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1.
J Mol Neurosci ; 73(11-12): 912-920, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37845428

ABSTRACT

Parkinson's disease (PD) is speculated with genetic and environmental factors. At molecular level, the mitochondrial impact is stated to be one of the causative reasons for PD. In this study, we investigated the mitochondrial membrane potential (MMP), reactive oxygen species (ROS) and adenosine triphosphate (ATP) levels along with mitochondrial tRNA alterations among three age categories of PD. By determining the genetic and organellar functionality using molecular techniques, the ROS levels were reported to be high with decreased MMP and ATP in the late-onset age group than in other two age categories. Likewise, the tRNA significancy in tRNAThr and tRNAGln was noticed with C4335T and G15927A mutations in late-onset and early-onset PD groups respectively. Therefore, from the findings, ageing has shown a disruption in tRNA metabolism leading to critical functioning of ATP synthesis and MMP, causing oxidative stress in PD patients. These physiological outcomes show that ageing has a keen role in the divergence of mitochondrial function, thereby proving a correlation with ageing and maintenance of mitochondrial homeostasis in PD.


Subject(s)
Parkinson Disease , RNA, Transfer, Thr , Humans , RNA, Transfer, Thr/genetics , RNA, Transfer, Thr/metabolism , RNA, Transfer, Gln/genetics , RNA, Transfer, Gln/metabolism , Parkinson Disease/genetics , Parkinson Disease/metabolism , Reactive Oxygen Species/metabolism , India , Mitochondria/genetics , Mitochondria/metabolism , Adenosine Triphosphate/metabolism
2.
FEBS Lett ; 597(12): 1638-1650, 2023 06.
Article in English | MEDLINE | ID: mdl-37079003

ABSTRACT

Each tRNA is aminoacylated (charged) with a genetic codon-specific amino acid. It remains unclear what factors are associated with tRNA charging and how tRNA charging is maintained. By using the individual tRNA acylation PCR method, we found that the charging ratio of tRNAGln (CUG) reflects cellular glutamine level. When uncharged tRNAGln (CUG) increased under amino acid starvation, the kinase GCN2, which is a key stimulator of the integrated stress response, was activated. Activation of GCN2 led to the upregulation of ubiquitin C (UBC) expression. Upregulated UBC, in turn, suppressed the further reduction in tRNAGln (CUG) charging levels. Thus, tRNA charging is sensitive to intracellular nutrient status and is an important initiator of intracellular signaling.


Subject(s)
Amino Acids , Saccharomyces cerevisiae Proteins , Amino Acids/metabolism , Glutamine/metabolism , Protein Serine-Threonine Kinases/metabolism , RNA, Transfer, Gln/metabolism , Ubiquitin C/genetics , Ubiquitin C/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Up-Regulation
3.
BMC Genomics ; 23(1): 793, 2022 Dec 01.
Article in English | MEDLINE | ID: mdl-36456909

ABSTRACT

BACKGROUND: Fruit flies (Diptera: Tephritidae) comprise species of agricultural and economic importance. Five such fruit fly species are known to affect commercial fruit production and export in South Africa: Ceratitis capitata, Ceratitis cosyra, Ceratitis rosa, Ceratitis quilicii, and Bactrocera dorsalis. Management practices for these pests include monitoring, application of pest control products, post-harvest disinfestation measures and inspection of consignments both prior to shipment and at ports of entry. In activities relating to monitoring and inspection, accurate identification of these pests to species level is required. While morphological keys for adult stages of these fruit fly species have been well developed, morphological keys for earlier life stages remain problematic. In instances where closely related species cannot be reliably distinguished morphologically, there is a need for molecular tools to assist in identifying these five fruit fly species during surveillance practices, where sequencing-based approaches would be beneficial. RESULTS: Two complete mitochondrial genomes were assembled for each fruit fly species investigated using high throughput sequencing data generated in this study. A single primer set was designed to amplify a region between tRNAile and tRNAmet. The amplicon consists of a partial segment of tRNAile, intergenic region I (tRNAile - tRNAgln), the complete sequence of tRNAgln, intergenic region II (tRNAgln - tRNAmet), and a partial segment of tRNAmet. PCR amplicons were generated for 20 specimens of each species, five of which were colony adult males, five colony larvae, and 10 wild, trap-collected specimens. Upon analysis of the amplicon, intergenic region I was identified as the most informative region, allowing for unambiguous identification of the five fruit fly species. The similarity in intergenic region II was too high between C. rosa and C. quilicii for accurate differentiation of these species. CONCLUSION: The identity of all five fruit flies investigated in this study can be determined through sequence analysis of the mitochondrial intergenic regions. Within the target amplicon, intergenic region I (tRNAile - tRNAgln) shows interspecific variation sufficient for species differentiation based on multiple sequence alignment. The variation in the length of intergenic region I is proposed as a potential tool for accurately identifying these five fruit flies in South Africa.


Subject(s)
Tephritidae , Male , Animals , Tephritidae/genetics , DNA, Intergenic/genetics , RNA, Transfer, Gln , South Africa , RNA, Transfer, Ile , RNA, Transfer, Met , Drosophila
4.
Genes (Basel) ; 13(10)2022 10 05.
Article in English | MEDLINE | ID: mdl-36292680

ABSTRACT

The mitochondrial 1555A>G mutation plays a critical role in aminoglycoside-induced and non-syndromic hearing loss (AINSHL). Previous studies have suggested that mitochondrial secondary variants may modulate the clinical expression of m.1555A>G-induced deafness, but the molecular mechanism has remained largely undetermined. In this study, we investigated the contribution of a deafness-associated tRNAGln 4394C>T mutation to the clinical expression of the m.1555A>G mutation. Interestingly, a three-generation family with both the m.1555A>G and m.4394C>T mutations exhibited a higher penetrance of hearing loss than another family harboring only the m.1555A>G mutation. At the molecular level, the m.4394C>T mutation resides within a very conserved nucleotide of tRNAGln, which forms a new base-pairing (7T-66A) and may affect tRNA structure and function. Using trans-mitochondrial cybrid cells derived from three subjects with both the m.1555A>G and m.4394C>T mutations, three patients with only the m.1555A>G mutation and three control subjects without these primary mutations, we observed that cells with both the m.1555A>G and m.4394C>T mutations exhibited more severely impaired mitochondrial functions than those with only the m.1555A>G mutation. Furthermore, a marked decrease in mitochondrial RNA transcripts and respiratory chain enzymes was observed in cells harboring both the m.1555A>G and m.4394C>T mutations. Thus, our data suggest that the m.4394C>T mutation may play a synergistic role in the m.1555A>G mutation, enhancing mitochondrial dysfunctions and contributing to a high penetrance of hearing loss in families with both mtDNA pathogenic mutations.


Subject(s)
Deafness , Hearing Loss , Humans , RNA, Mitochondrial , RNA, Transfer, Gln , Deafness/chemically induced , Deafness/genetics , Mutation , Hearing Loss/chemically induced , Hearing Loss/genetics , Aminoglycosides , DNA, Mitochondrial/genetics , Nucleotides/adverse effects
5.
Nucleic Acids Res ; 50(16): 9368-9381, 2022 09 09.
Article in English | MEDLINE | ID: mdl-36018806

ABSTRACT

Pseudouridine (Ψ) at position 55 in tRNAs plays an important role in their structure and function. This modification is catalyzed by TruB/Pus4/Cbf5 family of pseudouridine synthases in bacteria and yeast. However, the mechanism of TRUB family underlying the formation of Ψ55 in the mammalian tRNAs is largely unknown. In this report, the CMC/reverse transcription assays demonstrated the presence of Ψ55 in the human mitochondrial tRNAAsn, tRNAGln, tRNAGlu, tRNAPro, tRNAMet, tRNALeu(UUR) and tRNASer(UCN). TRUB1 knockout (KO) cell lines generated by CRISPR/Cas9 technology exhibited the loss of Ψ55 modification in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro but did not affect other 18 mitochondrial tRNAs. An in vitro assay revealed that recombinant TRUB1 protein can catalyze the efficient formation of Ψ55 in tRNAAsn and tRNAGln, but not in tRNAMet and tRNAArg. Notably, the overexpression of TRUB1 cDNA reversed the deficient Ψ55 modifications in these tRNAs in TRUB1KO HeLa cells. TRUB1 deficiency affected the base-pairing (18A/G-Ψ55), conformation and stability but not aminoacylation capacity of these tRNAs. Furthermore, TRUB1 deficiency impacted mitochondrial translation and biogenesis of oxidative phosphorylation system. Our findings demonstrated that human TRUB1 is a highly conserved mitochondrial pseudouridine synthase responsible for the Ψ55 modification in the mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro.


Subject(s)
Intramolecular Transferases , RNA, Transfer, Glu , Animals , Humans , RNA, Transfer, Gln , RNA, Transfer, Pro , RNA, Transfer, Asn , RNA, Transfer, Met , HeLa Cells , Intramolecular Transferases/genetics , Intramolecular Transferases/metabolism , Pseudouridine/genetics , Pseudouridine/metabolism , RNA, Transfer/metabolism , Mammals/genetics
6.
mBio ; 12(4): e0110021, 2021 08 31.
Article in English | MEDLINE | ID: mdl-34225495

ABSTRACT

Most bacteria employ a two-step indirect tRNA aminoacylation pathway for the synthesis of aminoacylated tRNAGln and tRNAAsn. The heterotrimeric enzyme GatCAB performs a critical amidotransferase reaction in the second step of this pathway. We have previously demonstrated in mycobacteria that this two-step pathway is error prone and translational errors contribute to adaptive phenotypes such as antibiotic tolerance. Furthermore, we identified clinical isolates of the globally important pathogen Mycobacterium tuberculosis with partial loss-of-function mutations in gatA, and demonstrated that these mutations result in high, specific rates of translational error and increased rifampin tolerance. However, the mechanisms by which these clinically derived mutations in gatA impact GatCAB function were unknown. Here, we describe biochemical and biophysical characterization of M. tuberculosis GatCAB, containing either wild-type gatA or one of two gatA mutants from clinical strains. We show that these mutations have minimal impact on enzymatic activity of GatCAB; however, they result in destabilization of the GatCAB complex as well as that of the ternary asparaginyl-transamidosome. Stabilizing complex formation with the solute trehalose increases specific translational fidelity of not only the mutant strains but also of wild-type mycobacteria. Therefore, our data suggest that alteration of GatCAB stability may be a mechanism for modulation of translational fidelity. IMPORTANCE Most bacteria use a two-step indirect pathway to aminoacylate tRNAGln and tRNAAsn, despite the fact that the indirect pathway consumes more energy and is error prone. We have previously shown that the higher protein synthesis errors from this indirect pathway in mycobacteria allow adaptation to hostile environments such as antibiotic treatment through generation of novel alternate proteins not coded by the genome. However, the precise mechanisms of how translational fidelity is tuned were not known. Here, we biochemically and biophysically characterize the critical enzyme of the Mycobacterium tuberculosis indirect pathway, GatCAB, as well as two mutant enzymes previously identified from clinical isolates that were associated with increased mistranslation. We show that the mutants dysregulate the pathway via destabilizing the enzyme complex. Importantly, increasing stability improves translational fidelity in both wild-type and mutant bacteria, demonstrating a mechanism by which mycobacteria may tune mistranslation rates.


Subject(s)
Gene Expression Regulation, Bacterial , Mutation , Mycobacterium smegmatis/enzymology , Mycobacterium smegmatis/genetics , Nitrogenous Group Transferases/genetics , Protein Biosynthesis/genetics , Humans , RNA, Transfer, Gln/metabolism , Transfer RNA Aminoacylation , Tuberculosis/microbiology
7.
Nucleic Acids Res ; 49(7): 3603-3616, 2021 04 19.
Article in English | MEDLINE | ID: mdl-33341895

ABSTRACT

During mRNA translation, tRNAs are charged by aminoacyl-tRNA synthetases and subsequently used by ribosomes. A multi-enzyme aminoacyl-tRNA synthetase complex (MSC) has been proposed to increase protein synthesis efficiency by passing charged tRNAs to ribosomes. An alternative function is that the MSC repurposes specific synthetases that are released from the MSC upon cues for functions independent of translation. To explore this, we generated mammalian cells in which arginyl-tRNA synthetase and/or glutaminyl-tRNA synthetase were absent from the MSC. Protein synthesis, under a variety of stress conditions, was unchanged. Most strikingly, levels of charged tRNAArg and tRNAGln remained unchanged and no ribosome pausing was observed at codons for arginine and glutamine. Thus, increasing or regulating protein synthesis efficiency is not dependent on arginyl-tRNA synthetase and glutaminyl-tRNA synthetase in the MSC. Alternatively, and consistent with previously reported ex-translational roles requiring changes in synthetase cellular localizations, our manipulations of the MSC visibly changed localization.


Subject(s)
Amino Acyl-tRNA Synthetases/metabolism , Protein Biosynthesis , RNA, Transfer, Arg/metabolism , RNA, Transfer, Gln/metabolism , Ribosomes/metabolism , Animals , Fibroblasts , HEK293 Cells , Humans , Mice
8.
Elife ; 92020 12 08.
Article in English | MEDLINE | ID: mdl-33289483

ABSTRACT

An inadequate supply of amino acids leads to accumulation of uncharged tRNAs, which can bind and activate GCN2 kinase to reduce translation. Here, we show that glutamine-specific tRNAs selectively become uncharged when extracellular amino acid availability is compromised. In contrast, all other tRNAs retain charging of their cognate amino acids in a manner that is dependent upon intact lysosomal function. In addition to GCN2 activation and reduced total translation, the reduced charging of tRNAGln in amino-acid-deprived cells also leads to specific depletion of proteins containing polyglutamine tracts including core-binding factor α1, mediator subunit 12, transcriptional coactivator CBP and TATA-box binding protein. Treating amino-acid-deprived cells with exogenous glutamine or glutaminase inhibitors restores tRNAGln charging and the levels of polyglutamine-containing proteins. Together, these results demonstrate that the activation of GCN2 and the translation of polyglutamine-encoding transcripts serve as key sensors of glutamine availability in mammalian cells.


Subject(s)
Amino Acids/deficiency , Protein Biosynthesis , RNA, Transfer, Gln/metabolism , Transfer RNA Aminoacylation , Animals , Cell Line, Tumor , Glutaminase/antagonists & inhibitors , Glutaminase/metabolism , Glutamine/metabolism , Humans , Mice , Peptides/metabolism
9.
J Biol Chem ; 295(32): 10885-10900, 2020 08 07.
Article in English | MEDLINE | ID: mdl-32487749

ABSTRACT

tRNA-derived small RNAs (tsRNAs) from spermatozoa could act as acquired epigenetic factors and contribute to offspring phenotypes. However, the roles of specific tsRNAs in early embryo development remain to be elucidated. Here, using pigs as a research model, we probed the tsRNA dynamics during spermatogenesis and sperm maturation and demonstrated the delivery of tsRNAs from semen-derived exosomes to spermatozoa. By microinjection of antisense sequences into in vitro fertilized oocytes and subsequent single-cell RNA-seq of embryos, we identified a specific functional tsRNA group (termed here Gln-TTGs) that participate in the early cleavage of porcine preimplantation embryos, probably by regulating cell cycle-associated genes and retrotransposons. We conclude that specific tsRNAs present in mature spermatozoa play significant roles in preimplantation embryo development.


Subject(s)
Blastocyst , Cell Division , RNA, Transfer, Gln/physiology , RNA/metabolism , Spermatozoa/metabolism , Animals , Embryonic Development , Female , Male , Microinjections , Pregnancy , Sperm Maturation , Spermatogenesis , Swine
10.
Nucleic Acids Res ; 48(6): 3071-3088, 2020 04 06.
Article in English | MEDLINE | ID: mdl-32016368

ABSTRACT

During protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies are incompletely characterised. To understand system responses to aaRS depletion, the yeast glutamine aaRS gene (GLN4) was transcriptionally regulated using doxycycline by tet-off control. Depletion of Gln4p inhibited growth, and induced a GCN4 amino acid starvation response, indicative of uncharged tRNA accumulation and Gcn2 kinase activation. Using a global model of translation that included aaRS recharging, Gln4p depletion was simulated, confirming slowed translation. Modelling also revealed that Gln4p depletion causes negative feedback that matches translational demand for Gln-tRNAGln to aaRS recharging capacity. This maintains normal charged tRNAGln levels despite Gln4p depletion, confirmed experimentally using tRNA Northern blotting. Model analysis resolves the paradox that Gln4p depletion triggers a GCN4 response, despite maintenance of tRNAGln charging levels, revealing that normally, the aaRS population can sequester free, uncharged tRNAs during aminoacylation. Gln4p depletion reduces this sequestration capacity, allowing uncharged tRNAGln to interact with Gcn2 kinase. The study sheds new light on mutant aaRS disease aetiologies, and explains how aaRS sequestration of uncharged tRNAs can prevent GCN4 activation under non-starvation conditions.


Subject(s)
Basic-Leucine Zipper Transcription Factors/genetics , Protein Serine-Threonine Kinases/genetics , RNA, Transfer, Gln/genetics , RNA, Transfer/genetics , Saccharomyces cerevisiae Proteins/genetics , Amino Acids/genetics , Amino Acids/metabolism , Amino Acyl-tRNA Synthetases/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Homeostasis , Phosphorylation , RNA, Transfer, Gln/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Starvation/genetics , Starvation/metabolism
11.
J Biomol Struct Dyn ; 38(6): 1575-1589, 2020 Apr.
Article in English | MEDLINE | ID: mdl-31084346

ABSTRACT

Aminoacyl-tRNA synthetases (aaRSs) are considered as important components in protein translation as they facilitate the attachment of specific transfer RNA (tRNA) to form aminoacyl-tRNAs. Our study focused on understanding the crystal structure of Glutaminyl-tRNA synthetase (GlnRS) from Thermus thermophilus HB8 (PDB ID:5ZDO) and mechanism of formation of enzyme-substrate complex using substrates and its analogs by applying molecular dynamics simulation (MDS) to investigate the conformational changes. Least energy structure of TtGlnRS was considered to dock the enzyme substrates such as glutamine (Gln), glutamic acid (Glu), adenosine monophosphate (AMP), adenosine triphosphate (ATP), QSI and various substrate analogs (2MA, 4SU and 5MU) onto the active site of the enzyme. We focused on comparative analysis of binding specificity between Gln and Glu; similarly, ATP and AMP. Active site organization as observed by MDS analysis showed interactive changes associated with substrate and catalytically important loops. Study found that when tRNAGln specific for GlnRS was docked into the active site of the TtGlnRS enzyme it interacts with 2' OH on the ribose acceptor end of the tRNA. Upon validation with 50 ns MDS, the maximum deviations and conformational changes of secondary structural elements were observed to be high in the loop regions of enzyme-substrate complexes. Binding affinity of ATP to TtGlnRS was further proved by isothermal titration calorimetry. AbbreviationsaaRSsaminoacyl-tRNA synthetasesAMPadenosine monophosphateATPadenosine triphosphateGlideGrid-based LIgand Docking with EnergeticGlnRSglutaminyl-tRNA synthetaseGRAVYGRand AVerage of hydropathicitYGROMACSGROingen Machine for Chemical SimulationsHADDOCKHigh Ambiguity Driven protein-protein DOCKingITCisothermal titration calorimetry2MA2-methyladenosine 5'-(dihydrogen phosphate)MDSmolecular dynamics simulation5MU5-methyluridine 5'-monophosphateNPTnumber of particles, pressure and temperatureNVTnumber of particles, volume and temperatureOPLS-AAoptimized potential for liquid simulation all atomPDBBrookhaven Protein DatabankPMEParticle-Mesh EwaldQSI5'-o-[n-(l-Glutaminyl)-sulfamoyl]adenosineRgradius of gyrationRMSDroot mean square deviationRMSFroot mean square fluctuation4SU4-thiouracil 5'-monophosphateSPCsimple point chargetRNAtransfer ribo nucleic acidTtThermus thermophilusXPextra precisionCommunicated by Ramaswamy H. Sarma.


Subject(s)
Amino Acyl-tRNA Synthetases , Molecular Dynamics Simulation , Amino Acyl-tRNA Synthetases/metabolism , Binding Sites , Molecular Docking Simulation , RNA, Transfer , RNA, Transfer, Gln
12.
Nucleic Acids Res ; 47(19): 10340-10356, 2019 11 04.
Article in English | MEDLINE | ID: mdl-31504769

ABSTRACT

Mitochondrial tRNA processing defects were associated with human diseases but their pathophysiology remains elusively. The hypertension-associated m.4401A>G mutation resided at a spacer between mitochondrial tRNAMet and tRNAGln genes. An in vitro processing experiment revealed that the m.4401A>G mutation caused 59% and 69% decreases in the 5' end processing efficiency of tRNAGln and tRNAMet precursors, catalyzed by RNase P, respectively. Using human umbilical vein endothelial cells-derived cybrids, we demonstrated that the m.4401A>G mutation caused the decreases of all 8 tRNAs and ND6 and increases of longer and uncleaved precursors from the Light-strand transcript. Conversely, the m.4401A>G mutation yielded the reduced levels of tRNAMet level but did not change the levels of other 13 tRNAs, 12 mRNAs including ND1, 12S rRNA and 16S rRNA from the Heavy-strand transcript. These implicated the asymmetrical processing mechanisms of H-strand and L-strand polycistronic transcripts. The tRNA processing defects play the determined roles in the impairing mitochondrial translation, respiratory deficiency, diminishing membrane potential, increasing production of reactive oxygen species and altering autophagy. Furthermore, the m.4401A>G mutation altered the angiogenesis, evidenced by aberrant wound regeneration and weaken tube formation in mutant cybrids. Our findings provide new insights into the pathophysiology of hypertension arising from mitochondrial tRNA processing defects.


Subject(s)
DNA, Mitochondrial/genetics , Hypertension/genetics , RNA, Transfer, Met/genetics , Transcription, Genetic , Human Umbilical Vein Endothelial Cells , Humans , Mutation/genetics , NADH Dehydrogenase/genetics , RNA Processing, Post-Transcriptional/genetics , RNA, Ribosomal/genetics , RNA, Ribosomal, 16S/genetics , RNA, Transfer, Gln/genetics
13.
Nucleic Acids Res ; 47(12): 6339-6350, 2019 07 09.
Article in English | MEDLINE | ID: mdl-31069379

ABSTRACT

Stop codon readthrough-the decoding of a stop codon by a near-cognate tRNA-is employed by viruses to balance levels of enzymatic and structural proteins and by eukaryotic cells to enable isoform-specific protein synthesis in response to external stimuli. Owing to the prevalence of premature termination codons in human disease, readthrough has emerged as an attractive therapeutic target. A growing list of various features, for example the +4 nucleotide immediately following the stop codon, modulate readthrough levels, underscoring the need for systematic investigation of readthrough. Here, we identified and described a complete group of yeast tRNAs that induce readthrough in the stop-codon tetranucleotide manner when overexpressed, designated readthrough-inducing tRNAs (rti-tRNAs). These rti-tRNAs are the keystones of YARIS (yeast applied readthrough inducing system), a reporter-based assay enabling simultaneous detection of readthrough levels at all twelve stop-codon tetranucleotides and as a function of the complete set of rti-tRNAs. We demonstrate the utility of YARIS for systematic study of translation readthrough by employing it to interrogate the effects of natural rti-tRNA modifications, as well as various readthrough-inducing drugs (RTIDs). This analysis identified a variety of genetic interactions demonstrating the power of YARIS to characterize existing and identify novel RTIDs.


Subject(s)
Codon, Terminator , Protein Biosynthesis , RNA, Transfer/metabolism , Aminoglycosides/pharmacology , Nucleotides/chemistry , Protein Biosynthesis/drug effects , RNA, Transfer, Gln , RNA, Transfer, Tyr , Saccharomyces cerevisiae/genetics
14.
J Biol Chem ; 294(23): 9308-9315, 2019 06 07.
Article in English | MEDLINE | ID: mdl-31010827

ABSTRACT

CRISPR/Cas9 nucleases are widely used for genome editing but can induce unwanted off-target mutations. High-fidelity Cas9 variants have been identified; however, they often have reduced activity, constraining their utility, which presents a major challenge for their use in research applications and therapeutics. Here we developed a tRNAGln-processing system to restore the activity of multiple high-fidelity Cas9 variants in human cells, including SpCas9-HF1, eSpCas9, and xCas9. Specifically, acting on previous observations that small guide RNAs (sgRNAs) harboring an extra A or G (A/G) in the first 5' nucleotide greatly affect the activity of high-fidelity Cas9 variants and that tRNA-sgRNA fusions improve Cas9 activity, we investigated whether a GN20 sgRNA fused to different tRNAs (G-tRNA-N20) could restore the activity of SpCas9 variants in human cells. Using flow cytometry, a T7E1 assay, deep sequencing-based DNA cleavage activity assays, and HEK-293 cells, we observed that a tRNAGln-sgRNA fusion system enhanced the activity of Cas9 variants, which could be harnessed for efficient correction of a pathogenic mutation in the retinoschisin 1 (RS1) gene, resulting in 6- to 8-fold improved Cas9 activity. We propose that the tRNA-processing system developed here specifically for human cells could facilitate high-fidelity Cas9-mediated human genome-editing applications.


Subject(s)
CRISPR-Cas Systems/genetics , Gene Editing/methods , RNA, Transfer, Gln/metabolism , DNA Cleavage , HEK293 Cells , Humans , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/metabolism
15.
Folia Neuropathol ; 57(4): 335-339, 2019.
Article in English | MEDLINE | ID: mdl-32337946

ABSTRACT

INTRODUCTION: Sporadic Parkinson's disease (PD) is a neurodegenerative disorder of unknown etiology. In recent years, it has been established that a genetic component underlies different forms of the disease. For instance, mitochondrial genome variants have been implicated in the pathogenesis of the PD. AIM OF THE STUDY: To determine the association of tRNA(Gln) 4336 and 8701A>G (ATP6: Thr59Ala) mitochondrial DNA polymorphisms with the presence of PD in Mexican mestizo patients. MATERIAL AND METHODS: This was a cross-sectional study in which patients were recruited from four tertiary-care level hospitals in Mexico. Genotyping was performed using real-time PCR with TaqMan genotyping assays. Genotypes were confirmed by automated sequencing. RESULTS: The 4336C allele of the tRNAGln gene was present at a low frequency, and the 8701G allele of the MT-ATP6 gene was not associated with PD. CONCLUSIONS: The 4336C variant of the tRNAGln gene was uncommon in the study population, and 8701A/G of MT-ATP6 was not associated with PD in Mexican Mestizos.


Subject(s)
DNA, Mitochondrial/genetics , Genetic Predisposition to Disease , Mitochondrial Proton-Translocating ATPases/genetics , Parkinson Disease/genetics , Female , Genotype , Humans , Male , Mexico/epidemiology , Mitochondria/metabolism , Parkinson Disease/epidemiology , Polymorphism, Genetic/genetics , RNA, Transfer, Gln
17.
RNA Biol ; 15(9): 1167-1173, 2018.
Article in English | MEDLINE | ID: mdl-30249152

ABSTRACT

The MnmE-MnmG complex of Escherichia coli uses either ammonium or glycine as a substrate to incorporate the 5-aminomethyl or 5-carboxymethylaminomethyl group into the wobble uridine of certain tRNAs. Both modifications can be converted into a 5-methylaminomethyl group by the independent oxidoreductase and methyltransferase activities of MnmC, which respectively reside in the MnmC(o) and MnmC(m) domains of this bifunctional enzyme. MnmE and MnmG, but not MnmC, are evolutionarily conserved. Bacillus subtilis lacks genes encoding MnmC(o) and/or MnmC(m) homologs. The glycine pathway has been considered predominant in this typical gram-positive species because only the 5-carboxymethylaminomethyl group has been detected in tRNALysUUU and bulk tRNA to date. Here, we show that the 5-methylaminomethyl modification is prevalent in B. subtilis tRNAGlnUUG and tRNAGluUUC. Our data indicate that B. subtilis has evolved MnmC(o)- and MnmC(m)-like activities that reside in non MnmC homologous protein(s), which suggests that both activities provide some sort of biological advantage.


Subject(s)
RNA, Transfer, Gln/metabolism , RNA, Transfer, Glu/metabolism , Uridine/metabolism , Bacillus subtilis/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Escherichia coli Proteins/metabolism , Multienzyme Complexes/metabolism , Mutation , One-Carbon Group Transferases/genetics , One-Carbon Group Transferases/metabolism , RNA Processing, Post-Transcriptional
18.
Gene ; 642: 299-306, 2018 Feb 05.
Article in English | MEDLINE | ID: mdl-29155328

ABSTRACT

Polycystic ovary syndrome (PCOS) is a very prevalent endocrine disease affecting reproductive women. Clinically, patients with this disorder are more vulnerable to develop type 2 diabetes mellitus (T2DM), cardiovascular events, as well as metabolic syndrome (MetS). To date, the molecular mechanism underlying PCOS remains largely unknown. Previously, we showed that mitochondrial dysfunction caused by mitochondrial DNA (mtDNA) mutation was an important cause for PCOS. In the current study, we described the clinical and biochemical features of a three-generation pedigree with maternally transmitted MetS, combined with PCOS. A total of three matrilineal relatives exhibited MetS including obesity, high triglyceride (TG) and Hemoglobin A1c (HbA1c) levels, and hypertension. Whereas one patient from the third generation manifestated PCOS. Mutational analysis of the whole mitochondrial genes from the affected individuals identified a set of genetic variations belonging to East Asia haplogroup B4b1c. Among these variants, the homoplasmic C3275T mutation disrupted a highly evolutionary conserved base-pairing (28A-46C) on the variable region of tRNALeu(UUR), whereas the T4363C mutation created a new base-pairing (31T-37A) in the anticodon stem of tRNAGln, furthermore, the A8343G mutation occurred at the very conserved position of tRNALys and may result the failure in mitochondrial tRNAs (mt-tRNAs) metabolism. Biochemical analysis revealed the deficiency in mitochondrial functions including lower levels of mitochondrial membrane potential (MMP), ATP production and mtDNA copy number, while a significantly increased reactive oxygen species (ROS) generation was observed in polymononuclear leukocytes (PMNs) from the individuals carrying these mt-tRNA mutations, suggesting that these mutations may cause mitochondrial dysfunction that was responsible for the clinical phenotypes. Taken together, our data indicated that mt-tRNA mutations were associated with MetS and PCOS in this family, which shaded additional light into the pathophysiology of PCOS that were manifestated by mitochondrial dysfunction.


Subject(s)
Metabolic Syndrome/genetics , Point Mutation , Polycystic Ovary Syndrome/genetics , RNA, Transfer, Gln/genetics , RNA, Transfer, Leu/genetics , RNA, Transfer, Lys/genetics , Adult , Asian People/genetics , DNA Mutational Analysis , Female , Genetic Association Studies , Genetic Predisposition to Disease , Haplotypes , Humans , Middle Aged , Mitochondria/genetics , Pedigree
19.
Mol Med Rep ; 16(5): 6029-6033, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28849157

ABSTRACT

Mitochondrial DNA mutations have been reported to be associated with essential hypertension. The present study reported the clinical and molecular features of a Chinese pedigree with maternally inherited hypertension. A total of 6 matrilineal relatives in this pedigree presented with variable degrees of hypertension; the age of onset ranged between 39 and 63 years, and the average age of onset was 53 years. Analysis of the mitochondrial genome in members of this family demonstrated the occurrence of a homoplasmic T4363C mutation in the transfer (t)RNAGln gene and 25 genetic polymorphisms belonging to mitochondrial haplogroup B4. Notably, the T4363C mutation was localized at the anticodon stem of tRNAGln, which is highly conserved across various species (conventional position 38). To determine its potential pathogenicity, RNA Fold software was used to predict the secondary structure of tRNAGln with and without this mutation. The results indicated that the T4363C mutation induced a significant alteration in the secondary structure of tRNAGln, and may reduce the steady­state levels of tRNAGln. Furthermore, matrilineal relatives carrying the T4363C mutation exhibited different age of onset and variable degrees of blood pressure, thus indicating that the T4363C mutation itself was insufficient to produce the clinical phenotype. Therefore, other modified factors, including environmental factors, and nuclear gene and epigenetic modifications, may be involved in the pathogenesis of hypertension. In conclusion, the present study provided valuable information regarding the association between tRNA mutations and hypertension.


Subject(s)
Genetic Predisposition to Disease , Hypertension/genetics , Point Mutation , RNA, Transfer, Gln/genetics , RNA/genetics , Adult , Aged , Asian People , Base Sequence , Female , Humans , Hypertension/ethnology , Hypertension/metabolism , Hypertension/physiopathology , Male , Maternal Inheritance , Middle Aged , Nucleic Acid Conformation , Pedigree , Phenotype , RNA/chemistry , RNA/metabolism , RNA, Mitochondrial , RNA, Transfer, Gln/chemistry , RNA, Transfer, Gln/metabolism
20.
Mol Med Rep ; 15(4): 1832-1836, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28259969

ABSTRACT

Mutations in mitochondrial (mt)transfer (t)RNA (mt­tRNA) have been reported to serve important roles in hypertension. To determine the underlying molecular mechanisms of mt­tRNA mutations in hypertension, the present study screened for mt­tRNA mutations in a Chinese family with a high incidence of essential hypertension. Sequence analysis of the mt­tRNA genes in this family revealed the presence of an A4401G mutation in the glycine­and methionine­tRNA genes, and a G5821A mutation in the cysteine­tRNA (tRNACys) gene. The G5821A mutation was located at a position conserved in various species, and disrupted G6­C67 base­pairing. It was hypothesized that the G5821A mutation may decrease the baseline expression levels of tRNACys, and consequently result in failure of tRNA metabolism. The A4401G mutation was reported to cause the mitochondrial dysfunction responsible for hypertension. Thus, the combination of G5821A and A4401G mutations may contribute to the high incidence of hypertension in this family. Mt­tRNA mutations may serve as potential biomarkers for hypertension.


Subject(s)
Hypertension/genetics , Mitochondria/genetics , Point Mutation , RNA, Transfer, Gln/genetics , RNA, Transfer, Met/genetics , Asian People/genetics , Base Sequence , China/epidemiology , Essential Hypertension , Female , Humans , Hypertension/epidemiology , Hypertension/pathology , Male , Middle Aged , Pedigree
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