Transfer RNA modifications and cellular thermotolerance.

RNA molecules are modified post-transcriptionally to acquire their diverse functions. Transfer RNA (tRNA) has the widest variety and largest numbers of RNA modifications. tRNA modifications are pivotal for decoding the genetic code and stabilizing the tertiary structure of tRNA molecules. Alternation of tRNA modifications directly modulates the structure and function of tRNAs and regulates gene expression. Notably, thermophilic organisms exhibit characteristic tRNA modifications that are dynamically regulated in response to varying growth temperatures, thereby bolstering fitness in extreme environments. Here, we review the history and latest findings regarding the functions and biogenesis of several tRNA modifications that contribute to the cellular thermotolerance of thermophiles.

Cryo-EM structure of the transposon-associated TnpB enzyme.

The class 2 type V CRISPR effector Cas12 is thought to have evolved from the IS200/IS605 superfamily of transposon-associated TnpB proteins1. Recent studies have identified TnpB proteins as miniature RNA-guided DNA endonucleases2,3. TnpB associates with a single, long RNA (ωRNA) and cleaves double-stranded DNA targets complementary to the ωRNA guide. However, the RNA-guided DNA cleavage mechanism of TnpB and its evolutionary relationship with Cas12 enzymes remain unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of Deinococcus radiodurans ISDra2 TnpB in complex with its cognate ωRNA and target DNA. In the structure, the ωRNA adopts an unexpected architecture and forms a pseudoknot, which is conserved among all guide RNAs of Cas12 enzymes. Furthermore, the structure, along with our functional analysis, reveals how the compact TnpB recognizes the ωRNA and cleaves target DNA complementary to the guide. A structural comparison of TnpB with Cas12 enzymes suggests that CRISPR-Cas12 effectors acquired an ability to recognize the protospacer-adjacent motif-distal end of the guide RNA-target DNA heteroduplex, by either asymmetric dimer formation or diverse REC2 insertions, enabling engagement in CRISPR-Cas adaptive immunity. Collectively, our findings provide mechanistic insights into TnpB function and advance our understanding of the evolution from transposon-encoded TnpB proteins to CRISPR-Cas12 effectors.

Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.

Post-transcriptional modifications have critical roles in tRNA stability and function1-4. In thermophiles, tRNAs are heavily modified to maintain their thermal stability under extreme growth temperatures5,6. Here we identified 2'-phosphouridine (Up) at position 47 of tRNAs from thermophilic archaea. Up47 confers thermal stability and nuclease resistance to tRNAs. Atomic structures of native archaeal tRNA showed a unique metastable core structure stabilized by Up47. The 2'-phosphate of Up47 protrudes from the tRNA core and prevents backbone rotation during thermal denaturation. In addition, we identified the arkI gene, which encodes an archaeal RNA kinase responsible for Up47 formation. Structural studies showed that ArkI has a non-canonical kinase motif surrounded by a positively charged patch for tRNA binding. A knockout strain of arkI grew slowly at high temperatures and exhibited a synthetic growth defect when a second tRNA-modifying enzyme was depleted. We also identified an archaeal homologue of KptA as an eraser that efficiently dephosphorylates Up47 in vitro and in vivo. Taken together, our findings show that Up47 is a reversible RNA modification mediated by ArkI and KptA that fine-tunes the structural rigidity of tRNAs under extreme environmental conditions.

Random mutagenesis of a hyperthermophilic archaeon identified tRNA modifications associated with cellular hyperthermotolerance.

Random mutagenesis for the hyperthermophilic archaeon Thermococcus kodakarensis was established by the insertion of an artificial transposon designed to allow easy identification of the transposon-inserted locus. The phenotypic screening was applied for the isolation of thermosensitive mutants of T. kodakarensis, which resulted in the isolation of 16 mutants showing defective growth at the supraoptimal temperature 93°C. The high occurrence of the mutants suggested that the high thermotolerance of hyperthermophiles was achieved by a combination of diverse gene functions. The transposon insertion sites in two-thirds of the mutants were identified in a group of genes responsible for tRNA modifications including 7-formamidino-7-deaza-guanosine (archaeosine), N1-methyladenosine/N1-methylinosine, N4-acetylcytidine, and N2-dimethylguanosine/N2,N2-dimethylguanosine. LC-MS/MS analyses of tRNA nucleosides and fragments exhibited disappearance of the corresponding modifications in the mutants. The melting temperature of total tRNA fraction isolated from the mutants lacking archaeosine or N1-methyladenosine/N1-methylinosine decreased significantly, suggesting that the thermosensitive phenotype of these mutants was attributed to low stability of the hypomodified tRNAs. Genes for metabolism, transporters, and hypothetical proteins were also identified in the thermosensitive mutants. The present results demonstrated the usefulness of random mutagenesis for the studies on the hyperthermophile, as well as crucial roles of tRNA modifications in cellular thermotolerance.

Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases.

S-adenosylmethionine (SAM)-dependent methyltransferases regulate a wide range of biological processes through the modification of proteins, nucleic acids, polysaccharides, as well as various metabolites. TYW3/Taw3 is a SAM-dependent methyltransferase responsible for the formation of a tRNA modification known as wybutosine and its derivatives that are required for accurate decoding in protein synthesis. Here, we report the crystal structure of Taw3, a homolog of TYW3 from Sulfolobus solfataricus, which revealed a novel α/ß fold. The sequence motif (S/T)xSSCxGR and invariant aspartate and histidine, conserved in TYW3/Taw3, cluster to form the catalytic center. These structural and sequence features indicate that TYW3/Taw3 proteins constitute a distinct class of SAM-dependent methyltransferases. Using site-directed mutagenesis along with in vivo complementation assays combined with mass spectrometry as well as ligand docking and cofactor binding assays, we have identified the active site of TYW3 and residues essential for cofactor binding and methyltransferase activity.

ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications.

ALKBH1 is a 2-oxoglutarate- and Fe2+-dependent dioxygenase responsible for multiple cellular functions. Here, we show that ALKBH1 is involved in biogenesis of 5-hydroxymethyl-2΄-O-methylcytidine (hm5Cm) and 5-formyl-2΄-O-methylcytidine (f5Cm) at the first position (position 34) of anticodon in cytoplasmic tRNALeu, as well as f5C at the same position in mitochondrial tRNAMet. Because f5C34 of mitochondrial tRNAMet is essential for translation of AUA, a non-universal codon in mammalian mitochondria, ALKBH1-knockout cells exhibited a strong reduction in mitochondrial translation and reduced respiratory complex activities, indicating that f5C34 formation mediated by ALKBH1 is required for efficient mitochondrial functions. We reconstituted formation of f5C34 on mitochondrial tRNAMetin vitro, and found that ALKBH1 first hydroxylated m5C34 to form hm5C34, and then oxidized hm5C34 to form f5C34. Moreover, we found that the frequency of 1-methyladenosine (m1A) in two mitochondrial tRNAs increased in ALKBH1-knockout cells, indicating that ALKBH1 also has demethylation activity toward m1A in mt-tRNAs. Based on these results, we conclude that nuclear and mitochondrial ALKBH1 play distinct roles in tRNA modification.

Precursors of tRNAs are stabilized by methylguanosine cap structures.

Efficient maturation of transfer RNAs (tRNAs) is required for rapid cell growth. However, the precise timing of tRNA processing in coordination with the order of tRNA modifications has not been thoroughly elucidated. To analyze the modification status of tRNA precursors (pre-tRNAs) during maturation, we isolated pre-tRNAs at various stages from Saccharomyces cerevisiae and subjected them to MS analysis. We detected methylated guanosine cap structures at the 5' termini of pre-tRNAs bearing 5' leader sequences. These capped pre-tRNAs accumulated substantially after inhibition of RNase P activity. Upon depletion of the capping enzyme Ceg1p, the steady state level of capped pre-tRNA was markedly reduced. In addition, a population of capped pre-tRNAs accumulated in strains in which 5' exonucleases were inhibited, indicating that the 5' cap structures protect pre-tRNAs from 5'-exonucleolytic degradation during maturation.

Upfront chemotherapy and subsequent resection for molecularly defined gliomas.

Functional preservation is critical in glioma surgery, and the extent of resection influences survival outcome. Neoadjuvant chemotherapy is a promising option because of its potential to facilitate tumor shrinkage and maximum tumor resection. The object of this study was to assess the utility of the neoadjuvant strategy in a prospective series of gliomas with favorable molecular status. Twenty-six consecutive cases of diffuse gliomas of WHO grade II or III with either 1p19q codeletion or MGMT methylation were treated with upfront chemotherapy following maximal safe removal. In cases of incomplete initial surgery, second-look resection was intended after tumor volume decrease by chemotherapy. Among 22 evaluable cases, chemotherapy led to a median change in the sum of the product of perpendicular diameters of -35 %, and 14 out of the 22 cases (64 %) showed objective response. Second-look resection after tumor volume decrease was performed in 12 out of 19 cases of incomplete initial surgery (GTR/STR 9, removal of residual methionine PET uptake 3). The median progression-free survival among the 22 patients with grade II tumors was 57 months, with some cases showing durable progression-free survival after second-look resection. MIB-1 indices of the second-look resected tumors were lower than those of the initial tumors, and the methylation status of the MGMT gene was unchanged. Neoadjuvant chemotherapy based on molecular guidance often produces significant volume decrease of incompletely resected gliomas. Radical second-look resection is an optional advantage of upfront chemotherapy for chemosensitive gliomas compared with initial radiotherapy.

Neuroendoscopic biopsy and the treatment of tumor-associated hydrocephalus of the ventricular and paraventricular region in pediatric patients: a nationwide study in Japan.

A neuroendoscopic biopsy is a minimally invasive and useful procedure for the diagnosis and initial management of tumor-associated hydrocephalus. We describe the nationwide investigation of the current status of neuroendoscopic biopsy for intra- and paraventricular tumors in children, as well as the treatment of tumor-associated hydrocephalus in pediatric patients. The main items examined included the patient's age and sex, location of the tumor, pathological diagnosis, complications, treatment and efficacy of treatment of the tumor-associated hydrocephalus, and the dissemination during the postoperative course. Two hundred twenty-one pediatric patients (mean 8.6 years) from 67 institutions were registered. Endoscopic tumor biopsies were performed in 206 patients (93.2 %), and a histopathological diagnosis could be performed in 195 of these 206 patients (94.7 %). The most frequently histopathologically diagnosed tumor was a germ cell tumor (41.5 %), followed by astrocytic tumors (24.1 %) and cystic lesions (15.9 %). Associated hydrocephalus was observed in 177 patients (80.1 %), 101 of whom underwent endoscopic third ventriculostomy (ETV). The efficacy rate of the ETV in the perioperative period was 99.0 %, and the long-term response rate was 90.1 %. Perioperative complications other than fever were found in 24 patients (10.9 %). In the statistical analysis, pediatric long-term response rate to ETV (p = 0.025) showed significantly more favorable results for pediatric than adult patients (p < 0.05). Neuroendoscopic procedures involving pediatric intra- and paraventricular tumors were considered to be very useful, with a low incidence of complication, and were associated with higher safety.

Repetitive transcranial magnetic stimulation once a week induces sustainable long-term relief of central poststroke pain.

OBJECTIVE: Central poststroke pain is a serious problem for some patients after stroke. Repetitive transcranial magnetic stimulation (rTMS) has been reported to relieve poststroke pain but its efficacy is still controversial. We tested the possibility that rTMS, when applied once a week, would induce sustainable relief of poststroke pain. MATERIALS AND METHODS: Eighteen patients with central poststroke pain were included in this study. rTMS (10 trains of 10-sec 5 Hz-rTMS) was delivered over the primary motor cortex on the affected side. The rTMS session was repeated once a week for 12 weeks, and for six patients the intervention was continued for one year. The degree of the pain was assessed before each weekly rTMS session to evaluate sustainable effects. RESULTS: The effects of the rTMS reached a plateau at the eighth week. At the 12th week, the rTMS was effective in 61.1% of the patients; 5 of the 18 patients showed more than 70% reduction based on a visual analog scale, 6 patients showed 40-69% reduction, and 7 remained at a pain reduction level of less than 40%. When patients were divided into two groups with or without severe dysesthesia, it was found that eight patients with severe dysesthesia showed less pain relief than those without. In the six patients who continued rTMS for one year, the pain relief effects also were sustained. CONCLUSION: Although this was an open-label study without a control group, our findings suggest that rTMS of the primary motor cortex, when maintained once a week, could help to relieve poststroke pain.

Decoding mechanism of non-universal genetic codes in Loligo bleekeri mitochondria.

Non-universal genetic codes are frequently found in animal mitochondrial decoding systems. In squid mitochondria, four codons deviate from the universal genetic code, namely AUA, UGA, and AGA/AGG (AGR) for Met, Trp, and Ser, respectively. To understand the molecular basis for establishing the non-universal genetic code, we isolated and analyzed five mitochondrial tRNAs from a squid, Loligo bleekeri. Primary structures of the isolated tRNAs, including their post-transcriptional modifications, were analyzed by mass spectrometry. tRNA(Met)(AUR) possessed an unmodified cytidine at the first position of the anticodon, suggesting that the AUA codon is deciphered by CAU anticodon via non-canonical A-C pairing. We identified 5-taurinomethyluridine (τm(5)U) at the first position of the anticodon in tRNA(Trp)(UGR). τm(5)U enables tRNA(Trp) to decipher UGR codons as Trp. In addition, 5-taurinomethyl-2-thiouridine (τm(5)s(2)U) was found in mitochondrial tRNAs for Leu(UUR) and Lys in L. bleekeri. This is the first discovery of τm(5)U and τm(5)s(2)U in molluscan mitochondrial tRNAs.

LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria.

In human mitochondria, 10 mRNAs species are generated from a long polycistronic precursor that is transcribed from the heavy chain of mitochondrial DNA, in theory yielding equal copy numbers of mRNA molecules. However, the steady-state levels of these mRNAs differ substantially. Through absolute quantification of mRNAs in HeLa cells, we show that the copy numbers of all mitochondrial mRNA species range from 6000 to 51,000 molecules per cell, indicating that mitochondria actively regulate mRNA metabolism. In addition, the copy numbers of mitochondrial mRNAs correlated with their cellular half-life. Previously, mRNAs with longer half-lives were shown to be stabilized by the LRPPRC/SLIRP complex, which we find that cotranscriptionally binds to coding sequences of mRNAs. We observed that the LRPPRC/SLIRP complex suppressed 3' exonucleolytic mRNA degradation mediated by PNPase and SUV3. Moreover, LRPPRC promoted the polyadenylation of mRNAs mediated by mitochondrial poly(A) polymerase (MTPAP) in vitro. These findings provide a framework for understanding the molecular mechanism of mRNA metabolism in human mitochondria.

Retrograde nuclear import of tRNA precursors is required for modified base biogenesis in yeast.

The retrograde movement of tRNAs from the cytoplasm to the nucleus occurs constitutively in eukaryotic cells but its functional significance remains unclear. We show evidence suggesting that in Saccharomyces cerevisiae, a spliced tRNA precursor must be imported into the nucleus before the biogenesis of a modified base can occur. Wybutosine (yW) is a modified base adjacent to the anticodon of tRNA(Phe) and is required for accurate decoding. Glucose starvation or overexpression of the nuclear tRNA binding protein Trz1p both caused nuclear retention of cytoplasmic tRNAs, impaired the yW synthesis, and induced the accumulation of its intermediate, N(1)-methylgunanosine (m(1)G), showing that the postspliced tRNA(Phe) is imported to the nucleus, where m(1)G is formed by Trm5p, after which it is reexported to the cytoplasm, where the yW synthesis is completed by cytoplasmic enzymes.

Usefulness of facial nerve monitoring for confirmation of greater superficial petrosal nerve in anterior transpetrosal approach.

INTRODUCTION: The greater superficial petrosal nerve (GSPN) is especially important in anterior transpetrosal approach (ATPA) as the most reliable superficial landmark of Kawase's triangle. The GSPN can be considered as the superficial lateral border of anterior petrosectomy on the middle fossa to avoid internal carotid artery (ICA) injury. Although experienced operators can find the GSPN, its confirmation is not always easy to achieve. METHODS: We introduce our recent GSPN confirmation methods using facial nerve monitoring. In 10 recent cases, antidromic GSPN stimulation and free-running facial muscle electromyography (EMG) monitoring were performed. RESULTS: Facial nerve evoked-EMG by antidromic GSPN stimulation confirmed the location of the GSPN course with precision in all cases. Free-running facial muscle EMG informed the mechanical stress of facial nerves through the GSPN. There was no postoperative facial palsy or dry eye in these cases. CONCLUSIONS: GSPN confirmation and preservation are not always easy to achieve. These monitoring methods are useful for the confirmation of the GSPN, which is a landmark for safe extradural anterior petrosectomy, and for the preservation of the GSPN itself.

Cerebral perfusion change of venous hypertension on near-infrared spectroscopy signals after operation for dural arteriovenous fistula.

A dural arteriovenous fistula (AVF) is an arteriovenous shunt in the dura and is associated with a risk of intracranial hemorrhage and neurologic deficit. The morbidity of this disease depends on venous hypertension, and the classification of this disease is based on the pattern of venous drainage. The pattern of venous drainage relates to the clinical features of the disease, especially to the probability of intracranial hemorrhage. We report 1 case of dural AVF with retrograde leptomeningeal venous drainage. Cerebral hemodynamics were monitored using near-infrared spectroscopy imaging before, during, and after the 2-stage operative treatment. Preoperative functional near-infrared spectroscopy (fNIRS) showed an increase in deoxyhemoglobin (HbR) during a motor task. After partial coil embolization of the shunt points (stage 1), HbR increased during the first half of the task and decreased later, whereas oxyhemoglobin (HbO2) decreased in the first half of the task and increased later. After complete embolization (stage 2), fNIRS showed a pattern similar to that of a normal adult. The patient's symptoms improved gradually, and angiography showed a reduction of the retrograde venous drainage and venous congestion after this 2-stage operation. The reduction in venous hypertension may be the underlying mechanism behind the changes observed with fNIRS.

Phase I/II Study of a Vascular Endothelial Growth Factor Receptor Vaccine in Patients With NF2-Related Schwannomatosis.

PURPOSE: The humanized antivascular endothelial growth factor (VEGF) antibody bevacizumab (Bev) is efficacious for the treatment of NF2-related schwannomatosis (NF2), previously known as neurofibromatosis type 2. This study evaluated the safety and efficacy of a VEGF receptor (VEGFR) vaccine containing VEGFR1 and VEGFR2 peptides in patients with NF2 with progressive schwannomas (jRCTs031180184). MATERIALS AND METHODS: VEGFR1 and VEGFR2 peptides were injected subcutaneously into infra-axillary and inguinal regions, once a week for 4 weeks and then once a month for 4 months. The primary end point was safety. Secondary end points included tolerability, hearing response, imaging response, and immunologic response. RESULTS: Sixteen patients with NF2 with progressive schwannomas completed treatment and were assessed. No severe vaccine-related adverse events occurred. Among the 13 patients with assessable hearing, word recognition score improved in five patients at 6 months and two at 12 months. Progression of average hearing level of pure tone was 0.168 dB/mo during the year of treatment period, whereas long-term progression was 0.364 dB/mo. Among all 16 patients, a partial response was observed in more than one schwannoma in four (including one in which Bev had not been effective), minor response in 5, and stable disease in 4. Both VEGFR1-specific and VEGFR2-specific cytotoxic T lymphocytes (CTLs) were induced in 11 patients. Two years after vaccination, a radiologic response was achieved in nine of 20 assessable schwannomas. CONCLUSION: This study demonstrated the safety and preliminary efficacy of VEGFR peptide vaccination in patients with NF2. Memory-induced CTLs after VEGFR vaccination may persistently suppress tumor progression.

The RIVET: a novel technique involving absorbable fixation for hydroxyapatite osteosynthesis.

Cranioplasty using custom-made hydroxyapatite (HAP) ceramic implants is a common procedure for the repair of skull defects. The advantages of using HAP are that it is nonmetallic, unlike titanium; biocompatible; and osteoconductive. Furthermore, it can be molded to any complex shape that may be needed. A disadvantage is that titanium screws and plates are in development for its fixation. We developed a technique for implant fixation using bioabsorbable screws and plates, and named this technique RIVET: resorbable immobilization for vacuolar en bloc technique.Before each operation, the implant was customized for the patient in question on the basis of models prepared using computed tomography data. The bioabsorbable plates were attached to the implant by drilling, tapping, and screwing, as shown in the video (http://links.lww.com/SCS/A43). The interior portion of the screw was then melted to flatten it against the internal surface of the implant, forming a rivet to join the plate and HAP implant.We used this technique for cranial reconstruction in 2 patients, with satisfying and functional results. We did not encounter any complications.In conclusion, the technique described here allows surgeons to fix implants and plates together more rigidly, giving a better result than possible with previous methods.

Dengue virus exploits the host tRNA epitranscriptome to promote viral replication.

The 40-50 RNA modifications of the epitranscriptome regulate posttranscriptional gene expression. Here we show that flaviviruses hijack the host tRNA epitranscriptome to promote expression of pro-viral proteins, with tRNA-modifying ALKBH1 acting as a host restriction factor in dengue virus infection. Early in the infection of human Huh-7 cells, ALKBH1 and its tRNA products 5-formylcytidine (f5C) and 2'-O-methyl-5-formylcytidine (f5Cm) were reduced. ALKBH1 knockdown mimicked viral infection, but caused increased viral NS3 protein levels during infection, while ALKBH1 overexpression reduced NS3 levels and viral replication, and increased f5C and f5Cm. Viral NS5, but not host FTSJ1, increased f5Cm levels late in infection. Consistent with reports of impaired decoding of leucine UUA codon by f5Cm-modified tRNALeu(CAA), ALKBH1 knockdown induced translation of UUA-deficient transcripts, most having pro-viral functions. Our findings support a dynamic ALKBH1/f5Cm axis during dengue infection, with virally-induced remodeling of the proteome by tRNA reprogramming and codon-biased translation.

A single m6A modification in U6 snRNA diversifies exon sequence at the 5' splice site.

N6-methyladenosine (m6A) is a modification that plays pivotal roles in RNA metabolism and function, although its functions in spliceosomal U6 snRNA remain unknown. To elucidate its role, we conduct a large-scale transcriptome analysis of a Schizosaccharomyces pombe strain lacking this modification and found a global change of pre-mRNA splicing. The most significantly impacted introns are enriched for adenosine at the fourth position pairing the m6A in U6 snRNA, and exon sequences weakly recognized by U5 snRNA. This suggests cooperative recognition of 5' splice site by U6 and U5 snRNPs, and also a role of m6A facilitating efficient recognition of the splice sites weakly interacting with U5 snRNA, indicating that U6 snRNA m6A relaxes the 5' exon constraint and allows protein sequence diversity along with explosively increasing number of introns over the course of eukaryotic evolution.

Trigeminal schwannomas: experience with 57 cases and a review of the literature.

Trigeminal schwannoma is a mostly benign tumor that can be cured by complete resection. Over the last few decades, several pioneers have developed surgical approaches enabling the total removal of such tumors. We analyzed 57 patients who underwent radical surgery, including 45 patients who underwent skull base surgery as their initial treatment, for removal of trigeminal schwannomas. Here, we report the surgical management of these cases. Since 1990, all such patients have been treated using three main types of middle fossa skull base approaches, which minimize the exposure of the brain: the anterior transpetrosal approach, subtemporal interdural approach (Dolenc), or a combination of these approaches. Before 1990, total tumor removal was achieved in only three of eight patients (38%). After 1990, the tumors were totally removed in 43 patients (90%) and were nearly completely removed in an additional three patients (6%). Among the patients who underwent skull base surgery as their initial treatment, a complete resection was achieved in 93% (42/45 patients) of the cases. However, total surgical removal after surgery and Gamma knife surgery was very difficult because of dense adhesions to the brain stem and cranial nerves. No surgery-related mortalities occurred in this series, and the individual KPS scores were more than 90% among the patients who underwent skull base surgery. No recurrences requiring additional surgery have occurred after an average follow-up period of 4.9 years. Most of the trigeminal schwannomas could be removed totally and safely during a single operation after the introduction of skull base surgery. Therefore, radiosurgery should not be applied as the treatment of first choice for younger patients. A correct anatomical knowledge is critical for minimizing brain exposure and avoiding surgical complications.