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Wang B, Zhang J, Liu X, Chai Q, Lu X, Yao X, Yang Z, Sun L, Johnson SF, Schwartz RC, Zheng YH. Protein disulfide isomerases (PDIs) negatively regulate ebolavirus structural glycoprotein expression in the endoplasmic reticulum (ER) via the autophagy-lysosomal pathway. Autophagy 2022; 18:2350-2367. [PMID: 35130104 PMCID: PMC9542513 DOI: 10.1080/15548627.2022.2031381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/09/2023] Open
Abstract
Zaire ebolavirus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates with high morbidity and mortality. EBOV infection is dependent on its structural glycoprotein (GP), but high levels of GP expression also trigger cell rounding, detachment, and downregulation of many surface molecules that is thought to contribute to its high pathogenicity. Thus, EBOV has evolved an RNA editing mechanism to reduce its GP expression and increase its fitness. We now report that the GP expression is also suppressed at the protein level in cells by protein disulfide isomerases (PDIs). Although PDIs promote oxidative protein folding by catalyzing correct disulfide formation in the endoplasmic reticulum (ER), PDIA3/ERp57 adversely triggered the GP misfolding by targeting GP cysteine residues and activated the unfolded protein response (UPR). Abnormally folded GP was targeted by ER-associated protein degradation (ERAD) machinery and, unexpectedly, was degraded via the macroautophagy/autophagy-lysosomal pathway, but not the proteasomal pathway. PDIA3 also decreased the GP expression from other ebolavirus species but increased the GP expression from Marburg virus (MARV), which is consistent with the observation that MARV-GP does not cause cell rounding and detachment, and MARV does not regulate its GP expression via RNA editing during infection. Furthermore, five other PDIs also had a similar inhibitory activity to EBOV-GP. Thus, PDIs negatively regulate ebolavirus glycoprotein expression, which balances the viral life cycle by maximizing their infection but minimizing their cellular effect. We suggest that ebolaviruses hijack the host protein folding and ERAD machinery to increase their fitness via reticulophagy during infection.Abbreviations: 3-MA: 3-methyladenine; 4-PBA: 4-phenylbutyrate; ACTB: β-actin; ATF: activating transcription factor; ATG: autophagy-related; BafA1: bafilomycin A1; BDBV: Bundibugyo ebolavirus; CALR: calreticulin; CANX: calnexin; CHX: cycloheximide; CMA: chaperone-mediated autophagy; ConA: concanamycin A; CRISPR: clusters of regularly interspaced short palindromic repeats; Cas9: CRISPR-associated protein 9; dsRNA: double-stranded RNA; EBOV: Zaire ebolavirus; EDEM: ER degradation enhancing alpha-mannosidase like protein; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; Env: envelope glycoprotein; ER: endoplasmic reticulum; ERAD: ER-associated protein degradation; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; GP: glycoprotein; HA: hemagglutinin; HDAC6: histone deacetylase 6; HMM: high-molecular-mass; HIV-1: human immunodeficiency virus type 1; HSPA5/BiP: heat shock protein family A (Hsp70) member 5; IAV: influenza A virus; IP: immunoprecipitation; KIF: kifenesine; Lac: lactacystin; LAMP: lysosomal associated membrane protein; MAN1B1/ERManI: mannosidase alpha class 1B member 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MARV: Marburg virus; MLD: mucin-like domain; NHK/SERPINA1: alpha1-antitrypsin variant null (Hong Kong); NTZ: nitazoxanide; PDI: protein disulfide isomerase; RAVV: Ravn virus; RESTV: Reston ebolavirus; SARS-CoV: severe acute respiratory syndrome coronavirus; SBOV: Sudan ebolavirus; sGP: soluble GP; SQSTM1/p62: sequestosome 1; ssGP: small soluble GP; TAFV: Taï Forest ebolavirus; TIZ: tizoxanide; TGN: thapsigargin; TLD: TXN (thioredoxin)-like domain; Ub: ubiquitin; UPR: unfolded protein response; VLP: virus-like particle; VSV: vesicular stomatitis virus; WB: Western blotting; WT: wild-type; XBP1: X-box binding protein 1.
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Affiliation(s)
- Bin Wang
- CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- MSD (Ningbo) Animal Health Technology Co., Ltd, Ningbo, China
| | - Jing Zhang
- CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xin Liu
- CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qingqing Chai
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Xiaoran Lu
- CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaoyu Yao
- CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Silas F. Johnson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Richard C Schwartz
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Yong-Hui Zheng
- CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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Memon F, Arif M, Kirmani S, Humayun KN. Wolcott-Rallison syndrome: a case series of three patients. Pediatr Endocrinol Diabetes Metab 2022; 28:238-240. [PMID: 36106422 PMCID: PMC10214929 DOI: 10.5114/pedm.2022.118325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/28/2022] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Neonatal diabetes is a rare disease with incidence estimated at 1 in 300,000 to 1 in 400,000 live births. Walcott-Rallison syndrome has been identified as the most common cause of permanent neonatal diabetes in consanguineous families caused by mutations in eukaryotic translation initiation factor 2-α kinase 3 (EIF2AK3), characterized by permanent neonatal diabetes associated with liver dysfunction, multiple epiphyseal dysplasia, and developmental delay. We herein report 3 cases of genetically proven Wolcott-Rallison syndrome with variable phenotype presentation. CASE SERIES All cases presented with high glucose levels and were treated with insulin. EIF2AK3 homozygous mutation was identified in all 3 on genetic analysis. Initial screening testing for associated comorbidities was normal, including X-ray examination, which did not show any signs of epiphyseal dysplasia in all cases. Case 2 and case 3 were both lost to follow-up and were later found to have expired at the ages of 18 months and 2 years, respectively, due to liver failure associated with intercurrent respiratory illness in hospitals in their native towns. Case one is now 2 years old on regular follow-up in paediatric Endocrine and neurology clinics and doing well so far. CONCLUSIONS Morbidity, as well as mortality, is high among children with WRS neonatal diabetes. It is crucial to screen for gene mutation in patients with diabetes diagnosed before 6 months. Close therapeutic monitoring is recommended in WRS because of the risk of acute episodes of hypoglycaemia and ketoacidosis.
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Affiliation(s)
- Fozia Memon
- Fozia Memon Pediatric and Child Health Section of Pediatric Endocrinology Aga Khan University Pakistan e-mail:
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Tomsic J, Caserta E, Pon CL, Gualerzi CO. Weakening the IF2-fMet-tRNA Interaction Suppresses the Lethal Phenotype Caused by GTPase Inactivation. Int J Mol Sci 2021; 22:ijms222413238. [PMID: 34948034 PMCID: PMC8709274 DOI: 10.3390/ijms222413238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/12/2023] Open
Abstract
Substitution of the conserved Histidine 448 present in one of the three consensus elements characterizing the guanosine nucleotide binding domain (IF2 G2) of Escherichia coli translation initiation factor IF2 resulted in impaired ribosome-dependent GTPase activity which prevented IF2 dissociation from the ribosome, caused a severe protein synthesis inhibition, and yielded a dominant lethal phenotype. A reduced IF2 affinity for the ribosome was previously shown to suppress this lethality. Here, we demonstrate that also a reduced IF2 affinity for fMet-tRNA can suppress this dominant lethal phenotype and allows IF2 to support faithful translation in the complete absence of GTP hydrolysis. These results strengthen the premise that the conformational changes of ribosome, IF2, and fMet-tRNA occurring during the late stages of translation initiation are thermally driven and that the energy generated by IF2-dependent GTP hydrolysis is not required for successful translation initiation and that the dissociation of the interaction between IF2 C2 and the acceptor end of fMet-tRNA, which represents the last tie anchoring the factor to the ribosome before the formation of an elongation-competent 70S complex, is rate limiting for both the adjustment of fMet-tRNA in a productive P site and the IF2 release from the ribosome.
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Affiliation(s)
- Jerneja Tomsic
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Enrico Caserta
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Cynthia L. Pon
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
| | - Claudio O. Gualerzi
- Laboratory of Genetics, Department of Bioscience and Biotechnology, University of Camerino, 62032 Camerino, Italy; (J.T.); (E.C.); (C.L.P.)
- Correspondence: ; Tel.: +39-3391602957
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Sellyei B, Bányai K, Bartha D, Hajtós I, Fodor L, Makrai L. Multilocus Sequencing of Corynebacterium pseudotuberculosis Biotype Ovis Strains. Biomed Res Int 2017; 2017:1762162. [PMID: 29159175 PMCID: PMC5660753 DOI: 10.1155/2017/1762162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/26/2017] [Accepted: 08/08/2017] [Indexed: 11/18/2022]
Abstract
Thirteen Corynebacterium pseudotuberculosis biotype ovis strains isolated from clinical cases of caseous lymphadenitis in Hungary were characterised using multilocus sequencing and their phylogenetic comparison was carried out on the basis of four housekeeping genes (groEL1, infB, dnaK, and leuA). The in silico analysis of the 16 frequently studied housekeeping genes showed that C. pseudotuberculosis strains could be readily distinguished from C. diphtheriae and C. ulcerans strains; however, sequences of the same genes in the two biotypes of the C. pseudotuberculosis were highly similar; the heterogeneity values were low. Genes dnaK, infB, groEL1, and leuA showed marked genetic variation within C. pseudotuberculosis, and strains of the two biotypes of C. pseudotuberculosis could be differentiated. Analysis of the individual genes showed a fairly conservative nature of C. pseudotuberculosis biotype ovis strains. The greatest genetic differentiation was seen in the dnaK and infB genes and concatenations of these two genes were very useful in the genetic separation of the studied strains.
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Affiliation(s)
- Boglárka Sellyei
- CAR, HAS, Institute for Veterinary Medical Research, P.O. Box 18, Budapest 1581, Hungary
| | - Krisztián Bányai
- CAR, HAS, Institute for Veterinary Medical Research, P.O. Box 18, Budapest 1581, Hungary
| | - Dániel Bartha
- CAR, HAS, Institute for Veterinary Medical Research, P.O. Box 18, Budapest 1581, Hungary
| | - István Hajtós
- Government Office for Borsod-Abaúj-Zemplén County, Vologda U. 1, Miskolc 3525, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, Budapest 1581, Hungary
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, Budapest 1581, Hungary
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Liu B, Luo J, Li W, Long XF, Zhang YQ, Zeng ZG, Tian YQ. Erwinia teleogrylli sp. nov., a Bacterial Isolate Associated with a Chinese Cricket. PLoS One 2016; 11:e0146596. [PMID: 26800121 PMCID: PMC4723187 DOI: 10.1371/journal.pone.0146596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 12/18/2015] [Indexed: 11/29/2022] Open
Abstract
A bacterial isolate (SCU-B244T) was obtained in China from crickets (Teleogryllus occipitalis) living in cropland deserted for approximately 10 years. The isolated bacteria were Gram-negative, facultatively anaerobic, oxidase-negative rods. A preliminary analysis of the 16S rRNA gene sequence indicated that the strain belongs to either the genus Erwinia or Pantoea. Analysis of multilocus sequence typing based on concatenated partial atpD, gyrB and infB gene sequences and physiological and biochemical characteristics indicated that the strain belonged to the genus Erwinia, as member of a new species as it was distinct from other known Erwinia species. Further analysis of the 16S rRNA gene showed SCU-B244T to have 94.71% identity to the closest species of that genus, Erwinia oleae (DSM 23398T), which is below the threshold of 97% used to discriminate bacterial species. DNA-DNA hybridization results (5.78±2.52%) between SCU-B244T and Erwinia oleae (DSM 23398T) confirmed that SCU-B244T and Erwinia oleae (DSM 23398T) represent different species combined with average nucleotide identity values which range from 72.42% to 74.41. The DNA G+C content of SCU-B244T was 55.32 mol%, which also differs from that of Erwinia oleae (54.7 to 54.9 mol%). The polyphasic taxonomic approach used here confirmed that the strain belongs to the Erwinia group and represents a novel species. The name Erwinia teleogrylli sp. nov. is proposed for this novel taxon, for which the type strain is SCU-B244T (= CGMCC 1.12772T = DSM 28222T = KCTC 42022T).
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Affiliation(s)
- Bo Liu
- Key laboratory of Leather Chemistry and engineering, College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu, Sichuan, P. R. China
- Department of Pharmaceutical and Biological Engineering, College of Chemical Engineering, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jin Luo
- Department of Pharmaceutical and Biological Engineering, College of Chemical Engineering, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Wei Li
- Department of Pharmaceutical and Biological Engineering, College of Chemical Engineering, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Xiu-Feng Long
- Key laboratory of Leather Chemistry and engineering, College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zhi-Gang Zeng
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, Sichuan, P. R. China
| | - Yong-Qiang Tian
- Key laboratory of Leather Chemistry and engineering, College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu, Sichuan, P. R. China
- * E-mail:
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Abstract
Enterobacter sakazakii is an opportunistic pathogen that causes meningitis and necrotizing enterocolitis in neonates. Here we characterized the thermal tolerance of E. sakazakii isolates obtained from powdered infant formula and other food products in Japan. Isolates were categorized into three classes according to their thermal tolerance, and differential gene expression analysis showed that the heat-resistant clones expressed a higher level of infB (which encodes a translation initiation factor), than did the heat-sensitive isolates. Gene expression and DNA polymorphism analyses suggested that this gene target might be useful to unequivocally detect and identify heat-resistant clones, permitting epidemiological surveillance for this pathogen.
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Affiliation(s)
- Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Tokyo, Japan
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Kuzmenko A, Atkinson GC, Levitskii S, Zenkin N, Tenson T, Hauryliuk V, Kamenski P. Mitochondrial translation initiation machinery: conservation and diversification. Biochimie 2013; 100:132-40. [PMID: 23954798 PMCID: PMC3978653 DOI: 10.1016/j.biochi.2013.07.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/29/2013] [Indexed: 11/29/2022]
Abstract
The highly streamlined mitochondrial genome encodes almost exclusively a handful of transmembrane components of the respiratory chain complex. In order to ensure the correct assembly of the respiratory chain, the products of these genes must be produced in the correct stoichiometry and inserted into the membrane, posing a unique challenge to the mitochondrial translational system. In this review we describe the proteins orchestrating mitochondrial translation initiation: bacterial-like general initiation factors mIF2 and mIF3, as well as mitochondria-specific components – mRNA-specific translational activators and mRNA-nonspecific accessory initiation factors. We consider how the fast rate of evolution in these organelles has not only created a system that is divergent from that of its bacterial ancestors, but has led to a huge diversity in lineage specific mechanistic features of mitochondrial translation initiation among eukaryotes. Mitochondrially-encoded proteins are mostly respiratory chain components. The mitochondrial translation system is thus organized in a very specific way. Initiation involves mRNA-specific activators and bacteria-like initiation factors. We show that Saccharomyces cerevisiae Aim23p is a functional ortholog of bacterial IF3. We review the lineage specific features of mitochondrial translation initiation.
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Affiliation(s)
- Anton Kuzmenko
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia; Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Gemma C Atkinson
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia
| | - Sergey Levitskii
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia; Department of Molecular Biology, Umeå University, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
| | - Piotr Kamenski
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia.
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Zhang H, Hu Y, Yang B, Xue F, Wang C, Kang Z, Ji W. Isolation and characterization of a wheat IF2 homolog required for innate immunity to stripe rust. Plant Cell Rep 2013; 32:591-600. [PMID: 23397275 DOI: 10.1007/s00299-013-1390-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 01/15/2013] [Indexed: 06/01/2023]
Abstract
The wheat eIF2 homolog, TaIF2, is induced by the stripe rust pathogen CYR 32 at an early stage of inoculation and is related to the innate immunity resistance level in wheat. The initiation of translation represents a critical control point in the regulation of gene expression in all organisms. We previously identified an upregulated EST S186 (EL773056) from an SSH-cDNA library of the Shaanmai 139 strain of wheat (Triticum aestivum) infected with Puccinia striiformis (Pst). In the present work, we isolated a cDNA clone and identified it as a wheat IF2 homolog. This cDNA consisted of 1,314 nucleotides and contained an open reading frame of 795 nucleotides encoding a polypeptide of 254 amino acids. The amino acids represent a conserved domain in EF-Tu, mtIF2-II, and mtIF2-Ivc. The alignment result showed that it maybe a partial cDNA of the initiation factor 2/eukaryotic initiation factor 5B (IF2/eIF5B) superfamily gene. Paradoxically, results of a Swiss-model analysis suggesting a low QMEAN Z-score implied that it was a membrane protein. Quantitative RT-PCR studies confirmed that the wheat eIF2 (TaIF2) homolog was differentially expressed in three near-isogenic lines. Critical time points for the induction of resistance by inoculation with Pst CYR32 in YrSM139-1B + YrSM139-2D immune resistance genotype occurred at 1 and 3 dpi (days post-infection). RNAi test showed that the inoculated BSMV-IF2 leaves of Shaanmai 139 showed obvious cell death after 15 days of inoculation with CYR 32. qRT-PCR analysis of the target gene in cDNA samples isolated from BSMV-IF2-Pst, BSMV-0-Pst and Pst infected leaves confirmed that the expression of TaIF2 is suppressed by BSMV-IF2 at 3 dpi. This suggested that TaIF2/eIF5B plays an important role in the mechanism of innate immunity to stripe rust pathogen.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas (Northwest A&F University), Yangling, 712100, China.
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Overcash RF, Chappell VA, Green T, Geyer CB, Asch AS, Ruiz-Echevarría MJ. Androgen signaling promotes translation of TMEFF2 in prostate cancer cells via phosphorylation of the α subunit of the translation initiation factor 2. PLoS One 2013; 8:e55257. [PMID: 23405127 PMCID: PMC3566213 DOI: 10.1371/journal.pone.0055257] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 12/27/2012] [Indexed: 01/21/2023] Open
Abstract
The type I transmembrane protein with epidermal growth factor and two follistatin motifs 2 (TMEFF2), is expressed mainly in brain and prostate. Expression of TMEFF2 is deregulated in prostate cancer, suggesting a role in this disease, but the molecular mechanism(s) involved in this effect are not clear. Although androgens promote tmeff2 transcription, androgen delivery to castrated animals carrying CWR22 xenografts increases TMEFF2 protein levels in the absence of mRNA changes, suggesting that TMEFF2 may also be post-transcriptionally regulated. Here we show that translation of TMEFF2 is regulated by androgens. Addition of physiological concentrations of dihydrotestosterone (DHT) to prostate cancer cell lines increases translation of endogenous TMEFF2 or transfected TMEFF2-Luciferase fusions, and this effect requires the presence of upstream open reading frames (uORFs) in the 5′-untranslated region (5′-UTR) of TMEFF2. Using chemical and siRNA inhibition of the androgen receptor (AR), we show that the androgen effect on TMEFF2 translation is mediated by the AR. Importantly, DHT also promotes phosphorylation of the α subunit of the translation initiation factor 2 (eIF2α) in an AR-dependent manner, paralleling the effect on TMEFF2 translation. Moreover, endoplasmic reticulum (ER) stress conditions, which promote eIF2α phosphorylation, also stimulate TMEFF2 translation. These results indicate that androgen signaling promotes eIF2α phosphorylation and subsequent translation of TMEFF2 via a mechanism that requires uORFs in the 5′-UTR of TMEFF2.
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Affiliation(s)
- Ryan F. Overcash
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
| | - Vesna A. Chappell
- Department of Anatomy and Cell Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
| | - Thomas Green
- Department of Internal Medicine, Division of Hematology/Oncology. Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
| | - Christopher B. Geyer
- Department of Anatomy and Cell Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
| | - Adam S. Asch
- Department of Internal Medicine, Division of Hematology/Oncology. Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Maria J. Ruiz-Echevarría
- Department of Anatomy and Cell Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
- Department of Internal Medicine, Division of Hematology/Oncology. Brody School of Medicine at East Carolina University, Greenville, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Madison KE, Abdelmeguid MR, Jones-Foster EN, Nakai H. A new role for translation initiation factor 2 in maintaining genome integrity. PLoS Genet 2012; 8:e1002648. [PMID: 22536160 PMCID: PMC3334882 DOI: 10.1371/journal.pgen.1002648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 02/24/2012] [Indexed: 11/25/2022] Open
Abstract
Escherichia coli translation initiation factor 2 (IF2) performs the unexpected function of promoting transition from recombination to replication during bacteriophage Mu transposition in vitro, leading to initiation by replication restart proteins. This function has suggested a role of IF2 in engaging cellular restart mechanisms and regulating the maintenance of genome integrity. To examine the potential effect of IF2 on restart mechanisms, we characterized its influence on cellular recovery following DNA damage by methyl methanesulfonate (MMS) and UV damage. Mutations that prevent expression of full-length IF2-1 or truncated IF2-2 and IF2-3 isoforms affected cellular growth or recovery following DNA damage differently, influencing different restart mechanisms. A deletion mutant (del1) expressing only IF2-2/3 was severely sensitive to growth in the presence of DNA-damaging agent MMS. Proficient as wild type in repairing DNA lesions and promoting replication restart upon removal of MMS, this mutant was nevertheless unable to sustain cell growth in the presence of MMS; however, growth in MMS could be partly restored by disruption of sulA, which encodes a cell division inhibitor induced during replication fork arrest. Moreover, such characteristics of del1 MMS sensitivity were shared by restart mutant priA300, which encodes a helicase-deficient restart protein. Epistasis analysis indicated that del1 in combination with priA300 had no further effects on cellular recovery from MMS and UV treatment; however, the del2/3 mutation, which allows expression of only IF2-1, synergistically increased UV sensitivity in combination with priA300. The results indicate that full-length IF2, in a function distinct from truncated forms, influences the engagement or activity of restart functions dependent on PriA helicase, allowing cellular growth when a DNA–damaging agent is present. Translation Initiation Factor 2 (IF2) is a bacterial protein that plays an essential role in the initiation of protein synthesis. As such, it not only has an important influence on cellular growth but also is subject to regulation in response to physiological conditions such as nutritional deprivation. Biochemical characterization of IF2's function in replicating movable genetic elements has suggested a new role in the maintenance of genome integrity, potentially regulating replication restart. The parasitic elements exploit the cellular replication restart system to duplicate themselves as they transpose to new positions of the chromosome. In this process, IF2 makes way for action of restart proteins, which assemble replication enzymes for initiation of DNA synthesis. For the bacterial cell, the restart system is the means by which it copes with accidents that result in arrest of chromosomal replication, promoting resumption of replication. We present evidence for an IF2 function associated with restart proteins, allowing chromosomal replication in the presence of DNA–damaging agents. As the IF2 function is a highly conserved one found in all organisms, the findings have implications for understanding the maintenance of genome integrity with respect to physiological status, which can be sensed by the translation apparatus.
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Affiliation(s)
| | | | | | - Hiroshi Nakai
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D.C, United States of America
- * E-mail:
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11
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Abstract
Nutrient sensing and the capacity to respond to starvation is tightly regulated as a means of cell survival. Among the features of the starvation response are induction of both translational repression and autophagy. Despite the fact that intracellular parasite like Toxoplasma gondii within a host cell predicted to be nutrient rich, they encode genes involved in both translational repression and autophagy. We therefore examined the consequence of starvation, a classic trigger of autophagy, on intracellular parasites. As expected, starvation results in the activation of the translational repression system as evidenced by elevation of phosphorylated TgIF2α (TgIF2α-P). Surprisingly, we also observe a rapid and selective fragmentation of the single parasite mitochondrion that leads irreversibly to parasite death. This profound effect was dependent primarily on the limitation of amino acids and involved signalling by the parasite TOR homologue. Notably, the effective blockade of mitochondrial fragmentation by the autophagy inhibitor 3-methyl adenine (3-MA) suggests an autophagic mechanism. In the absence of a documented apoptotic cascade in T. gondii, the data suggest that autophagy is the primary mechanism of programmed cell death in T. gondii and potentially other related parasites.
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Affiliation(s)
- Debasish Ghosh
- Department of Microbiology, Immunology and Molecular Genetics; University of Kentucky College of Medicine, Lexington KY 40536, USA
| | - Julia L. Walton
- Department of Microbiology, Immunology and Molecular Genetics; University of Kentucky College of Medicine, Lexington KY 40536, USA
| | - Paul D. Roepe
- Departments of Chemistry, Biochemistry and Cellular and Molecular Biology, Georgetown University, Washington DC. 20057, USA
| | - Anthony P. Sinai
- Department of Microbiology, Immunology and Molecular Genetics; University of Kentucky College of Medicine, Lexington KY 40536, USA
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12
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Bylund GO, Nord S, Lövgren JM, Wikström PM. Alterations in the β flap and β' dock domains of the RNA polymerase abolish NusA-mediated feedback regulation of the metY-nusA-infB operon. J Bacteriol 2011; 193:4113-22. [PMID: 21685293 PMCID: PMC3147696 DOI: 10.1128/jb.00196-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/04/2011] [Indexed: 11/20/2022] Open
Abstract
The RimM protein in Escherichia coli is important for the in vivo maturation of 30S ribosomal subunits and a ΔrimM mutant grows poorly due to assembly and translational defects. These deficiencies are suppressed partially by mutations that increase the synthesis of another assembly protein, RbfA, encoded by the metY-nusA-infB operon. Among these suppressors are mutations in nusA that impair the NusA-mediated negative-feedback regulation at internal intrinsic transcriptional terminators of the metY-nusA-infB operon. We describe here the isolation of two new mutations, one in rpoB and one in rpoC (encoding the β and β' subunits of the RNA polymerase, respectively), that increase the synthesis of RbfA by preventing NusA from stimulating termination at the internal intrinsic transcriptional terminators of the metY-nusA-infB operon. The rpoB2063 mutation changed the isoleucine in position 905 of the β flap-tip helix to a serine, while the rpoC2064 mutation duplicated positions 415 to 416 (valine-isoleucine) at the base of the β' dock domain. These findings support previously published in vitro results, which have suggested that the β flap-tip helix and β' dock domain at either side of the RNA exit tunnel mediate the binding to NusA during transcriptional pausing and termination.
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Affiliation(s)
| | | | | | - P. Mikael Wikström
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
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13
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Zorzet A, Pavlov MY, Nilsson AI, Ehrenberg M, Andersson DI. Error-prone initiation factor 2 mutations reduce the fitness cost of antibiotic resistance. Mol Microbiol 2010; 75:1299-313. [PMID: 20132454 PMCID: PMC2859245 DOI: 10.1111/j.1365-2958.2010.07057.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2010] [Indexed: 11/27/2022]
Abstract
Mutations in the fmt gene (encoding formyl methionine transferase) that eliminate formylation of initiator tRNA (Met-tRNA(i)) confer resistance to the novel antibiotic class of peptide deformylase inhibitors (PDFIs) while concomitantly reducing bacterial fitness. Here we show in Salmonella typhimurium that novel mutations in initiation factor 2 (IF2) located outside the initiator tRNA binding domain can partly restore fitness of fmt mutants without loss of antibiotic resistance. Analysis of initiation of protein synthesis in vitro showed that with non-formylated Met-tRNA(i) IF2 mutants initiated much faster than wild-type IF2, whereas with formylated fMet-tRNA(i) the initiation rates were similar. Moreover, the increase in initiation rates with Met-tRNA(i) conferred by IF2 mutations in vitro correlated well with the increase in growth rate conferred by the same mutations in vivo, suggesting that the mutations in IF2 compensate formylation deficiency by increasing the rate of in vivo initiation with Met-tRNA(i). IF2 mutants had also a high propensity for erroneous initiation with elongator tRNAs in vitro, which could account for their reduced fitness in vivo in a formylation-proficient strain. More generally, our results suggest that bacterial protein synthesis is mRNA-limited and that compensatory mutations in IF2 could increase the persistence of PDFI-resistant bacteria in clinical settings.
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Affiliation(s)
- Anna Zorzet
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityBox 582, SE-751 23 Uppsala, Sweden
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala UniversityBox 596, SE-751 24 Uppsala, Sweden
| | - Annika I Nilsson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityBox 582, SE-751 23 Uppsala, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala UniversityBox 596, SE-751 24 Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala UniversityBox 582, SE-751 23 Uppsala, Sweden
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14
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Stolboushkina EA, Nikonov OS, Garber MB. Isolation and crystallization of heterotrimeric translation initiation factor 2 from Sulfolobus solfataricus. Biochemistry (Mosc) 2009; 74:54-60. [PMID: 19232049 DOI: 10.1134/s0006297909010088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The structure of the intact heterotrimeric translation initiation factor 2 (e/aIF2) is of great interest due to its key role in the initiator tRNA delivery to the ribosome and in translation initiation regulation in eukaryotes and archaea. We have chosen aIF2 from the hyperthermophilic archaeobacterium Sulfolobus solfataricus (SsoIF2) as an object for crystallization and structural investigations. Genes of the SsoIF2 subunits alpha, beta, and gamma were cloned and superexpressed. A method for heterotrimer SsoIF2alphabetagamma purification was elaborated with at least 95% purity. Highly ordered crystals of the full-sized SsoIF2, reflecting X-rays at the resolution up to 2.8 A, were obtained for the first time.
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Affiliation(s)
- E A Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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15
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Nakakido M, Tanaka Y, Sokabe M, Tsumoto K. Thermodynamic analysis reveals that GTP binding affects the interaction between the alpha- and gamma-subunits of translation initiation factor 2. Biochem Biophys Res Commun 2008; 371:596-9. [PMID: 18381064 DOI: 10.1016/j.bbrc.2008.03.101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 03/17/2008] [Indexed: 11/17/2022]
Abstract
Eukaryotic and archaeal translation initiation factors 2, heterotrimers that consist of alpha-, beta-, and gamma-subunits, deliver methionylated initiator tRNA to a small ribosomal subunit in a manner that depends on GTP. To evaluate correlation of the function and association of the subunits, we used isothermal titration calorimetry to analyze the thermodynamics of the interactions between the alpha- and gamma-subunits in the presence or absence of a nonhydrolyzable GTP analog or GDP. The alpha-subunits bound to the gamma-subunit with large heat capacity change (DeltaC(p)) values. The DeltaH and DeltaC(p) values for the interaction between the alpha- and gamma-subunits varied in the presence of the GTP analog but not in the presence of GDP. These results suggest that the binding of both the alpha-subunit and GTP changes the conformation of the switch region of the gamma-subunit and increases the affinity of the gamma-subunit for tRNA.
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Affiliation(s)
- Makoto Nakakido
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 301 FBS-Building, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan
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16
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Gaur R, Grasso D, Datta PP, Krishna PDV, Das G, Spencer A, Agrawal RK, Spremulli L, Varshney U. A single mammalian mitochondrial translation initiation factor functionally replaces two bacterial factors. Mol Cell 2008; 29:180-90. [PMID: 18243113 DOI: 10.1016/j.molcel.2007.11.021] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 08/30/2007] [Accepted: 11/05/2007] [Indexed: 11/19/2022]
Abstract
The mechanism of translation in eubacteria and organelles is thought to be similar. In eubacteria, the three initiation factors IF1, IF2, and IF3 are vital. Although the homologs of IF2 and IF3 are found in mammalian mitochondria, an IF1 homolog has never been detected. Here, we show that bovine mitochondrial IF2 (IF2(mt)) complements E. coli containing a deletion of the IF2 gene (E. coli DeltainfB). We find that IF1 is no longer essential in an IF2(mt)-supported E. coli DeltainfB strain. Furthermore, biochemical and molecular modeling data show that a conserved insertion of 37 amino acids in the IF2(mt) substitutes for the function of IF1. Deletion of this insertion from IF2(mt) supports E. coli for the essential function of IF2. However, in this background, IF1 remains essential. These observations provide strong evidence that a single factor (IF2(mt)) in mammalian mitochondria performs the functions of two eubacterial factors, IF1 and IF2.
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Affiliation(s)
- Rahul Gaur
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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17
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Rasheedi S, Ghosh S, Suragani M, Tuteja N, Sopory SK, Hasnain SE, Ehtesham NZ. Pisum sativum contains a factor with strong homology to eIF5B. Gene 2007; 399:144-51. [PMID: 17582707 DOI: 10.1016/j.gene.2007.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 04/19/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
Immunoscreening of a cDNA expression library, prepared from 7 days old young shoots of pea (Pisum sativum), identified a novel gene comprising of 2586 bp open reading frame (ORF) with 381 bp and 532 bp 5' and 3'untranslated regions (UTRs), respectively. Sequence analysis of this gene, termed as PeIF5B, revealed striking homology to eukaryotic translation initiation factor eIF5B - a sequence homologue of prokaryotic translation initiation factor IF2. Southern blot analyses indicated that PeIF5B exists as a single copy gene in P. sativum genome. Northern blot hybridization revealed the presence of a 7 kb transcript in pea plant. In vitro translation using rabbit reticulocyte lysate system yielded a protein corresponding to 116 kDa which was higher than the calculated value of 96 kDa. Phylogenetic analyses of PeIF5B placed it closer to eIF5B from yeast, human and Drosophila. Pfam domain search analysis pointed to its likely role as a translation initiation factor. The presence of an eIF5B-like factor in a plant system will aid in better understanding of the mechanism of translation initiation in plants.
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Affiliation(s)
- Sheeba Rasheedi
- Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 076, India
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18
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Hayashi R, Ueda T, Farwell MA, Takeuchi N. Nuclear respiratory factor 2 activates transcription of human mitochondrial translation initiation factor 2 gene. Mitochondrion 2006; 7:195-203. [PMID: 17161026 DOI: 10.1016/j.mito.2006.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Revised: 10/20/2006] [Accepted: 10/26/2006] [Indexed: 11/18/2022]
Abstract
We studied the transcriptional regulation of the human mitochondrial translation initiation factor 2 (IF2mt) gene. The minimal promoter region for the human IF2mt gene contains binding sites for Nuclear Respiratory Factor 2 (NRF-2), which is often involved in the transcription of mitochondrial-related genes. Electrophoresis mobility shift assay (EMSA) analyses indicated that NRF-2alpha/beta binds to the IF2mt promoter. Reporter assays, where HEK293T cells were co-transfected with an NRF-2alpha/beta-expressing vector and/or an IF2mt promoter reporter vector, revealed that NRF-2 trans-activates the IF2mt promoter. NRF-2 sites were also found in the promoters of several other mitochondrial translation factors, which suggests NRF-2 may play a key role in the regulation of mitochondrial protein synthesis.
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Affiliation(s)
- Rippei Hayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Building FSB-401, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan
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19
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Milon P, Tischenko E, Tomšic J, Caserta E, Folkers G, La Teana A, Rodnina MV, Pon CL, Boelens R, Gualerzi CO. The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proc Natl Acad Sci U S A 2006; 103:13962-7. [PMID: 16968770 PMCID: PMC1599896 DOI: 10.1073/pnas.0606384103] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Indexed: 11/18/2022] Open
Abstract
Translational initiation factor 2 (IF2) is a guanine nucleotide-binding protein that can bind guanosine 3',5'-(bis) diphosphate (ppGpp), an alarmone involved in stringent response in bacteria. In cells growing under optimal conditions, the GTP concentration is very high, and that of ppGpp very low. However, under stress conditions, the GTP concentration may decline by as much as 50%, and that of ppGpp can attain levels comparable to those of GTP. Here we show that IF2 binds ppGpp at the same nucleotide-binding site and with similar affinity as GTP. Thus, GTP and the alarmone ppGpp can be considered two alternative physiologically relevant IF2 ligands. ppGpp interferes with IF2-dependent initiation complex formation, severely inhibits initiation dipeptide formation, and blocks the initiation step of translation. Our data suggest that IF2 has the properties of a cellular metabolic sensor and regulator that oscillates between an active GTP-bound form under conditions allowing active protein syntheses and an inactive ppGpp-bound form when shortage of nutrients would be detrimental, if not accompanied by slackening of this synthesis.
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Affiliation(s)
- Pohl Milon
- *Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
- Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany
| | - Eugene Tischenko
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Jerneja Tomšic
- *Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
- Institute of Biochemistry, Polytechnic University of “The Marche,” 60131 Ancona, Italy; and
| | - Enrico Caserta
- *Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
- Institute of Biochemistry, Polytechnic University of “The Marche,” 60131 Ancona, Italy; and
| | - Gert Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Anna La Teana
- Institute of Biochemistry, Polytechnic University of “The Marche,” 60131 Ancona, Italy; and
| | - Marina V. Rodnina
- Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany
| | - Cynthia L. Pon
- *Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Claudio O. Gualerzi
- *Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
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20
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Spencer AC, Spremulli LL. The interaction of mitochondrial translational initiation factor 2 with the small ribosomal subunit. Biochim Biophys Acta 2005; 1750:69-81. [PMID: 15935986 DOI: 10.1016/j.bbapap.2005.03.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 03/03/2005] [Accepted: 03/07/2005] [Indexed: 10/25/2022]
Abstract
Bovine mitochondrial translational initiation factor 2 (IF-2(mt)) is organized into four domains, an N-terminal domain, a central G-domain and two C-terminal domains. These domains correspond to domains III-VI in the six-domain model of Escherichia coli IF-2. Variants in IF-2(mt) were prepared and tested for their abilities to bind the small (28S) subunit of the mitochondrial ribosome. The binding of wild-type IF-2(mt) was strong (K(d) approximately 10-20 nM) and was not affected by fMet-tRNA. Deletion of the N-terminal domain substantially reduced the binding of IF-2(mt) to 28S subunits. However, the addition of fMet-tRNA stimulated the binding of this variant at least 2-fold demonstrating that contacts between fMet-tRNA and IF-2(mt) can stabilize the binding of this factor to 28S subunits. No binding was observed for IF-2(mt) variants lacking the G-domain which probably plays a critical role in organizing the structure of IF-2(mt). IF-2(mt) contains a 37-amino acid insertion region between domains V and VI that is not found in the prokaryotic factors. Mutations in this region caused a significant reduction in the ability of the factor to promote initiation complex formation and to bind 28S subunits.
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Affiliation(s)
- Angela C Spencer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
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21
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Christensen H, Bisgaard M, Angen O, Frederiksen W, Olsen JE. Characterization of sucrose-negative Pasteurella multocida variants, including isolates from large-cat bite wounds. J Clin Microbiol 2005; 43:259-70. [PMID: 15634981 PMCID: PMC540169 DOI: 10.1128/jcm.43.1.259-270.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To validate the identification of Pasteurella multocida-like bacteria negative for acid formation from sucrose, including isolates from bite wounds caused by large cats, 17 strains were phenotypically and genotypically characterized. Phylogenetic analysis of partially sequenced rpoB and infB genes showed the monophyly of the strains characterized and the reference strains of P. multocida. The sucrose-negative strains formed two groups, one related to reference strains of P. multocida and the other related to a separate species-like group (taxon 45 of Bisgaard). DNA-DNA hybridization further documented the species-like nature of this group. Ribotyping showed the heterogeneity of all strains except four strains that shared the same ribotype and that were isolated from bovine lungs. Phylogenetic analysis by 16S rRNA sequence comparison showed the monophyly of the strains characterized and the reference strains of P. multocida. Two strains isolated from leopard bite wounds were related to the type strain of P. dagmatis; however, they represented a new taxon (taxon 46 of Bisgaard), in accordance with their distinct phenotypic and genotypic identifications. The present study documents that sucrose-negative strains of P. multocida-like bacteria belong to two genotypically distinct groups. The study further confirms the phenotypic heterogeneity of P. multocida strains and documents two new species-like taxa of Pasteurella related to P. multocida. Until diagnostic tools have been further elaborated, special care should be taken in the identification of Pasteurella-like bacteria isolated from bite wounds caused by large cats. The evidence of phenotypic and genotypic divergence calls for the further development of PCR tests and DNA sequencing to document doubtful isolates.
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Affiliation(s)
- Henrik Christensen
- Department of Veterinary Pathobiology, The Royal Danish Veterinary and Agricultural University, Stigbøjlen 4, 1870 Frederiksberg C, Denmark.
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22
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Christensen H, Kuhnert P, Olsen JE, Bisgaard M. Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol 2005; 54:1601-1609. [PMID: 15388716 DOI: 10.1099/ijs.0.03018-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. The monophyly of representatives of the genus Gallibacterium was recognized by analysis of all housekeeping genes, while members of Mannheimia, Actinobacillus sensu stricto and the core group of Pasteurella sensu stricto formed monophyletic groups with two out of three housekeeping genes. Representatives of Mannheimia, Actinobacillus sensu stricto, [Haemophilus] ducreyi and [Pasteurella] trehalosi formed a monophyletic unit by analysis of all three housekeeping genes, which was in contrast to the 16S rRNA gene-derived phylogeny, where these taxa occurred at separate positions in the phylogenetic tree. Representatives of the Rodent, Avian and Aphrophilus-Haemophilus 16S rRNA gene groups were weakly supported by phylogenetic analysis of housekeeping genes. Phylogenies derived by comparison of the housekeeping genes diverged significantly from the 16S rRNA gene-derived phylogeny as evaluated by the likelihood ratio test. A low degree of congruence was also observed between the individual housekeeping gene-derived phylogenies. Estimates on speciation derived from 16S rRNA and housekeeping gene sequence comparisons resulted in quite different evolutionary scenarios for members of the Pasteurellaceae. The phylogeny based on the housekeeping genes supported observed host associations between Mannheimia, Actinobacillus sensu stricto and [Pasteurella] trehalosi and animals with paired hooves.
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MESH Headings
- Actinobacillus/genetics
- Bacterial Proteins/genetics
- Biological Evolution
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA-Directed RNA Polymerases/genetics
- Genes, Bacterial
- Genes, rRNA
- Haemophilus/genetics
- Mannheimia/genetics
- Molecular Sequence Data
- Pasteurella/genetics
- Pasteurellaceae/classification
- Pasteurellaceae/genetics
- Phylogeny
- Prokaryotic Initiation Factor-2/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Transcription Factors/genetics
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Affiliation(s)
- Henrik Christensen
- Department of Veterinary Microbiology, Stigbøjlen 4, Royal Danish Veterinary and Agricultural University, 1870 Frederiksberg C, Denmark
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, University of Bern, Laenggass-Strasse 122, CH-3012 Bern, Switzerland
| | - John Elmerdahl Olsen
- Department of Veterinary Microbiology, Stigbøjlen 4, Royal Danish Veterinary and Agricultural University, 1870 Frederiksberg C, Denmark
| | - Magne Bisgaard
- Department of Veterinary Microbiology, Stigbøjlen 4, Royal Danish Veterinary and Agricultural University, 1870 Frederiksberg C, Denmark
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23
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Layfield LJ, Willmore-Payne C, Shimada H, Holden JA. Assessment of NMYC amplification: a comparison of FISH, quantitative PCR monoplexing and traditional blotting methods used with formalin-fixed, paraffin-embedded neuroblastomas. Anal Quant Cytol Histol 2005; 27:5-14. [PMID: 15794447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
OBJECTIVE To determine the degree of agreement between fluorescence in situ hybridization (FISH), Southern blot analysis and LightCycler monoplex polymerase chain reaction (PCR) analysis in the assessment of NMYC gene amplification status in neuroblastoma. STUDY DESIGN We performed a retrospective analysis of NMYC amplification, using FISH, LightCycler monoplex PCR and Southern blot techniques to assess NMYC amplification in a series of 18 neuroblastomas and 20 histologically normal tissues (15 lymph nodes, 2 pancreas specimens, 1 section each of thyroid, prostate and uterus). RESULTS Nine neuroblastomas were NMYC amplified, and the remaining cases were nonamplified. All cases yielded interpretable results by Southern blotting and PCR monoplexing techniques. A single case of neuroblastoma was difficult to interpret by FISH due to high background debris. A single case demonstrated low-level NMYC amplification by LightCycler PCR monoplexing but was nonamplified by the other 2 techniques. FISH analysis in 1 case showed amplification, while the other 2 techniques demonstrated nonamplified status. The case in which FISH analysis incorrectly demonstrated amplification was the same one in which there was high background debris. The Southern blot results were reported as amplified or nonamplified, while numeric amplification ratios were obtained by both FISH and PCR LightCycler monoplex analysis. Comparison of these techniques demonstrated FISH to underestimate the degree of amplification in cases in which the amplification level was high by PCR. In fact, FISH appeared to saturate at amplification ratios > 10. CONCLUSION The study revealed a high level of concordance between the 3 techniques for assessment of NMYC amplification status. However, FISH analysis has the advantage of allowing concurrent assessment of NMYC amplification status and architecture. LightCycler PCR monoplexing appears to have the advantage of more accurately quantitating high levels of NMYC amplification, including those amplified 20-fold or higher. Both FISH and PCR LightCycler monoplexing have the advantage of being performable on formalin-fixed, paraffin-embedded tissue.
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Affiliation(s)
- Lester J Layfield
- Department of Pathology, University of Utah School of Medicine, and ARUP Laboratories, Salt Lake City, Utah, USA.
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24
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Bohnsack JF, Whiting AA, Martinez G, Jones N, Adderson EE, Detrick S, Blaschke-Bonkowsky AJ, Bisharat N, Gottschalk M. Serotype III Streptococcus agalactiae from bovine milk and human neonatal infections. Emerg Infect Dis 2004; 10:1412-9. [PMID: 15496242 PMCID: PMC3320405 DOI: 10.3201/eid1008.030917] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Although largely unrelated, many bovine type III GBS appear to share a common ancestor with an important human clone. Streptococcus agalactiae (group B streptococcus [GBS]) causes invasive human infections and bovine mastitis. This study examined the genetic relationship between bovine and human serotype III GBS by using molecular techniques that classify human serotype III GBS into four distinct phylogenetic lineages. Bovine serotype III GBS were largely contained in two lineages, which are distinct from the two major lineages (restriction digest types III-2 and III-3) that infect human neonates. One of the bovine lineages closely resembles the human III-1 lineage, whose members occasionally cause human neonatal infections. The bovine strains in the other lineage characteristically have an initiation factor IF2 gene (infB) H allele and multilocus sequence types that are not found in human GBS strains. Evidence suggests that this “H allele” lineage is related to the human III-3 lineage. These results support the assertion that human and bovine GBS are largely unrelated and provide further insight into the genetic relation between human and bovine GBS.
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Affiliation(s)
- John F Bohnsack
- Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA.
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25
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Steiner-Mosonyi M, Creuzenet C, Keates RAB, Strub BR, Mangroo D. The Pseudomonas aeruginosa initiation factor IF-2 is responsible for formylation-independent protein initiation in P. aeruginosa. J Biol Chem 2004; 279:52262-9. [PMID: 15385567 DOI: 10.1074/jbc.m408086200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formylation of the initiator methionyl-tRNA (Met-tRNAfMet) was generally thought to be essential for initiation of protein synthesis in all eubacteria based on studies conducted primarily in Escherichia coli. However, this view of eubacterial protein initiation has changed because some bacteria have been demonstrated to have the capacity to initiate protein synthesis with the unformylated Met-tRNAfMet. Here we show that the Pseudomonas aeruginosa initiation factor IF-2 is required for formylation-independent protein initiation in P. aeruginosa, the first bacterium shown to have the ability to initiate protein synthesis with both the initiator formyl-methionyl-tRNA (fMet-tRNAfMet) and Met-tRNAfMet. The E. coli IF-2, which participates exclusively in formylation-dependent protein initiation in E. coli, was unable to facilitate utilization of Met-tRNAfMet in initiation in P. aeruginosa. However, the E. coli IF-2 was made to function in formylation-independent protein initiation in P. aeruginosa by decreasing the positive charge potential of the cleft that binds the amino end of the amino acid attached to the tRNA. Furthermore increasing the positive charge potential of this cleft in the P. aeruginosa IF-2 prevented the protein from participating in formylation-independent protein initiation. Thus, this is the first demonstration of a eubacterial IF-2 with an inherent capacity to facilitate utilization of Met-tRNAfMet in protein initiation, discounting the dogma that eubacterial IF-2 can only allow the use of fMet-tRNAfMet in protein initiation. Furthermore these findings give important clues to the basis for discriminating the initiator Met-tRNA by IF-2 and for the evolution of alternative mechanisms for discrimination.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- DNA, Bacterial/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Genetic Complementation Test
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Peptide Chain Initiation, Translational
- Prokaryotic Initiation Factor-2/chemistry
- Prokaryotic Initiation Factor-2/genetics
- Prokaryotic Initiation Factor-2/metabolism
- Protein Structure, Tertiary
- Pseudomonas aeruginosa/genetics
- Pseudomonas aeruginosa/metabolism
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- Sequence Homology, Amino Acid
- Static Electricity
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Affiliation(s)
- Marta Steiner-Mosonyi
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
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26
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Laursen BS, Kjaergaard AC, Mortensen KK, Hoffman DW, Sperling-Petersen HU. The N-terminal domain (IF2N) of bacterial translation initiation factor IF2 is connected to the conserved C-terminal domains by a flexible linker. Protein Sci 2004; 13:230-9. [PMID: 14691238 PMCID: PMC2286522 DOI: 10.1110/ps.03337604] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Bacterial translation initiation factor IF2 is a multidomain protein that is an essential component of a system for ensuring that protein synthesis begins at the correct codon within a messenger RNA. Full-length IF2 from Escherichia coli and seven fragments of the protein were expressed, purified, and characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) methods. Interestingly, resonances of the 6 kD IF2N domain located at the extreme N terminus of IF2 can be clearly identified within the NMR spectra of the full-length 97-kD protein. (15)N NMR relaxation rate data indicate that (1) the IF2N domain is internally well ordered and tumbles in solution in a manner that is independent of the other domains of the IF2 protein, and (2) the IF2N domain is connected to the C-terminal regions of IF2 by a flexible linker. Chemical shifts of resonances within the isolated IF2N domain do not significantly differ from those of the corresponding residues within the context of the full-length 97-kD protein, indicating that IF2N is a structurally independent unit that does not strongly interact with other regions of IF2. CD and NMR data together provide evidence that Domains I-III of IF2 have unstructured and flexible regions as well as substantial helical content; CD data indicate that the helical content of these regions decreases significantly at temperatures above 35 degrees C. The features of structurally well-ordered N- and C-terminal domains connected by a flexible linker with significant helical content are reminiscent of another translation initiation factor, IF3.
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27
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Fleming KE, Bohnsack JF, Palacios GC, Takahashi S, Adderson EE. Equivalence of high-virulence clonotypes of serotype III group B Streptococcus agalactiae (GBS). J Med Microbiol 2004; 53:505-508. [PMID: 15150329 DOI: 10.1099/jmm.0.05443-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of growth characteristics, multilocus enzyme electrophoresis, restriction digest pattern (RDP) typing and multilocus sequence typing have identified clonotypes of serotype III group B Streptococcus agalactiae (GBS) associated with invasive infection in neonates. This study sought to unify phenotypic and genotypic classifications of type III GBS strains associated with increased virulence in newborns. High-virulence clonotype (HVC) strains possessed the translation initiation factor 2 (infB) C allele, found in RDP type III-3 strains, and hybridized with the RDP type III-3-specific probe AA3.6, whereas non-HVC strains shared the infB A allele and genomic DNA from these strains did not hybridize with the AA3.6 probe. The characteristic growth lag of HVC GBS at 40 degrees C has been attributed to the presence of a heat-labile fructose-1,6-bisphosphate aldolase (Fba) enzyme in these strains. The deduced amino acid sequence of fba genes of both HVC and non-HVC strains, however, were identical. HVC and RDP type III-3 represent the same genetically related group of bacteria. The characteristic growth differences of virulent strains of type III GBS, however, are not directly attributable to differences in fba.
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Affiliation(s)
- Katherine E Fleming
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA 2Departments of Pediatrics and Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA 3Instituto Mexicano del Seguro Social, Mexico City, Mexico 4Department of Microbiology, Joshi-Eiyoh University, Sakano, Japan
| | - John F Bohnsack
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA 2Departments of Pediatrics and Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA 3Instituto Mexicano del Seguro Social, Mexico City, Mexico 4Department of Microbiology, Joshi-Eiyoh University, Sakano, Japan
| | - Geraldo C Palacios
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA 2Departments of Pediatrics and Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA 3Instituto Mexicano del Seguro Social, Mexico City, Mexico 4Department of Microbiology, Joshi-Eiyoh University, Sakano, Japan
| | - Shinji Takahashi
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA 2Departments of Pediatrics and Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA 3Instituto Mexicano del Seguro Social, Mexico City, Mexico 4Department of Microbiology, Joshi-Eiyoh University, Sakano, Japan
| | - Elisabeth E Adderson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA 2Departments of Pediatrics and Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA 3Instituto Mexicano del Seguro Social, Mexico City, Mexico 4Department of Microbiology, Joshi-Eiyoh University, Sakano, Japan
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Nørskov-Lauritsen N, Christensen H, Okkels H, Kilian M, Bruun B. Delineation of the genus Actinobacillus by comparison of partial infB sequences. Int J Syst Evol Microbiol 2004; 54:635-644. [PMID: 15143001 DOI: 10.1099/ijs.0.02785-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A 426 bp fragment of infB, a housekeeping gene that encodes translation initiation factor 2, was sequenced from 59 clinical isolates and type strains of Actinobacillus species and sequences were compared. Partial sequences of 16S rRNA genes were also obtained. By comparing infB sequences, Actinobacillus pleuropneumoniae, Actinobacillus equuli, Actinobacillus suis, Actinobacillus ureae, Actinobacillus arthritidis, Actinobacillus hominis and two unnamed genomospecies showed more than 85 % similarity to the type strain of the type species of the genus, Actinobacillus lignieresii. The taxonomic position of Actinobacillus capsulatus was unresolved; this species is more remotely related to A. lignieresii. The two species A. lignieresii and A. pleuropneumoniae could not be clearly separated by infB sequence analysis. The phylogeny of the genus Actinobacillus based on infB analysis was essentially congruent with relationships inferred from 16S rRNA sequence comparisons and DNA hybridization studies. Discrepancies were encountered with single strains or taxa at the periphery of the genus. Greater intraspecies variation was observed with infB sequences than with 16S rRNA gene sequences, with notable exceptions. The apparent subdivision of some species by 16S rRNA analysis was most likely caused by RNA operon heterogeneity.
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Affiliation(s)
- Niels Nørskov-Lauritsen
- Department of Medical Microbiology and Immunology, University of Aarhus, Aarhus, Denmark
- Department of Clinical Microbiology, Aalborg Hospital, Aalborg, Denmark
| | - Henrik Christensen
- Department of Veterinary Microbiology, The Royal Veterinary and Agricultural University, Copenhagen, Denmark
| | - Henrik Okkels
- Department of Clinical Biochemistry, Aalborg Hospital, Aalborg, Denmark
| | - Mogens Kilian
- Department of Medical Microbiology and Immunology, University of Aarhus, Aarhus, Denmark
| | - Brita Bruun
- Department of Clinical Microbiology, State Serum Institute, Copenhagen, Denmark
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29
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Sørensen HP, Sperling-Petersen HU, Mortensen KK. A favorable solubility partner for the recombinant expression of streptavidin. Protein Expr Purif 2004; 32:252-9. [PMID: 14965771 DOI: 10.1016/j.pep.2003.07.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Revised: 07/02/2003] [Indexed: 11/16/2022]
Abstract
Recombinant streptavidin is extremely difficult to express at high levels in the cytoplasm of Escherichia coli without the formation of inclusion bodies. Fusing a solubility enhancing partner to an aggregation prone protein is a widely used tool to circumvent inclusion body formation. Here, we use streptavidin as a target protein to test the properties of N-terminal fragments of translation initiation factor IF2 from E. coli as a solubility partner. Domain I (residue 1-158) of IF2 is superior to the well-established solubility partners maltose-binding protein (MBP) and NusA for soluble expression of active streptavidin. The number of active streptavidin molecules isolated by chromatography is increased threefold when domain I is used as solubility partner as compared to MBP or NusA. The relatively small size, high expressivity, and extreme solubility make domain I of IF2 an ideal partner for streptavidin and may also prevent other recombinant proteins such as ScFv antibodies from being expressed as insoluble aggregates in the cytoplasm of E. coli.
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Affiliation(s)
- Hans Peter Sørensen
- Laboratory of BioDesign, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
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30
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Abstract
Eukaryotic and archaeal initiation factors 2 (e/aIF2) are heterotrimeric proteins (alphabetagamma) carrying methionylated initiator tRNA to the small subunit of the ribosome. The three-dimensional structure of aIF2gamma from the Archaea Pyrococcus abyssi was previously solved. This subunit forms the core of the heterotrimer. The alpha and beta subunits bind the gamma, but do not interact together. aIF2gamma shows a high resemblance with elongation factor EF1-A. In this study, we characterize the role of each subunit in the binding of the methionylated initiator tRNA. Studying various aminoacyl-tRNA ligands shows that the methionyl group is a major determinant for recognition by aIF2. aIF2gamma alone is able to specifically bind Met-tRNAiMet, although with a reduced affinity as compared with the intact trimer. Site-directed mutagenesis confirms a binding mode of the tRNA molecule similar to that observed with the elongation factor. Under our assay conditions, aIF2beta is not involved in the docking of the tRNA molecule. In contrast, aIF2alpha provides the heterotrimer its full tRNA binding affinity. Furthermore, the isolated C-domain of aIF2alpha is responsible for binding of the alpha subunit to gamma. This binding involves an idiosyncratic loop of domain 2 of aIF2gamma. Association of the C-domain of aIF2alpha to aIF2gamma is enough to retrieve the binding affinity of tRNA for aIF2. The N-terminal and central domains of aIF2alpha do not interfere with tRNA binding. However, the N-domain of aIF2alpha interacts with RNA unspecifically. Based on this property, a possible contribution of aIF2alpha to formation of a productive complex between aIF2 and the small ribosomal subunit is envisaged.
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Affiliation(s)
- Laure Yatime
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France
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31
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Tibbetts AS, Oesterlin L, Chan SY, Kramer G, Hardesty B, Appling DR. Mammalian mitochondrial initiation factor 2 supports yeast mitochondrial translation without formylated initiator tRNA. J Biol Chem 2003; 278:31774-80. [PMID: 12799364 DOI: 10.1074/jbc.m304962200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Initiation of protein synthesis in mitochondria and chloroplasts is widely believed to require a formylated initiator methionyl-tRNA (fMet-tRNAfMet) in a process involving initiation factor 2 (IF2). However, yeast strains disrupted at the FMT1 locus, encoding mitochondrial methionyl-tRNA formyltransferase, lack detectable fMet-tRNAfMet but exhibit normal mitochondrial function as evidenced by normal growth on non-fermentable carbon sources. Here we show that mitochondrial translation products in Saccharomyces cerevisiae were synthesized in the absence of formylated initiator tRNA. ifm1 mutants, lacking the mitochondrial initiation factor 2 (mIF2), are unable to respire, indicative of defective mitochondrial protein synthesis, but their respiratory defect could be complemented by plasmid-borne copies of either the yeast IFM1 gene or a cDNA encoding bovine mIF2. Moreover, the bovine mIF2 sustained normal respiration in ifm1 fmt1 double mutants. Bovine mIF2 supported the same pattern of mitochondrial translation products as yeast mIF2, and the pattern did not change in cells lacking formylated Met-tRNAfMet. Mutant yeast lacking any mIF2 retained the ability to synthesize low levels of a subset of mitochondrially encoded proteins. The ifm1 null mutant was used to analyze the domain structure of yeast mIF2. Contrary to a previous report, the C terminus of yeast mIF2 is required for its function in vivo, whereas the N-terminal domain could be deleted. Our results indicate that formylation of initiator methionyl-tRNA is not required for mitochondrial protein synthesis. The ability of bovine mIF2 to support mitochondrial translation in the yeast fmt1 mutant suggests that this phenomenon may extend to mammalian mitochondria as well.
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Affiliation(s)
- Anne S Tibbetts
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
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32
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Abstract
Rapid protein synthesis in bacteria requires the G proteins IF2, EF-Tu, EF-G, and RF3. These factors catalyze all major steps of mRNA translation in a GTP-dependent manner. Here, it is shown how the position of peptidyl-tRNA in the ribosome and presence of its peptide control the binding and GTPase activity of these translation factors. The results explain how idling GTPase activity and negative interference between different translation factors are avoided and suggest that hybrid sites for tRNA on the ribosome play essential roles in translocation of tRNAs, recycling of class 1 release factors by RF3, and recycling of ribosomes back to a new round of initiation. We also propose a model for translocation of tRNAs in two separate steps, which clarifies the roles of EF-G.GTP and GTP hydrolysis in this process.
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Affiliation(s)
- Andrey V Zavialov
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, S-75124 Uppsala, Sweden.
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33
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Dever TE, Roll-Mecak A, Choi SK, Lee JH, Cao C, Shin BS, Burley SK. Universal translation initiation factor IF2/eIF5B. Cold Spring Harb Symp Quant Biol 2003; 66:417-24. [PMID: 12762044 DOI: 10.1101/sqb.2001.66.417] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- T E Dever
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-2716, USA
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34
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Laursen BS, de A Steffensen SA, Hedegaard J, Moreno JMP, Mortensen KK, Sperling-Petersen HU. Structural requirements of the mRNA for intracistronic translation initiation of the enterobacterial infB gene. Genes Cells 2003; 7:901-10. [PMID: 12296821 DOI: 10.1046/j.1365-2443.2002.00571.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The gene infB encodes the prokaryotic translation initiation factor IF2, a central macromolecular component in the formation of the ribosomal 70S initiation complex. In Escherichia coli, infB encodes three forms of IF2: IF2alpha, IF2beta and IF2gamma. The expression of IF2beta and IF2gamma is a tandem translation from intact infB mRNA and not merely a translation of post-transcriptionally truncated mRNA. The molecular mechanism responsible for the ribosomal recognition of the two intracistronic translation initiation sites in E. coli infB is not well characterized. RESULTS We found three different forms of IF2 in Enterobacter cloacae, Klebsiella oxytoca, Salmonella enterica, Salmonella typhimurium, and two different forms in Proteus vulgaris. We identified the intracistronic translation initiation sites of the mRNA by isolation and N-terminal sequencing of the shorter isoforms of IF2 in S. enterica and S. typhimurium. A further search in the readily available public sequence databases revealed that infB from Yersinia pestis also contains an intracistronic in-frame initiation site used for the translation of IF2beta. The base composition in a part of the 5' end of the DNA coding strand of the enterobacterial infB gene shows a strong preference for adenine (A) over thymine (T) with a maximum ratio of A-to-T around the intracistronic initiation sites. We demonstrate that the mRNA has an open structure around the ribosomal binding region. CONCLUSION Efficient intracistronic translation initiation of the infB gene is suggested to require an mRNA with this special base composition that results in an open, single-stranded structure at the ribosomal binding region.
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Affiliation(s)
- Brian Søgaard Laursen
- Laboratory of BioDesign, Department of Molecular and Structural Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
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Laursen BS, Siwanowicz I, Larigauderie G, Hedegaard J, Ito K, Nakamura Y, Kenney JM, Mortensen KK, Sperling-Petersen HU. Characterization of mutations in the GTP-binding domain of IF2 resulting in cold-sensitive growth of Escherichia coli. J Mol Biol 2003; 326:543-51. [PMID: 12559921 DOI: 10.1016/s0022-2836(02)01367-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The infB gene encodes translation initiation factor IF2. We have determined the entire sequence of infB from two cold-sensitive Escherichia coli strains IQ489 and IQ490. These two strains have been isolated as suppressor strains for the temperature-sensitive secretion mutation secY24. The mutations causing the suppression phenotype are located within infB. The only variations from the wild-type (wt) infB found in the two mutant strains are a replacement of Asp409 with Glu in strain IQ489 and an insertion of Gly between Ala421 and Gly422 in strain IQ490. Both positions are located in the GTP-binding G-domain of IF2. A model of the G-domain of E.coli IF2 is presented in. Physiological quantities of the recombinant mutant proteins were expressed in vivo in E.coli strains from which the chromosomal infB gene has been inactivated. At 42 degrees C, the mutants sustained normal cell growth, whereas a significant decrease in growth rate was found at 25 degrees C for both mutants as compared to wt IF2 expressed in the control strain. Circular dichroism spectra were recorded of the wt and the two mutant proteins to investigate the structural properties of the proteins. The spectra are characteristic of alpha-helix dominated structure, and reveal a significant different behavior between the wt and mutant IF2s with respect to temperature-induced conformational changes. The temperature-induced conformational change of the wt IF2 is a two-state process. In a ribosome-dependent GTPase assay in vitro the two mutants showed practically no activity at temperatures below 10 degrees C and a reduced activity at all temperatures up to 45 degrees C, as compared to wt IF2. The results indicate that the amino acid residues, Asp409 and Gly422, are located in important regions of the IF2 G-domain and demonstrate the importance of GTP hydrolysis in translation initiation for optimal cell growth.
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Shin BS, Maag D, Roll-Mecak A, Arefin MS, Burley SK, Lorsch JR, Dever TE. Uncoupling of initiation factor eIF5B/IF2 GTPase and translational activities by mutations that lower ribosome affinity. Cell 2002; 111:1015-25. [PMID: 12507428 DOI: 10.1016/s0092-8674(02)01171-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Translation initiation factor eIF5B/IF2 is a GTPase that promotes ribosomal subunit joining. We show that eIF5B mutations in Switch I, an element conserved in all GTP binding domains, impair GTP hydrolysis and general translation but not eIF5B subunit joining function. Intragenic suppressors of the Switch I mutation restore general translation, but not eIF5B GTPase activity. These suppressor mutations reduce the ribosome affinity of eIF5B and increase AUG skipping/leaky scanning. The uncoupling of translation and eIF5B GTPase activity suggests a regulatory rather than mechanical function for eIF5B GTP hydrolysis in translation initiation. The translational defect suggests eIF5B stabilizes Met-tRNA(i)(Met) binding and that GTP hydrolysis by eIF5B is a checkpoint monitoring 80S ribosome assembly in the final step of translation initiation.
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Affiliation(s)
- Byung-Sik Shin
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Takahashi S, Detrick S, Whiting AA, Blaschke-Bonkowksy AJ, Aoyagi Y, Adderson EE, Bohnsack JF. Correlation of phylogenetic lineages of group B Streptococci, identified by analysis of restriction-digestion patterns of genomic DNA, with infB alleles and mobile genetic elements. J Infect Dis 2002; 186:1034-8. [PMID: 12232847 DOI: 10.1086/342950] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2002] [Revised: 06/04/2002] [Indexed: 11/03/2022] Open
Abstract
Phylogenetic lineages of pathogenic Streptococcus agalactiae (group B streptococci [GBS]) can be identified by analysis of restriction-digestion patterns (RDPs) of chromosomal DNA. The purpose of the present study was to correlate GBS RDP types and (1) alleles of the highly conserved gene encoding translation-initiation factor IF2, infB, and/or (2) the inserted elements IS1548 and GBSi1. Only 1 combination of serotype and infB allele was found within each RDP type. Strains within a particular RDP type also tend to have the same inserted elements in each of 3 loci examined. A novel insertion sequence, designated "IS1563," was found within all RDP type II-2 strains. Most RDP types could be identified by a combination of serotype, infB allele, and inserted elements at each of the loci. These molecular markers can be used to identify GBS populations and to correlate RDP types and phylogenetic lineages identified by different methods.
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Affiliation(s)
- Shinji Takahashi
- Division of Microbiology, Joshi-Eiyoh University, Chiyoda, Sakado, Saitama, Japan
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