion:RARS2 promotes cell proliferation, invasion, migration and chemoresistance of pancreatic cancer, and expression of RARS2 is positively correlated with gemcitabine concentration and treatment time.

Efficient gene editing in a medaka (Oryzias latipes) cell line and embryos by SpCas9/tRNA-gRNA / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Generation of mutants with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is commonly carried out in fish species by co-injecting a mixture of Cas9 messenger RNA (mRNA) or protein and transcribed guide RNA (gRNA). However, the appropriate expression system to produce functional gRNAs in fish embryos and cells is rarely present. In this study, we employed a poly-transfer RNA (tRNA)-gRNA (PTG) system driven by cytomegalovirus (CMV) promoter to target the medaka (Oryzias latipes) endogenous gene tyrosinase(tyr) or paired box 6.1 (pax6.1) and illustrated its function in a medaka cell line and embryos. The PTG system was combined with the CRISPR/Cas9 system under high levels of promoter to successfully induce gene editing in medaka. This is a valuable step forward in potential application of the CRISPR/Cas9 system in medaka and other teleosts.

Identification of tRNA-Derived Fragments and Their Regulatory Mechanisms on Target Molecules / 中国生物化学与分子生物学报

With the development of sequencing technology and in-depth research on tRNA-derived small molecules (tsRNAs)‚ more and more tRNAs and their functions have been identified in various species. tsRNAs can be divided into tRNA-derived fragment (tRF) and tRNA-derived stress-induced RNA (tiRNA) according to different cleavage sites. And we will focus on tRF‚ which is a kind of non-coding RNA with regulatory function. To deepen the research of tRF‚ a large number of tRF identification methods based on sequencing data and corresponding databases are being constructed in recent years. The former mainly includes the method of Telonis et al. and tDRmapper‚ while the latter mainly includes tRFdb‚ tRF2Cancer and MINTbase. At the same time‚ both provide a more effective tool for the in-depth research of tRF. The regulation mechanisms of tRF are also being illustrated in many studies. tRF mainly regulates the expression of RNA‚ DNA and proteins in a miRNA-like manner. With further investigations‚ researchers have found that tRF also plays a specific regulatory role in various biological processes of human diseases‚ suggesting its role as a potential biomarker. Herein we mainly summarize the identification methods‚ databases‚ regulation mechanisms of tRF and its role in human diseases.

IARS2 regulates proliferation, migration, and angiogenesis of human umbilical vein endothelial cells

SUMMARY OBJECTIVE: In this study, we aimed at investigating the role of isoleucyl-tRNA synthetase in the growth, migration, and angiogenesis of human umbilical vein endothelial cells and the underlying molecular mechanism. METHODS: To assess the role of isoleucyl-tRNA synthetase, we silenced isoleucyl-tRNA synthetase in human umbilical vein endothelial cells using lentiviral 2 specific short hairpin RNAs (short hairpin RNAs 1 and 2) and examined silencing efficiency using real time quantitative polymerase chain reaction and western blot analyses. Short hairpin RNAs 1-isoleucyl-tRNA synthetase had greater knockdown efficiency, it was used in the entire downstream analysis. Short hairpin RNAs 1- isoleucyl-tRNA synthetase silencing effects on cell proliferation, cell colony generation, cell migration, as well as angiogenesis were assessed using cell counting kit-8, colony development, cell migration, and angiogenesis tube formation assays, respectively. RESULTS: Compared to the control group, anti-isoleucyl-tRNA synthetase short hairpin RNAs significantly silenced isoleucyl-tRNA synthetase expression in human umbilical vein endothelial cells, and suppressed their proliferation, migration, and angiogenic capacity. To characterize the underlying mechanism, western blot analyses showed that isoleucyl-tRNA synthetase knockdown suppressed phosphorylation of extracellular-regulated kinase ½ and protein-serine- threonine kinase, as well as expression of vascular endothelial growth factor, GSK-3β, and β-catenin. CONCLUSIONS: We have shown, for the first time, the critical role of isoleucyl-tRNA synthetase in human umbilical vein endothelial cells. Our data show that isoleucyl-tRNA synthetase knockdown suppresses human umbilical vein endothelial cell proliferation, migration, and angiogenesis. We have also shown that isoleucyl-tRNA synthetase knockdown suppresses phosphorylation of extracellular-regulated kinase ½ and protein-serine- threonine kinase, as well as expression of vascular endothelial growth factor, GSK-3β, and β-catenin. Together, these data highlight isoleucyl-tRNA synthetase as a potential antitumor anti-angiogenic target.

Triple-negative breast cancer cells respond to T cells severely at the alternative splicing layer

BACKGROUND: Cross talk of tumor­immune cells at the gene expression level has been an area of intense research. However, it is largely unknown at the alternative splicing level which has been found to play important roles in the tumor­immune microenvironment. RESULTS: Here, we re-exploited one transcriptomic dataset to gain insight into tumor­immune interactions from the point of AS level. Our results showed that the AS profiles of triple-negative breast cancer cells co-cultured with activated T cells were significantly changed but not Estrogen receptor positive cells. We further suggested that the alteration in AS profiles in triple-negative breast cancer cells was largely caused by activated T cells rather than paracrine factors from activated T cells. Biological pathway analyses showed that translation initiation and tRNA aminoacylation pathways were most disturbed with T cell treatment. We also established an approach largely based on the AS factor­AS events associations and identified LSM7, an alternative splicing factor, may be responsible for the major altered events. CONCLUSIONS: Our study reveals the notable differences of response to T cells among breast cancer types which may facilitate the development or improvement of tumor immunotherapy.

Progress of RNA N6-methyladenosine modification in malignant tumors of digestive system / 肿瘤研究与临床

RNA N6-methyladenosine (m6A) modification is an important gene expression regulation mechanism of eukaryotes. The m6A modification mainly mediates the methylation of adenosine N6. It is a reversible epigenetic modification that not only occurs in messenger RNA (mRNA), but also occurs in non-coding RNA (ncRNA). In addition, RNA m6A modification participates in many physiological and pathological processes, and also plays an important role in the occurrence and development of tumors. This article reviews the role of RNA m6A modification in malignant tumors of the digestive system.

Alanyl-transfer ribonucleic acid synthetase 2 gene mutation producing leukodystrophy: a case report / 中华神经科杂志

Objective:To investigate the clinical features, imaging features and gene mutation of a paitent with alanyl-transfer ribonucleic acid synthetase 2 (AARS2) gene mutation- related leukodystrophy and further improve the understanding of this rare disease.Methods:Clinical data of a patient with leukodystrophy associated with AARS2 gene mutation diagnosed in October 2020 at Xiamen Hospital of Beijing University of Chinese Medicine and Huashan Hospital of Fudan University were collected.Results:The male patient, 25 years old, was admitted with the clinical manifestations, including chronic onset dyskinesia, ataxia, nystagmus and psoriasis. Head magnetic resonance imaging (MRI) showed bilateral white matter lesions and cerebellar atrophy. Spine MRI showed vertebral body incomplete fusion. Gene detection showed heterozygous compound AARS2 gene mutation [c.985C>T chr6:44275041(p.R329C) and c.452T>C chr6:44279256(p.M151T)].Conclusions:AARS2 gene mutation-related leukodystrophy is a rare mitochondrial disease in clinical practice. The patient presented with progressive motor deficits in the lower limbs, ataxia, relatively retained cognitive function. MRI revealed abnormal symmetry of corpus callosum and bilateral paraventricular white matter. Heterozygous compound AARS2 gene mutations [c.985C>T chr6:44275041 (p.R329C) and c.452T>C chr6:44279256 (p.M151T)] are one of the pathogenic factors leading to hereditary leukodystrophy.

Overexpression of a leucine transfer RNA gene tL(CAA)K improves the acetic acid tolerance of Saccharomyces cerevisiae / 生物工程学报

Acetic acid is a common inhibitor present in lignocellulosic hydrolysate. Development of acetic acid tolerant strains may improve the production of biofuels and bio-based chemicals using lignocellulosic biomass as raw materials. Current studies on stress tolerance of yeast Saccharomyces cerevisiae have mainly focused on transcription control, but the role of transfer RNA (tRNA) was rarely investigated. We found that some tRNA genes showed elevated transcription levels in a stress tolerant yeast strain. In this study, we further investigated the effects of overexpressing an arginine transfer RNA gene tR(ACG)D and a leucine transfer RNA gene tL(CAA)K on cell growth and ethanol production of S. cerevisiae BY4741 under acetic acid stress. The tL(CAA)K overexpression strain showed a better growth and a 29.41% higher ethanol productivity than that of the control strain. However, overexpression of tR(ACG)D showed negative influence on cell growth and ethanol production. Further studies revealed that the transcriptional levels of HAA1, MSN2, and MSN4, which encode transcription regulators related to stress tolerance, were up-regulated in tL(CAA)K overexpressed strain. This study provides an alternative strategy to develop robust yeast strains for cellulosic biorefinery, and also provides a basis for investigating how yeast stress tolerance is regulated by tRNA genes.

Effects of tRNA and tRNA-derived Fragments on Skeletal Muscle Development / 中国生物化学与分子生物学报

Skeletal muscle is an important tissue of human and livestock. The study of the muscle development is of great significance for treating muscle diseases and improving livestock meat quality. The process of muscle development is controlled by several myogenic transcription factors and signaling pathways. In addition, recent findings established that several noncoding RNAs play a critical role in the regulation of muscle development such as long non-coding RNA (lncRNA), microRNA (miRNA) and circu- lar RNA (circRNA), etc. The detailed mechanism of muscle development is not well understood. Transfer RNAs (tRNAs) are fundamental components in the translation machinery as an adaptor molecule, and tRNA pool could be differentially exploited to modulate expression of mRNAs. In addition, tRNA can be cleaved into tRNA-derived fragments (tRFs) by a variety of ribonucleases (RNases) upon various stress conditions. Unlike the post-transcriptional regulation of lncRNA and miRNA on muscle development, tRNA has been implicated in various aspects of muscle development. Mitochondria play a central role in a plethora of processes related to the maintenance of muscle cellular homeostasis and genomic integrity. Mitochondrial tRNA(mt-tRNA) gene mutations lead to multiple myopathy because human mitochondrial genome is extremely small. The regulation of tRF is similar to miRNAs in regards to the related physiological processes, but are more conservative than miRNA. It is generally believed that tRF has strong tissue specificity, disease specificity and temporal specificity. Some skeletal muscle-specific tRFs could act posttranscriptionally via RNAi or targeting related genes. However, the tRF-sequencing analysis and functional mechanism of tRF are rarely studied in skeletal muscles. The myopathy caused by mitochondrial tRNA gene mutations are particularly complex, which are one of the challenges to diagnose, treat, or prevent diseases. Compared with other noncoding RNAs, the structural complexity of tRF also brings great challenges to data mining and analysis. In this review, we summarize the formation and function of tRNA and tRF especially in muscle development, which will deepen our understandings of related myopathy, and provide new ideas and directions for the investigation of skeletal muscle.

Deciphering the interaction of benzoxaborole inhibitor AN2690 with connective polypeptide 1 (CP1) editing domain of Leishmania donovani leucyl-tRNA synthetase

Leucyl-tRNA synthetases (LRS) catalyze the linkage of leucine with tRNALeu. A large insertion CP1 domain(Connective Polypeptide 1) in LRS is responsible for post-transfer editing of mis-charged aminoacyl-tRNAs.Here, we characterized the CP1 domain of Leishmania donovani, a protozoan parasite, and its role in editingactivity and interaction with broad spectrum anti-fungal, AN2690. The deletion mutant of LRS, devoid of CP1domain (LRS-CP1D) was constructed, followed by determination of its role in editing and aminoacylation.Binding of AN2690 and different amino acids with CP1 deletion mutant and full length LRS was evaluatedusing isothermal titration calorimetry (ITC) and molecular dynamics simulations. The recombinant LRS-CP1Dprotein did not catalyze the aminoacylation and the editing reaction when compared to full-length LRS. Thus,indicating that CP1 domain was imperative for both aminoacylation and editing activities of LRS. Bindingstudies with different amino acids indicated selectivity of isoleucine by CP1 domain over other amino acids.These studies also indicated high affinity of AN2690 with the editing domain. Molecular docking studiesindicated that AN2690-CP1 domain complex was stabilized by hydrogen bonding and hydrophobic interactions resulting in high binding affinity between the two. Our data suggests CP1 is crucial for the function of L.donovani LRS.

Exploring tRNA gene cluster in archaea

BACKGROUND Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain. OBJECTIVE Explore the occurrence of tRNA gene clusters in archaea. METHODS In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements. FINDINGS We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer. MAIN CONCLUSIONS tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.