ArcS from Thermococcus kodakarensis transfers L-lysine to preQ0 nucleoside derivatives as minimum substrate RNAs.

Archaeosine (G+) is an archaea-specific tRNA modification synthesized via multiple steps. In the first step, archaeosine tRNA guanine transglucosylase (ArcTGT) exchanges the G15 base in tRNA with 7-cyano-7-deazaguanine (preQ0). In Euryarchaea, preQ015 in tRNA is further modified by archaeosine synthase (ArcS). Thermococcus kodakarensis ArcS catalyzes a lysine-transfer reaction to produce preQ0-lysine (preQ0-Lys) as an intermediate. The resulting preQ0-Lys15 in tRNA is converted to G+15 by a radical S-adenosyl-L-methionine enzyme for archaeosine formation (RaSEA), which forms a complex with ArcS. Here, we focus on the substrate tRNA recognition mechanism of ArcS. Kinetic parameters of ArcS for lysine and tRNA-preQ0 were determined using purified enzyme. RNA fragments containing preQ0 were prepared from Saccharomyces cerevisiae tRNAPhe-preQ015. ArcS transferred 14C-labeled lysine to RNA fragments. Furthermore, ArcS transferred lysine to preQ0 nucleoside and preQ0 nucleoside 5'-monophosphate. Thus, the L-shaped structure and the sequence of tRNA are not essential for the lysine-transfer reaction by ArcS. However, the presence of D-arm structure accelerates the lysine-transfer reaction. Because ArcTGT from thermophilic archaea recognizes the common D-arm structure, we expected the combination of T. kodakarensis ArcTGT and ArcS and RaSEA complex would result in the formation of preQ0-Lys15 in all tRNAs. This hypothesis was confirmed using 46 T. kodakarensis tRNA transcripts and three H. volcanii tRNA transcripts. In addition, ArcTGT did not exchange the preQ0-Lys15 in tRNA with guanine or preQ0 base, showing that formation of tRNA-preQ0-Lys by ArcS plays a role in preventing the reverse reaction in G+ biosynthesis.

Stratification of Stage II Colon Cancer Using Recurrence Prediction Value: A Multi-institutional International Retrospective Study.

OBJECTIVE: To create a recurrence prediction value (RPV) of high-risk factor and identify the patients with high risk of cancer recurrence. SUMMARY BACKGROUND DATA: There are several high-risk factors known to lead to poor outcomes. Weighting each high-risk factor based on their association with increased risk of cancer recurrence can provide a more precise understanding of risk of recurrence. METHODS: We performed a multi-institutional international retrospective analysis of patients with Stage II colon cancer patients who underwent surgery from 2010 to 2020. Patient data from a multi-institutional database were used as the Training data, and data from a completely separate international database from two countries were used as the Validation data. The primary endpoint was recurrence-free survival (RFS). RESULTS: A total of 739 patients were included from Training data. To validate the feasibility of RPV, 467 patients were included from Validation data. Training data patients were divided into RPV low (n = 564) and RPV high (n = 175). Multivariate analysis revealed that risk of recurrence was significantly higher in the RPV high than the RPV low (Hazard ratio (HR) 2.628; 95% confidence interval (CI) 1.887-3.660; P < 0.001). Validation data patients were divided into two groups (RPV low, n = 420) and RPV high (n = 47). Multivariate analysis revealed that risk of recurrence was significantly higher in the RPV high than the RPV low (HR 3.053; 95% CI 1.962-4.750; P < 0.001). CONCLUSIONS: RPV can identify Stage II colon cancer patients with high risk of cancer recurrence world-wide.

Prognostic Impact of Main Lymph Node Metastasis in Patients with Colon Cancer.

BACKGROUND: Although extended lymph node dissection during colon cancer surgery is recommended in both Western and Eastern countries, the perception and clinical significance of main lymph node metastasis (MLNM) remains controversial. METHODS: In total, 1557 patients with colon cancer who underwent curative resection with D3 dissection were retrospectively analyzed. Clinicopathological factors associated with MLNM were analyzed. Kaplan-Meier survival analysis and log-rank tests were used to compare the prognosis between the MLNM and non-MLNM groups. RESULTS: Multivariate analysis showed that overall survival (OS) [hazard ratio, 2.117 (0.939-4.774), p = 0.071] and recurrence-free survival (RFS) [hazard ratio, 2.183 (1.182-4.031), p = 0.013] were affected by the MLNM status independent of the TNM stage. Survival analysis demonstrated that among patients with stage III disease, the OS and RFS rates were significantly different between patients with and without MLNM (OS: p = 0.0147, RFS: p = 0.0001). However, the OS and RFS rates were not significantly different between patients who had stage III disease with MLNM and patients who had stage IV disease (OS: p = 0.5901, RFS: p = 0.9610). CONCLUSIONS: MLNM is an independent prognostic factor for patients with colon cancer. The addition of the MLNM status to the current TNM classification may enhance the prognostic value of the TNM staging system and the clinical efficacy of adjuvant therapy in patients with colon cancer.

Long-term changes in the refractive effect of a toric intraocular lens on astigmatism correction.

PURPOSE: To examine the long-term changes in the astigmatism-correcting effect of a toric intraocular lens (IOL) after stabilization of surgically induced astigmatic changes due to cataract surgery. METHODS: Unilateral eyes of 120 patients that received a toric IOL for against-the-rule (ATR) or with-the-rule (WTR) astigmatism were enrolled. Manifest refractive and anterior corneal astigmatism, and ocular residual astigmatism which is mainly derived from internal optics were examined preoperatively, at approximately 2 months postoperatively (baseline) and at 5 ~ 10 years postbaseline. The astigmatism was decomposed to vertical/horizontal (Rx) and oblique components (Ry), which was compared between baseline and 5 ~ 10 years postbaseline. RESULTS: In the eyes having ATR astigmatism, the mean Rx and Ry of the manifest refractive and corneal astigmatism significantly changed toward ATR astigmatism between the baseline and 5 ~ 10 years postbaseline (p ≤ 0.0304), but those of ocular residual astigmatism did not change significantly between the 2 time points. In the eyes having WTR astigmatism, the Rx and Ry of refractive, corneal, and ocular residual astigmatism did not change significantly between the 2 time points. Double-angle plots revealed an ATR shift in refractive and corneal astigmatism and no marked change in the ocular residual astigmatism in the eyes with ATR astigmatism, and there is no change in this astigmatism in the eyes with WTR astigmatism. CONCLUSION: The long-term changes with age in the effect of a toric IOL significantly deteriorated due to an ATR shift of corneal astigmatism in the eyes having ATR astigmatism, while it was maintained in eyes having WTR astigmatism, suggesting that ATR astigmatism should be overcorrected.

Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine-N2-) Methyltransferase (Trm11-Trm112 Complex).

The Saccharomyces cerevisiae Trm11 and Trm112 complex (Trm11-Trm112) methylates the 2-amino group of guanosine at position 10 in tRNA and forms N2-methylguanosine. To determine the elements required in tRNA for methylation by Trm11-Trm112, we prepared 60 tRNA transcript variants and tested them for methylation by Trm11-Trm112. The results show that the precursor tRNA is not a substrate for Trm11-Trm112. Furthermore, the CCA terminus is essential for methylation by Trm11-Trm112, and Trm11-Trm112 also only methylates tRNAs with a regular-size variable region. In addition, the G10-C25 base pair is required for methylation by Trm11-Trm112. The data also demonstrated that Trm11-Trm112 recognizes the anticodon-loop and that U38 in tRNAAla acts negatively in terms of methylation. Likewise, the U32-A38 base pair in tRNACys negatively affects methylation. The only exception in our in vitro study was tRNAValAAC1. Our experiments showed that the tRNAValAAC1 transcript was slowly methylated by Trm11-Trm112. However, position 10 in this tRNA was reported to be unmodified G. We purified tRNAValAAC1 from wild-type and trm11 gene deletion strains and confirmed that a portion of tRNAValAAC1 is methylated by Trm11-Trm112 in S. cerevisiae. Thus, our study explains the m2G10 modification pattern of all S. cerevisiae class I tRNAs and elucidates the Trm11-Trm112 binding sites.

Identification of a radical SAM enzyme involved in the synthesis of archaeosine.

Archaeosine (G+), 7-formamidino-7-deazaguanosine, is an archaea-specific modified nucleoside found at the 15th position of tRNAs. In Euryarchaeota, 7-cyano-7-deazaguanine (preQ0)-containing tRNA (q0N-tRNA), synthesized by archaeal tRNA-guanine transglycosylase (ArcTGT), has been believed to be converted to G+-containing tRNA (G+-tRNA) by the paralog of ArcTGT, ArcS. However, we found that several euryarchaeal ArcSs have lysine transfer activity to q0N-tRNA to form q0kN-tRNA, which has a preQ0 lysine adduct as a base. Through comparative genomics and biochemical experiments, we found that ArcS forms a robust complex with a radical S-adenosylmethionine (SAM) enzyme named RaSEA. The ArcS-RaSEA complex anaerobically converted q0N-tRNA to G+-tRNA in the presence of SAM and lysine via q0kN-tRNA. We propose that ArcS and RaSEA should be considered an archaeosine synthase α-subunit (lysine transferase) and ß-subunit (q0kN-tRNA lyase), respectively.

Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.

The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 complex. Purified recombinant Trm7-Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7-Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7-Trm734. Small angle X-ray scattering reveals that Trm7-Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 ß-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7-Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.

Verifying the M1c category of CRC: analysis of the data from a Japanese multi-institutional database.

BACKGROUND/AIMS: In the TNM classification 8th edition, colorectal cancer (CRC) with peritoneal metastasis, one of the most poor prognostic factors, is classified as M1c (stage IVC), regardless of the presence/absence of other distant metastasis. Several cases with peritoneal metastasis have been successfully managed by surgical treatment; therefore, there is need to give more consideration for uniform differentiation of peritoneal metastasis. This study was aimed at verifying the classification of M1c in CRC. MATERIALS AND METHODS: Data from a multi-institutional retrospective cohort of 2929 CRC patients who were diagnosed as having stage IV CRC from 1997 to 2007 were analyzed. Peritoneal metastasis alone was defined as M1c1 and peritoneal metastasis with other organ metastasis was defined as M1c2. RESULTS: The 3-year OS of patients with M1c1 was significantly higher than that of patients with M1b (25.6% vs. 18.1%; HR 0.77; 95% confidence interval (CI) 0.65-0.92; p = 0.005); in particular, the prognosis of patients with M1c1 with localized peritoneal metastasis and R0 resection was equivalent to that of patients with M1a (3-year OS 40.5% vs. 39.2%, p = 0.41). On the other hand, among the stage IV cases, patients with M1c2 had a low R0 resection rate (5.9%) and the worst prognosis (3-year OS, 9.1%). CONCLUSIONS: The prognosis of M1c1 with localized peritoneal metastasis is relatively good, and can be further improved by surgical intervention. Combined evaluation of the M1c1/2 classification with the peritoneal metastasis grade may help in establishing more individualized treatment strategies.

The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity.

Four different types (α4, α'2, (αß)2 and ϵ2) of RNA-splicing endonucleases (EndAs) for RNA processing are known to exist in the Archaea. Only the (αß)2 and ϵ2 types can cleave non-canonical introns in precursor (pre)-tRNA. Both enzyme types possess an insert associated with a specific loop, allowing broad substrate specificity in the catalytic α units. Here, the hyperthermophilic euryarchaeon Methanopyrus kandleri (MKA) was predicted to harbor an (αß)2-type EndA lacking the specific loop. To characterize MKA EndA enzymatic activity, we constructed a fusion protein derived from MKA α and ß subunits (fMKA EndA). In vitro assessment demonstrated complete removal of the canonical bulge-helix-bulge (BHB) intron structure from MKA pre-tRNAAsn. However, removal of the relaxed BHB structure in MKA pre-tRNAGlu was inefficient compared to crenarchaeal (αß)2 EndA, and the ability to process the relaxed intron within mini-helix RNA was not detected. fMKA EndA X-ray structure revealed a shape similar to that of other EndA types, with no specific loop. Mapping of EndA types and their specific loops and the tRNA gene diversity among various Archaea suggest that MKA EndA is evolutionarily related to other (αß)2-type EndAs found in the Thaumarchaeota, Crenarchaeota and Aigarchaeota but uniquely represents constrained substrate specificity.

Distinct Modified Nucleosides in tRNATrp from the Hyperthermophilic Archaeon Thermococcus kodakarensis and Requirement of tRNA m2G10/m22G10 Methyltransferase (Archaeal Trm11) for Survival at High Temperatures.

tRNA m2G10/m22G10 methyltransferase (archaeal Trm11) methylates the 2-amino group in guanosine at position 10 in tRNA and forms N2,N2-dimethylguanosine (m22G10) via N2-methylguanosine (m2G10). We determined the complete sequence of tRNATrp, one of the substrate tRNAs for archaeal Trm11 from Thermococcus kodakarensis, a hyperthermophilic archaeon. Liquid chromatography/mass spectrometry following enzymatic digestion of tRNATrp identified 15 types of modified nucleoside at 21 positions. Several modifications were found at novel positions in tRNA, including 2'-O-methylcytidine at position 6, 2-thiocytidine at position 17, 2'-O-methyluridine at position 20, 5,2'-O-dimethylcytidine at position 32, and 2'-O-methylguanosine at position 42. Furthermore, methylwyosine was found at position 37 in this tRNATrp, although 1-methylguanosine is generally found at this location in tRNATrp from other archaea. We constructed trm11 (Δtrm11) and some gene disruptant strains and compared their tRNATrp with that of the wild-type strain, which confirmed the absence of m22G10 and other corresponding modifications, respectively. The lack of 2-methylguanosine (m2G) at position 67 in the trm11 trm14 double disruptant strain suggested that this methylation is mediated by Trm14, which was previously identified as an m2G6 methyltransferase. The Δtrm11 strain grew poorly at 95°C, indicating that archaeal Trm11 is required for T. kodakarensis survival at high temperatures. The m22G10 modification might have effects on stabilization of tRNA and/or correct folding of tRNA at the high temperatures. Collectively, these results provide new clues to the function of modifications and the substrate specificities of modification enzymes in archaeal tRNA, enabling us to propose a strategy for tRNA stabilization of this archaeon at high temperatures.IMPORTANCEThermococcus kodakarensis is a hyperthermophilic archaeon that can grow at 60 to 100°C. The sequence of tRNATrp from this archaeon was determined by liquid chromatography/mass spectrometry. Fifteen types of modified nucleoside were observed at 21 positions, including 5 modifications at novel positions; in addition, methylwyosine at position 37 was newly observed in an archaeal tRNATrp The construction of trm11 (Δtrm11) and other gene disruptant strains confirmed the enzymes responsible for modifications in this tRNA. The lack of 2-methylguanosine (m2G) at position 67 in the trm11 trm14 double disruptant strain suggested that this position is methylated by Trm14, which was previously identified as an m2G6 methyltransferase. The Δtrm11 strain grew poorly at 95°C, indicating that archaeal Trm11 is required for T. kodakarensis survival at high temperatures.

Relationship between the morphology of the foveal avascular zone and the degree of aniseikonia before and after vitrectomy in patients with unilateral epiretinal membrane.

PURPOSE: Persistent metamorphopsia, particularly aniseikonia, is a troublesome problem which may occur after epiretinal membrane (ERM) surgery. To clarify if the preoperative foveal avascular zone (FAZ) morphology can be used as a predictor of postoperative residual aniseikonia, the morphological changes in the FAZ and the degree of aniseikonia between before and 12 months after vitrectomy for epiretinal membrane (ERM) were measured and analyzed. METHODS: Thirty patients, each with a unilateral idiopathic ERM, who underwent treatment between September 2016 and March 2017 were enrolled for this prospective case series study. Best-corrected visual acuity (BCVA), the degree of aniseikonia, central foveal thickness (CFT), FAZ area (FAZa), perimeter (FAZp), and circularity in ERM eyes were examined before and 1, 3, 6 and 12 months after surgery. The fellow eye without an ERM was also examined and used as the control. The interocular ratios of the CFT, FAZa, and FAZp in ERM eyes with those in control eyes were also calculated. Multiple regression analysis was performed on preoperative parameters that were found to be significantly correlated with the 12-month aniseikonia in univariate analyses. RESULTS: The BCVA in the ERM eyes was significantly improved at 1 month after surgery (P < .0001) The degree of aniseikonia was significantly reduced only after 12 months (P = .004). The CFT had decreased significantly by 3 months after the surgery and continued decreasing thereafter (P < .0001). Both FAZa and FAZp were significantly smaller in the ERM eyes than in the control eyes throughout the study period (P < .0001 and P < .0001, respectively), with no change in either parameter over the study period. Correlation analyses revealed that the degree of aniseikonia was significantly correlated with pre- and postoperative CFT, CFT ratio, FAZa, FAZa ratio, FAZp, and FAZp ratio. Within preoperative OCT parameters, FAZa ratio remained significant after multiple regression analysis was performed (P < .0001). CONCLUSIONS: Aniseikonia changed little over the long term following ERM surgery. Preoperative FAZ area ratio was identified as a significant predictor of postoperative aniseikonia.

Anatomical and functional changes in paravascular abnormalities after epiretinal membrane removal.

PURPOSE: To investigate the anatomical and functional changes in areas containing paravascular abnormalities (PVA) in eyes with epiretinal membrane (ERM) after surgery. METHODS: Twenty-eight eyes with concurrent idiopathic ERM and PVA were enrolled in this prospective study. Best-corrected visual acuity (BCVA), central macular thickness (CMT), and areas of PVA in the superficial and deep capillary levels detected on en face optical coherence tomography were measured preoperatively and 1, 3, and 6 months postoperatively. Retinal sensitivity in selected PVA lesions was evaluated by microperimetry preoperatively and 1 and 6 months postoperatively. RESULTS: The areas of PVA at the superficial capillary level before and 1, 3, and 6 months after surgery measured 1.65 ± 1.27, 0.44 ± 0.62, 0.40 ± 0.64, and 0.38 ± 0.62 mm2, respectively, while those at the deep capillary level measured 0.27 ± 0.57, 0.10 ± 0.26, 0.09 ± 0.29, and 0.05 ± 0.15 mm2, respectively. The areas of PVA in the superficial and deep capillary levels were significantly smaller postoperatively (all p < 0.001 at the superficial capillary level and p = 0.010 at the deep capillary level). Average retinal sensitivity values in the PVA lesions before and 1 and 6 months after surgery were 11.2 ± 3.5, 12.9 ± 3.2, and 13.2 ± 2.7 dB, respectively; the values at postoperative months 1 and 6 were significantly improved (p = 0.045 and p < 0.001, respectively). BCVA and CMT were significantly improved postoperatively. CONCLUSION: PVA not only improves anatomically but also functionally after ERM surgery. Vitrectomy can improve not only central vision but also retinal sensitivity in areas of PVA.

CORRELATIONS BETWEEN EXPERIMENTAL MYOPIA MODELS AND HUMAN PATHOLOGIC MYOPIA.

PURPOSE: To analyze the hallmark features of pathologic myopia developed in animal models and compare them with those seen in patients. METHODS: A literature review was performed to identify animal models that exhibited key features of pathologic myopia, namely posterior staphyloma, myopic maculopathy, lacquer cracks, and choroidal neovascularization, either spontaneously or induced by monocular deprivation. Using imaging modalities, such as optical coherence tomography, confocal scanning laser ophthalmoscopy, fluorescein angiography, and electron microscopy, these features were compared with those found in myopic maculopathy of patients. RESULTS: Three types of animals were identified. The LRP2 knockout mice exhibited posterior staphylomas and chorioretinal atrophy at 21 and 60 days after birth, respectively. Retinopathy globe enlarged (rge) chicks and normal lid-sutured chicks developed lacquer cracks and chorioretinal atrophy. Lacquer cracks detected in rge chicks subsequently progressed to patchy chorioretinal atrophy, which is also commonly seen in patients with pathologic myopia. CONCLUSION: The LRP2 knockout mice, retinopathy globe enlarged (rge) chicks, and normal lid-sutured chicks exhibit features typical for myopic maculopathy in patients and could serve to further elucidate the pathogenesis of myopic maculopathy.

Changes in the rate of and trends in colectomy for ulcerative colitis during the era of biologics and calcineurin inhibitors based on a Japanese nationwide cohort study.

PURPOSE: We evaluated the recent incidence of surgery and the changing surgery trends for ulcerative colitis (UC) in Japan due to the increasing use of anti-tumor necrosis factor (TNF) agents. METHODS: A questionnaire survey was performed to assess the number of surgeries, surgical indications, surgical timing, and immunosuppressive treatments before surgery between 2007 and 2017. RESULTS: A total of 3801 surgical cases were reported over 11 years. The prevalence of UC surgery decreased over the period studied. The rate of prednisolone (PSL) use did not change. The prevalence of both calcineurin inhibitors (CNIs) and anti-TNF agents increased during the period studied (p < 0.01). The prevalence of urgent/emergent surgery did not change. The most distinctive change in surgical indications was the increase in cancer/dysplasia (CAC), the prevalence of which increased from 20.2% in 2007 to 34.8%. CONCLUSION: The prevalence of UC surgery seems to be decreasing according to the increasing rate of anti-TNF agent and CNI administration. However, the indication of CAC significantly increased. Further research should evaluate whether or not long-term remission maintained with several agents can lead to increasing CAC.

A Phase II Study of Irinotecan for Patients with Previously Treated Small-Cell Lung Cancer.

OBJECTIVE: Chemotherapy with irinotecan plus cisplatin has shown promise in chemo-naïve small-cell lung cancer (SCLC) patients. However, irinotecan treatment for relapsed or refractory SCLC has not been adequately evaluated. This phase II study evaluated the appropriate treatment schedule of irinotecan as a single agent. This study was designed to determine the antitumor activity, toxicity, and survival in previously treated SCLC patients. METHODS: Previously treated SCLC patients with at least one platinum-based regimen received irinotecan (100 mg/m2) on days 1 and 8, every 3 weeks, until disease progression. The assessment of the response rate was the primary endpoint. RESULTS: Thirty patients were enrolled, with an objective response rate of 41.3% (95% confidence interval [CI] 25.5-59.3), and a disease control rate of 69%. Median progression-free and overall survival was 4.1 months (95% CI, 2.2-5.4) and 10.4 months (95% CI, 8.1-14), respectively. The grade 3/4 hematological toxicities were neutropenia (36.7%), thrombocytopenia (3.3%), anemia (13.3%), and febrile neutropenia (6.6%). There were no grade 4 nonhematological toxicities. Frequent grade 3 nonhematological toxicities included diarrhea (10%), anorexia (6.6%), and hyponatremia (6.6%). CONCLUSIONS: This phase II study showed a high objective response rate and long survival. Irinotecan monotherapy schedule used was well tolerated, and could be an active treatment option for these patients.

Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules.

N(2)-methylguanosine is one of the most universal modified nucleosides required for proper function in transfer RNA (tRNA) molecules. In archaeal tRNA species, a specific S-adenosyl-L-methionine (SAM)-dependent tRNA methyltransferase (MTase), aTrm11, catalyzes formation of N(2)-methylguanosine and N(2),N(2)-dimethylguanosine at position 10. Here, we report the first X-ray crystal structures of aTrm11 from Thermococcus kodakarensis (Tko), of the apo-form, and of its complex with SAM. The structures show that TkoTrm11 consists of three domains: an N-terminal ferredoxinlike domain (NFLD), THUMP domain and Rossmann-fold MTase (RFM) domain. A linker region connects the THUMP-NFLD and RFM domains. One SAM molecule is bound in the pocket of the RFM domain, suggesting that TkoTrm11 uses a catalytic mechanism similar to that of other tRNA MTases containing an RFM domain. Furthermore, the conformation of NFLD and THUMP domains in TkoTrm11 resembles that of other tRNA-modifying enzymes specifically recognizing the tRNA acceptor stem. Our docking model of TkoTrm11-SAM in complex with tRNA, combined with biochemical analyses and pre-existing evidence, provides insights into the substrate tRNA recognition mechanism: The THUMP domain recognizes a 3'-ACCA end, and the linker region and RFM domain recognize the T-stem, acceptor stem and V-loop of tRNA, thereby causing TkoTrm11 to specifically identify its methylation site.

Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon.

Archaeosine (G(+)), which is found only at position 15 in many archaeal tRNA, is formed by two steps, the replacement of the guanine base with preQ0 by archaeosine tRNA-guanine transglycosylase (ArcTGT) and the subsequent modification of preQ0 to G(+) by archaeosine synthase. However, tRNA(Leu) from Thermoplasma acidophilum, a thermo-acidophilic archaeon, exceptionally has two G(+)13 and G(+)15 modifications. In this study, we focused on the biosynthesis mechanism of G(+)13 and G(+)15 modifications in this tRNA(Leu). Purified ArcTGT from Pyrococcus horikoshii, for which the tRNA recognition mechanism and structure were previously characterized, exchanged only the G15 base in a tRNA(Leu) transcript with (14)C-guanine. In contrast, T. acidophilum cell extract exchanged both G13 and G15 bases. Because T. acidophilum ArcTGT could not be expressed as a soluble protein in Escherichia coli, we employed an expression system using another thermophilic archaeon, Thermococcus kodakarensis. The arcTGT gene in T. kodakarensis was disrupted, complemented with the T. acidophilum arcTGT gene, and tRNA(Leu) variants were expressed. Mass spectrometry analysis of purified tRNA(Leu) variants revealed the modifications of G(+)13 and G(+)15 in the wild-type tRNA(Leu). Thus, T. acidophilum ArcTGT has a multisite specificity and is responsible for the formation of both G(+)13 and G(+)15 modifications.

Folate-/FAD-dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures.

TrmFO is a N(5) , N(10) -methylenetetrahydrofolate (CH2 THF)-/FAD-dependent tRNA methyltransferase, which synthesizes 5-methyluridine at position 54 (m(5) U54) in tRNA. Thermus thermophilus is an extreme-thermophilic eubacterium, which grows in a wide range of temperatures (50-83 °C). In T. thermophilus, modified nucleosides in tRNA and modification enzymes form a network, in which one modification regulates the degrees of other modifications and controls the flexibility of tRNA. To clarify the role of m(5) U54 and TrmFO in the network, we constructed the trmFO gene disruptant (∆trmFO) strain of T. thermophilus. Although this strain did not show any growth retardation at 70 °C, it showed a slow-growth phenotype at 50 °C. Nucleoside analysis showed increase in 2'-O-methylguanosine at position 18 and decrease in N(1) -methyladenosine at position 58 in the tRNA mixture from the ∆trmFO strain at 50 °C. These in vivo results were reproduced by in vitro experiments with purified enzymes. Thus, we concluded that the m(5) U54 modification have effects on the other modifications in tRNA through the network at 50 °C. (35) S incorporations into proteins showed that the protein synthesis activity of ∆trmFO strain was inferior to the wild-type strain at 50 °C, suggesting that the growth delay at 50 °C was caused by the inferior protein synthesis activity.

Incorporation of serum carcinoembryonic antigen levels into the prognostic grouping system of colon cancer.

PURPOSE: This study aimed to clarify the significance of preoperative serum carcinoembryonic antigen (CEA) on disease-free survival (DFS) in colon cancer and propose a new prognostic grouping system. METHODS: A multiinstitutional retrospective cohort of 7296 colon cancer patients who underwent R0 surgery between 1997 and 2006 was analyzed. We stratified preoperative serum CEA values into three categories (C-stages): C0 (normal CEA), C1A (up to double the cutoff value), and C1B (more than double the cutoff value) and stratified each TNM stage by C-stage. Multivariate analyses using Cox regression models were used to analyze the significance of C-stage on 5-year DFS. RESULTS: CEA level was an independent factor affecting DFS; the 5-year DFS of patients with C0 and C1, as well as those with C1A and C1B, differed significantly (C0 84.6%, C1 69.8%, C1A 72.7%, and C1B 66.4%, P < 0.0001). Additionally, the DFS of pStages IIC and C1B was significantly lower than of pStages IIIA and C0 (65.8 vs. 87.7%, respectively; hazard ratio 3.44, 95% confidence interval 1.97-5.88, P < 0.0001). Moreover, the 5-year DFS of pStages IIIA and C0 or C1A did not differ significantly from pStages I and C1A (87.7 vs. 87.7%, P = 0.90 and 86.4 vs. 87.7%, P = 0.78, respectively). CONCLUSIONS: pStage IIC and C1B disease should be considered candidates for intensive adjuvant chemotherapy. Conversely, pStages IIIA and C0 or C1A could be exempted from adjuvant chemotherapy. Incorporating C-stage into the current TNM staging system may facilitate decision making regarding the use of adjuvant chemotherapy in colon cancer patients.

Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI).

TrmI generates N(1)-methyladenosine at position 58 (m(1)A58) in tRNA. The Thermus thermophilus tRNA(Phe) transcript was methylated efficiently by T. thermophilus TrmI, whereas the yeast tRNA(Phe) transcript was poorly methylated. Fourteen chimeric tRNA transcripts derived from these two tRNAs revealed that TrmI recognized the combination of aminoacyl stem, variable region, and T-loop. This was confirmed by 10 deletion tRNA variants: TrmI methylated transcripts containing the aminoacyl stem, variable region, and T-arm. The requirement for the T-stem itself was confirmed by disrupting the T-stem. Disrupting the interaction between T- and D-arms accelerated the methylation, suggesting that this disruption is included in part of the reaction. Experiments with 17 point mutant transcripts elucidated the positive sequence determinants C56, purine 57, A58, and U60. Replacing A58 with inosine and 2-aminopurine completely abrogated methylation, demonstrating that the 6-amino group in A58 is recognized by TrmI. T. thermophilus tRNAGGU(Thr)GGU(Thr) contains C60 instead of U60. The tRNAGGU(Thr) transcript was poorly methylated by TrmI, and replacing C60 with U increased the methylation, consistent with the point mutation experiments. A gel shift assay revealed that tRNAGGU(Thr) had a low affinity for TrmI than tRNA(Phe). Furthermore, analysis of tRNAGGU(Thr) purified from the trmI gene disruptant strain revealed that the other modifications in tRNA accelerated the formation of m(1)A58 by TrmI. Moreover, nucleoside analysis of tRNAGGU(Thr) from the wild-type strain indicated that less than 50% of tRNAGG(Thr) contained m(1)A58. Thus, the results from the in vitro experiments were confirmed by the in vivo methylation patterns.