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1.
Life Sci Alliance ; 7(9)2024 Sep.
Article in English | MEDLINE | ID: mdl-38955468

ABSTRACT

In addition to mitochondrial DNA, mitochondrial double-stranded RNA (mtdsRNA) is exported from mitochondria. However, specific channels for RNA transport have not been demonstrated. Here, we begin to characterize channel candidates for mtdsRNA export from the mitochondrial matrix to the cytosol. Down-regulation of SUV3 resulted in the accumulation of mtdsRNAs in the matrix, whereas down-regulation of PNPase resulted in the export of mtdsRNAs to the cytosol. Targeting experiments show that PNPase functions in both the intermembrane space and matrix. Strand-specific sequencing of the double-stranded RNA confirms the mitochondrial origin. Inhibiting or down-regulating outer membrane proteins VDAC1/2 and BAK/BAX or inner membrane proteins PHB1/2 strongly attenuated the export of mtdsRNAs to the cytosol. The cytosolic mtdsRNAs subsequently localized to large granules containing the stress protein TIA-1 and activated the type 1 interferon stress response pathway. Abundant mtdsRNAs were detected in a subset of non-small-cell lung cancer cell lines that were glycolytic, indicating relevance in cancer biology. Thus, we propose that mtdsRNA is a new damage-associated molecular pattern that is exported from mitochondria in a regulated manner.


Subject(s)
Cytosol , Mitochondria , Prohibitins , RNA, Double-Stranded , RNA, Mitochondrial , Humans , Cytosol/metabolism , Mitochondria/metabolism , RNA, Double-Stranded/metabolism , RNA, Mitochondrial/metabolism , RNA, Mitochondrial/genetics , Cell Line, Tumor , Repressor Proteins/metabolism , Repressor Proteins/genetics , RNA Transport , Exoribonucleases/metabolism , Exoribonucleases/genetics , Voltage-Dependent Anion Channel 1/metabolism , Voltage-Dependent Anion Channel 1/genetics , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Mitochondrial Proteins
2.
Biochem Soc Trans ; 52(3): 1243-1251, 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38884788

ABSTRACT

Mitochondrial DNA replication is initiated by the transcription of mitochondrial RNA polymerase (mtRNAP), as mitochondria lack a dedicated primase. However, the mechanism determining the switch between continuous transcription and premature termination to generate RNA primers for mitochondrial DNA (mtDNA) replication remains unclear. The pentatricopeptide repeat domain of mtRNAP exhibits exoribonuclease activity, which is required for the initiation of mtDNA replication in Drosophila. In this review, we explain how this exonuclease activity contributes to primer synthesis in strand-coupled mtDNA replication, and discuss how its regulation might co-ordinate mtDNA replication and transcription in both Drosophila and mammals.


Subject(s)
DNA Replication , DNA, Mitochondrial , Mitochondria , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , Animals , Mitochondria/metabolism , Mitochondria/genetics , Humans , DNA-Directed RNA Polymerases/metabolism , Transcription, Genetic , Drosophila/genetics , Drosophila/metabolism , Exoribonucleases/metabolism , Exoribonucleases/genetics , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism
3.
Yeast ; 41(7): 458-472, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38874348

ABSTRACT

The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5' → 3' exoribonuclease paralogs. In yeast, they are called Xrn1, which shuttles between the nucleus and the cytoplasm, and executes major cytoplasmic messenger RNA (mRNA) decay, and Rat1, which carries a strong nuclear localization sequence (NLS) and localizes to the nucleus. Xrn1 is 30% identical to Rat1 but has an extra ~500 amino acids C-terminal extension. In the cytoplasm, Xrn1 can degrade decapped mRNAs during the last round of translation by ribosomes, a process referred to as "cotranslational mRNA decay." The division of labor between the two enzymes is still enigmatic and serves as a paradigm for the subfunctionalization of many other paralogs. Here we show that Rat1 is capable of functioning in cytoplasmic mRNA decay, provided that Rat1 remains cytoplasmic due to its NLS disruption (cRat1). This indicates that the physical segregation of the two paralogs plays roles in their specific functions. However, reversing segregation is not sufficient to fully complement the Xrn1 function. Specifically, cRat1 can partially restore the cell volume, mRNA stability, the proliferation rate, and 5' → 3' decay alterations that characterize xrn1Δ cells. Nevertheless, cotranslational decay is only slightly complemented by cRat1. The use of the AlphaFold prediction for cRat1 and its subsequent docking with the ribosome complex and the sequence conservation between cRat1 and Xrn1 suggest that the tight interaction with the ribosome observed for Xrn1 is not maintained in cRat1. Adding the Xrn1 C-terminal domain to Rat1 does not improve phenotypes, which indicates that lack of the C-terminal is not responsible for partial complementation. Overall, during evolution, it appears that the two paralogs have acquired specific characteristics to make functional partitioning beneficial.


Subject(s)
Exoribonucleases , RNA Stability , RNA, Messenger , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Exoribonucleases/metabolism , Exoribonucleases/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/enzymology , RNA, Messenger/genetics , RNA, Messenger/metabolism , Cytoplasm/metabolism , Protein Biosynthesis
4.
Aging (Albany NY) ; 16(11): 9727-9752, 2024 06 05.
Article in English | MEDLINE | ID: mdl-38843383

ABSTRACT

This study explored the role of 14-3-3σ in carbon ion-irradiated pancreatic adenocarcinoma (PAAD) cells and xenografts and clarified the underlying mechanism. The clinical significance of 14-3-3σ in patients with PAAD was explored using publicly available databases. 14-3-3σ was silenced or overexpressed and combined with carbon ions to measure cell proliferation, cell cycle, and DNA damage repair. Immunoblotting and immunofluorescence (IF) assays were used to determine the underlying mechanisms of 14-3-3σ toward carbon ion radioresistance. We used the BALB/c mice to evaluate the biological behavior of 14-3-3σ in combination with carbon ions. Bioinformatic analysis revealed that PAAD expressed higher 14-3-3σ than normal pancreatic tissues; its overexpression was related to invasive clinicopathological features and a worse prognosis. Knockdown or overexpression of 14-3-3σ demonstrated that 14-3-3σ promoted the survival of PAAD cells after carbon ion irradiation. And 14-3-3σ was upregulated in PAAD cells during DNA damage (carbon ion irradiation, DNA damaging agent) and promotes cell recovery. We found that 14-3-3σ resulted in carbon ion radioresistance by promoting RPA2 and RAD51 accumulation in the nucleus in PAAD cells, thereby increasing homologous recombination repair (HRR) efficiency. Blocking the HR pathway consistently reduced 14-3-3σ overexpression-induced carbon ion radioresistance in PAAD cells. The enhanced radiosensitivity of 14-3-3σ depletion on carbon ion irradiation was also demonstrated in vivo. Altogether, 14-3-3σ functions in tumor progression and can be a potential target for developing biomarkers and treatment strategies for PAAD along with incorporating carbon ion irradiation.


Subject(s)
14-3-3 Proteins , Mice, Inbred BALB C , Pancreatic Neoplasms , Recombinational DNA Repair , 14-3-3 Proteins/metabolism , 14-3-3 Proteins/genetics , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/radiotherapy , Animals , Humans , Mice , Cell Line, Tumor , Down-Regulation , Radiation Tolerance/genetics , Exoribonucleases/metabolism , Exoribonucleases/genetics , Heavy Ion Radiotherapy , Carbon , Cell Proliferation/genetics , Gene Expression Regulation, Neoplastic , Male , DNA Damage , Female
5.
Nucleic Acids Res ; 52(10): 5841-5851, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38716877

ABSTRACT

Therapeutic fluoropyrimidines 5-fluorouracil (5-FU) and 5-fluorocytosine (5-FC) are in long use for treatment of human cancers and severe invasive fungal infections, respectively. 5-Fluorouridine triphosphate represents a bioactive metabolite of both drugs and is incorporated into target cells' RNA. Here we use the model fungus Saccharomyces cerevisiae to define fluorinated tRNA as a key mediator of 5-FU and 5-FC cytotoxicity when specific tRNA methylations are absent. tRNA methylation deficiency caused by loss of Trm4 and Trm8 was previously shown to trigger an RNA quality control mechanism resulting in partial destabilization of hypomodified tRNAValAAC. We demonstrate that, following incorporation into tRNA, fluoropyrimidines strongly enhance degradation of yeast tRNAValAAC lacking Trm4 and Trm8 dependent methylations. At elevated temperature, such effect occurs already in absence of Trm8 alone. Genetic approaches and quantification of tRNA modification levels reveal that enhanced fluoropyrimidine cytotoxicity results from additional, drug induced uridine modification loss and activation of tRNAValAAC decay involving the exonuclease Xrn1. These results suggest that inhibition of tRNA methylation may be exploited to boost therapeutic efficiency of 5-FU and 5-FC.


Subject(s)
Flucytosine , Fluorouracil , RNA, Transfer , Saccharomyces cerevisiae , Exoribonucleases/metabolism , Exoribonucleases/genetics , Flucytosine/pharmacology , Fluorouracil/pharmacology , Methylation , RNA Stability/drug effects , RNA, Transfer/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , tRNA Methyltransferases/metabolism , tRNA Methyltransferases/genetics , Uridine/metabolism
6.
Mol Cell ; 84(9): 1711-1726.e11, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38569554

ABSTRACT

N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.


Subject(s)
Adenosine , Adenosine/analogs & derivatives , DEAD-box RNA Helicases , Exoribonucleases , Genomic Instability , Methyltransferases , R-Loop Structures , RNA Polymerase II , Transcription Termination, Genetic , Humans , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , Methyltransferases/metabolism , Methyltransferases/genetics , Adenosine/metabolism , Adenosine/genetics , Exoribonucleases/metabolism , Exoribonucleases/genetics , RNA Polymerase II/metabolism , RNA Polymerase II/genetics , HEK293 Cells , Chromatin/metabolism , Chromatin/genetics , DNA Damage , HeLa Cells , RNA/metabolism , RNA/genetics , Transcription, Genetic , RNA Methylation
7.
Exp Mol Med ; 56(5): 1080-1106, 2024 May.
Article in English | MEDLINE | ID: mdl-38689093

ABSTRACT

Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.


Subject(s)
Exoribonucleases , Gene Expression Regulation, Neoplastic , Hepacivirus , MicroRNAs , Neoplasms , RNA-Binding Proteins , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Neoplasms/genetics , Neoplasms/metabolism , Exoribonucleases/metabolism , Exoribonucleases/genetics , Animals , Hepacivirus/genetics , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/pathology , Hepatitis C/metabolism , Hepatitis C/genetics , Hepatitis C/virology
8.
Biochem J ; 481(7): 481-498, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38440860

ABSTRACT

The protein kinase Gcn2 and its effector protein Gcn1 are part of the general amino acid control signalling (GAAC) pathway best known in yeast for its function in maintaining amino acid homeostasis. Under amino acid limitation, Gcn2 becomes activated, subsequently increasing the levels of phosphorylated eIF2α (eIF2α-P). This leads to the increased translation of transcriptional regulators, such as Gcn4 in yeast and ATF4 in mammals, and subsequent re-programming of the cell's gene transcription profile, thereby allowing cells to cope with starvation. Xrn1 is involved in RNA decay, quality control and processing. We found that Xrn1 co-precipitates Gcn1 and Gcn2, suggesting that these three proteins are in the same complex. Growth under starvation conditions was dependent on Xrn1 but not on Xrn1-ribosome association, and this correlated with reduced eIF2α-P levels. Constitutively active Gcn2 leads to a growth defect due to eIF2α-hyperphosphorylation, and we found that this phenotype was independent of Xrn1, suggesting that xrn1 deletion does not enhance eIF2α de-phosphorylation. Our study provides evidence that Xrn1 is required for efficient Gcn2 activation, directly or indirectly. Thus, we have uncovered a potential new link between RNA metabolism and the GAAC.


Subject(s)
Eukaryotic Initiation Factor-2 , Exoribonucleases , Peptide Elongation Factors , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Amino Acids/metabolism , Eukaryotic Initiation Factor-2/genetics , Eukaryotic Initiation Factor-2/metabolism , Mammals/metabolism , Peptide Elongation Factors/genetics , Peptide Elongation Factors/metabolism , Phosphorylation , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Exoribonucleases/genetics , Exoribonucleases/metabolism
9.
RNA ; 30(6): 662-679, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38443115

ABSTRACT

Despite being predicted to lack coding potential, cytoplasmic long noncoding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNA translation remain poorly studied. In yeast, cytoplasmic Xrn1-sensitive unstable transcripts (XUTs) are targeted by nonsense-mediated mRNA decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Ribo-seq confirmed ribosomes binding to XUTs and identified ribosome-associated 5'-proximal small ORFs. Mechanistically, the NMD-sensitivity of XUTs mainly depends on the 3'-untranslated region length. Finally, we show that the peptide resulting from the translation of an NMD-sensitive XUT reporter exists in NMD-competent cells. Our work highlights the role of translation in the posttranscriptional metabolism of XUTs. We propose that XUT-derived peptides could be exposed to natural selection, while NMD restricts XUT levels.


Subject(s)
Exoribonucleases , Nonsense Mediated mRNA Decay , Protein Biosynthesis , RNA, Long Noncoding , Ribosomes , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Exoribonucleases/metabolism , Exoribonucleases/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Ribosomes/metabolism , Ribosomes/genetics , 3' Untranslated Regions , Open Reading Frames , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA Stability
10.
Nucleic Acids Res ; 52(11): 6441-6458, 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38499483

ABSTRACT

Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex upon significant allosteric change. This interaction is expected to encourage the formation of mature capped viral mRNA, modulating nsp14's exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.


Subject(s)
Methyltransferases , RNA, Viral , SARS-CoV-2 , Viral Nonstructural Proteins , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Viral Nonstructural Proteins/metabolism , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/chemistry , Methyltransferases/metabolism , Methyltransferases/genetics , Methyltransferases/chemistry , Methylation , RNA, Viral/metabolism , RNA, Viral/chemistry , RNA, Viral/genetics , Exoribonucleases/metabolism , Exoribonucleases/genetics , Humans , Protein Binding , RNA Caps/metabolism , RNA Caps/genetics , Allosteric Regulation , COVID-19/virology , COVID-19/genetics , Protein Multimerization , Virus Replication/genetics , RNA, Messenger/metabolism , RNA, Messenger/genetics , RNA, Messenger/chemistry , Viral Regulatory and Accessory Proteins
11.
Cancer Lett ; 592: 216761, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38490326

ABSTRACT

Hepatocellular carcinoma (HCC) is a highly aggressive malignant tumor with limited treatment options and poor prognosis. In this study, we reveal the pivotal role of Stratifin (SFN), also recognized as 14-3-3σ, in driving HCC progression. Our investigation underscores a substantial upregulation of SFN within HCC tissues, manifesting a significant association with worse prognostic outcomes among HCC patients. In vitro and in vivo experiments reveal that SFN overexpression significantly amplifies proliferation, mitigates sorafenib-induced effects on HCC cells, and enhances tumorigenesis. While SFN silencing exerts converse effects on HCC progression. Additionally, we unveil a critical interaction between SFN and AKT, where SFN boosts AKT kinase activity by disrupting the binding of PHLPP2 and AKT, thereby intensifying the malignant progression of HCC cells. In conclusion, this study identifies the oncogenic role of SFN and elucidates the regulatory mechanism of the SFN/AKT axis in HCC, which may provide valuable insights into the mechanisms of HCC progression and potential targets for therapeutic intervention.


Subject(s)
14-3-3 Proteins , Carcinoma, Hepatocellular , Cell Proliferation , Disease Progression , Exoribonucleases , Liver Neoplasms , Proto-Oncogene Proteins c-akt , Signal Transduction , Animals , Female , Humans , Male , Mice , 14-3-3 Proteins/metabolism , 14-3-3 Proteins/genetics , Carcinoma, Hepatocellular/pathology , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/genetics , Cell Line, Tumor , Exoribonucleases/metabolism , Exoribonucleases/genetics , Gene Expression Regulation, Neoplastic , Liver Neoplasms/pathology , Liver Neoplasms/metabolism , Liver Neoplasms/genetics , Prognosis , Proto-Oncogene Proteins c-akt/metabolism , Middle Aged
12.
Front Biosci (Elite Ed) ; 16(1): 1, 2024 Jan 31.
Article in English | MEDLINE | ID: mdl-38538525

ABSTRACT

BACKGROUND: Xrn1 exoribonuclease is the major mRNA degradation enzyme in Saccharomyces cerevisiae. In exponentially growing cells, Xrn1 is localised in the yeast cells and directs the degradation of mRNA molecules. Xrn1 is gradually deposited and presumably inactivated in the processing bodies (P-bodies) as the yeast population ages. Xrn1 can also localise to the membrane compartment of the arginine permease Can1/eisosome compartment at the yeast plasma membrane. This localisation correlates with the metabolic (diauxic) shift from glucose fermentation to respiration, although the relevance of this Xrn1 localisation remains unknown. METHODS: We monitored the growth rates and morphology of Xrn1-green fluorescent protein (GFP) cells compared to wild-type and Δxrn1 cells and observed the Xrn1-GFP localisation pattern in different media types for up to 72 hours using fluorescence microscopy. RESULTS: We present the dynamic changes in the localisation of Xrn1 as a versatile tool for monitoring the growth of yeast populations at the single-cell level using fluorescence microscopy. CONCLUSIONS: The dynamic changes in the localisation of Xrn1 can be a versatile tool for monitoring the growth of yeast populations at the single-cell level. Simultaneously, Xrn1 localisation outside of P-bodies in post-diauxic cells supports its storage and cytoprotective function, yet the role of P-bodies in cell metabolism has still not yet been entirely elucidated.


Subject(s)
Exoribonucleases , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Exoribonucleases/genetics , Exoribonucleases/metabolism , Population Growth , RNA, Messenger/metabolism
13.
Life Sci Alliance ; 7(5)2024 May.
Article in English | MEDLINE | ID: mdl-38418089

ABSTRACT

ISG20 is an IFN-induced 3'-5' RNA exonuclease that acts as a broad antiviral factor. At present, the features that expose RNA to ISG20 remain unclear, although recent studies have pointed to the modulatory role of epitranscriptomic modifications in the susceptibility of target RNAs to ISG20. These findings raise the question as to how cellular RNAs, on which these modifications are abundant, cope with ISG20. To obtain an unbiased perspective on this topic, we used RNA-seq and biochemical assays to identify elements that regulate the behavior of RNAs against ISG20. RNA-seq analyses not only indicate a general preservation of the cell transcriptome, but they also highlight a small, but detectable, decrease in the levels of histone mRNAs. Contrarily to all other cellular ones, histone mRNAs are non-polyadenylated and possess a short stem-loop at their 3' end, prompting us to examine the relationship between these features and ISG20 degradation. The results we have obtained indicate that poly(A)-binding protein loading on the RNA 3' tail provides a primal protection against ISG20, easily explaining the overall protection of cellular mRNAs observed by RNA-seq. Terminal stem-loop RNA structures have been associated with ISG20 protection before. Here, we re-examined this question and found that the balance between resistance and susceptibility to ISG20 depends on their thermodynamic stability. These results shed new light on the complex interplay that regulates the susceptibility of different classes of viruses against ISG20.


Subject(s)
Exonucleases , Exoribonucleases , Exonucleases/genetics , Exonucleases/metabolism , Exoribonucleases/genetics , Exoribonucleases/metabolism , RNA, Viral/genetics , RNA, Viral/metabolism , Histones , Virus Replication/physiology
14.
J Mol Biol ; 436(6): 168487, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38341172

ABSTRACT

Synonymous mutations in messenger RNAs (mRNAs) can reduce protein-protein binding substantially without changing the protein's amino acid sequence. Here, we use coarse-grain simulations of protein synthesis, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of two E. coli homodimers, oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs in silico and calculate the ensemble-averaged interaction energy between the resulting dimers. We find synonymous mutations alter oligoribonuclease's dimer properties. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-translating mRNAs. Ribonuclease T dimerization, however, is insensitive to synonymous mutations. The structural and kinetic origin of these changes are misfolded states containing non-covalent lasso-entanglements, many of which structurally perturb the dimer interface, and whose probability of occurrence depends on translation speed. These entangled states are kinetic traps that persist for long time scales. Entanglements cause altered dimerization energies for oligoribonuclease, as there is a large association (odds ratio: 52) between the co-occurrence of non-native self-entanglements and weak-binding dimer conformations. Simulated at all-atom resolution, these entangled structures persist for long timescales, indicating the conclusions are independent of model resolution. Finally, we show that regions of the protein we predict to have changes in entanglement are also structurally perturbed during refolding, as detected by limited-proteolysis mass spectrometry. Thus, non-native changes in entanglement at dimer interfaces is a mechanism through which oligomer structure and stability can be altered.


Subject(s)
Cell Membrane , Escherichia coli , Exoribonucleases , Protein Multimerization , Silent Mutation , Escherichia coli/enzymology , Exoribonucleases/chemistry , Exoribonucleases/genetics , Kinetics , Protein Folding , Protein Multimerization/genetics , Cell Membrane/enzymology
15.
Genome Biol ; 25(1): 54, 2024 02 22.
Article in English | MEDLINE | ID: mdl-38388963

ABSTRACT

BACKGROUND: RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among other processes. 3' untranslated regions (3' UTRs) of mRNA also hold the key for many aspects of gene regulation. However, there are often contradictory results regarding the roles of RSS in 3' UTRs in gene expression in different organisms and/or contexts. RESULTS: Here, we incidentally observe that the primary substrate of miR159a (pri-miR159a), when embedded in a 3' UTR, could promote mRNA accumulation. The enhanced expression is attributed to the earlier polyadenylation of the transcript within the hybrid pri-miR159a-3' UTR and, resultantly, a poorly structured 3' UTR. RNA decay assays indicate that poorly structured 3' UTRs could promote mRNA stability, whereas highly structured 3' UTRs destabilize mRNA in vivo. Genome-wide DMS-MaPseq also reveals the prevailing inverse relationship between 3' UTRs' RSS and transcript accumulation in the transcriptomes of Arabidopsis, rice, and even human. Mechanistically, transcripts with highly structured 3' UTRs are preferentially degraded by 3'-5' exoribonuclease SOV and 5'-3' exoribonuclease XRN4, leading to decreased expression in Arabidopsis. Finally, we engineer different structured 3' UTRs to an endogenous FT gene and alter the FT-regulated flowering time in Arabidopsis. CONCLUSIONS: We conclude that highly structured 3' UTRs typically cause reduced accumulation of the harbored transcripts in Arabidopsis. This pattern extends to rice and even mammals. Furthermore, our study provides a new strategy of engineering the 3' UTRs' RSS to modify plant traits in agricultural production and mRNA stability in biotechnology.


Subject(s)
Arabidopsis , Exoribonucleases , Animals , Humans , 3' Untranslated Regions , RNA, Messenger/genetics , RNA, Messenger/metabolism , Exoribonucleases/genetics , Exoribonucleases/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Gene Expression Regulation , Mammals/genetics
16.
Comput Biol Med ; 170: 107899, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38232455

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional Nonstructural protein 14 (NSP14) enzyme, possessing exonuclease and messenger RNA (mRNA) capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscoresthe dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development.


Subject(s)
COVID-19 , Exoribonucleases , SARS-CoV-2 , Viral Nonstructural Proteins , Humans , COVID-19/genetics , Exoribonucleases/chemistry , Exoribonucleases/genetics , Exoribonucleases/metabolism , Mutation/genetics , Pandemics , Phylogeny , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Virus Replication/genetics , Viral Nonstructural Proteins/metabolism
17.
Cell Mol Life Sci ; 81(1): 58, 2024 Jan 27.
Article in English | MEDLINE | ID: mdl-38279024

ABSTRACT

Reduced oxygen availability (hypoxia) triggers adaptive cellular responses via hypoxia-inducible factor (HIF)-dependent transcriptional activation. Adaptation to hypoxia also involves transcription-independent processes like post-translational modifications; however, these mechanisms are poorly characterized. Investigating the involvement of protein SUMOylation in response to hypoxia, we discovered that hypoxia strongly decreases the SUMOylation of Exosome subunit 10 (EXOSC10), the catalytic subunit of the RNA exosome, in an HIF-independent manner. EXOSC10 is a multifunctional exoribonuclease enriched in the nucleolus that mediates the processing and degradation of various RNA species. We demonstrate that the ubiquitin-specific protease 36 (USP36) SUMOylates EXOSC10 and we reveal SUMO1/sentrin-specific peptidase 3 (SENP3) as the enzyme-mediating deSUMOylation of EXOSC10. Under hypoxia, EXOSC10 dissociates from USP36 and translocates from the nucleolus to the nucleoplasm concomitant with its deSUMOylation. Loss of EXOSC10 SUMOylation does not detectably affect rRNA maturation but affects the mRNA transcriptome by modulating the expression levels of hypoxia-related genes. Our data suggest that dynamic modulation of EXOSC10 SUMOylation and localization under hypoxia regulates the RNA degradation machinery to facilitate cellular adaptation to low oxygen conditions.


Subject(s)
Exosomes , Transcriptome , Humans , Exosomes/metabolism , Hypoxia/genetics , Hypoxia/metabolism , Transcriptional Activation , Oxygen/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Sumoylation , Exoribonucleases/genetics , Exoribonucleases/metabolism , Exosome Multienzyme Ribonuclease Complex/genetics , Exosome Multienzyme Ribonuclease Complex/metabolism , Cysteine Endopeptidases/metabolism , Ubiquitin Thiolesterase/metabolism
18.
New Phytol ; 241(2): 861-877, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37897070

ABSTRACT

In plants, exoribonuclease-resistant RNAs (xrRNAs) are produced by many viruses. Whereas xrRNAs contribute to the pathogenicity of these viruses, the role of xrRNAs in the virus infectious cycle remains elusive. Here, we show that xrRNAs produced by a benyvirus (a multipartite RNA virus with four genomic segments) in plants are involved in the formation of monocistronic coat protein (CP)-encoding chimeric RNAs. Naturally occurring chimeric RNAs, we discovered, are composed of 5'-end of RNA 2 and 3'-end of either RNA 3 or RNA 4 bearing conservative exoribonuclease-resistant 'coremin' region. Using computational tools and site-directed mutagenesis, we show that de novo formation of chimeric RNAs requires intermolecular base-pairing interaction between 'coremin' and 3'-proximal part of the CP gene of RNA 2 as well as a stem-loop structure immediately adjacent to the CP gene. Moreover, knockdown of the expression of the XRN4 gene, encoding 5'→3' exoribonuclease, inhibits biogenesis of both xrRNAs and chimeric RNAs. Our findings suggest a novel mechanism involving a unique tropology of the intermolecular base-pairing complex between xrRNAs and RNA2 to promote formation of chimeric RNAs in plants. XrRNAs, essential for chimeric RNA biogenesis, are generated through the action of cytoplasmic Xrn 4 5'→3' exoribonuclease conserved in all plant species.


Subject(s)
Exoribonucleases , RNA, Viral , RNA, Viral/genetics , RNA, Viral/metabolism , Exoribonucleases/genetics , Exoribonucleases/metabolism , RNA, Untranslated/genetics
19.
Appl Environ Microbiol ; 89(11): e0116823, 2023 11 29.
Article in English | MEDLINE | ID: mdl-37905926

ABSTRACT

IMPORTANCE: Bacterial exoribonucleases play a crucial role in RNA maturation, degradation, quality control, and turnover. In this study, we have uncovered a previously unknown role of 3'-5' exoribonuclease RNase R of Pseudomonas syringae Lz4W in DNA damage and oxidative stress response. Here, we show that neither the exoribonuclease function of RNase R nor its association with the RNA degradosome complex is essential for this function. Interestingly, in P. syringae Lz4W, hydrolytic RNase R exhibits physiological roles similar to phosphorolytic 3'-5' exoribonuclease PNPase of E. coli. Our data suggest that during the course of evolution, mesophilic E. coli and psychrotrophic P. syringae have apparently swapped these exoribonucleases to adapt to their respective environmental growth conditions.


Subject(s)
Escherichia coli , Exoribonucleases , Exoribonucleases/genetics , Exoribonucleases/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Pseudomonas syringae/genetics , Pseudomonas syringae/metabolism , Antarctic Regions , DNA Damage , Oxidative Stress , RNA, Bacterial/genetics
20.
Development ; 150(21)2023 11 01.
Article in English | MEDLINE | ID: mdl-37767629

ABSTRACT

Control of mRNA poly(A) tails is essential for regulation of mRNA metabolism, specifically translation efficiency and mRNA stability. Gene expression in maturing oocytes relies largely on post-transcriptional regulation, as genes are transcriptionally silent during oocyte maturation. The CCR4-NOT complex is a major mammalian deadenylase, which regulates poly(A) tails of maternal mRNAs; however, the function of the CCR4-NOT complex in translational regulation has not been well understood. Here, we show that this complex suppresses translational activity of maternal mRNAs during oocyte maturation. Oocytes lacking all CCR4-NOT deadenylase activity owing to genetic deletion of its catalytic subunits, Cnot7 and Cnot8, showed a large-scale gene expression change caused by increased translational activity during oocyte maturation. Developmental arrest during meiosis I in these oocytes resulted in sterility of oocyte-specific Cnot7 and Cnot8 knockout female mice. We further showed that recruitment of CCR4-NOT to maternal mRNAs is mediated by the 3'UTR element CPE, which suppresses translational activation of maternal mRNAs. We propose that suppression of untimely translational activation of maternal mRNAs via deadenylation by CCR4-NOT is essential for proper oocyte maturation.


Subject(s)
Oocytes , RNA, Messenger, Stored , Animals , Mice , Female , RNA, Messenger, Stored/metabolism , Oocytes/metabolism , Oogenesis/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Meiosis , Mice, Knockout , Mammals/genetics , Exoribonucleases/genetics , Exoribonucleases/metabolism , Repressor Proteins/metabolism
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