1
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Soung GY, Miller JL, Koc H, Koc EC. Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes. J Proteome Res 2009; 8:3390-402. [PMID: 19469554 DOI: 10.1021/pr900042e] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Phosphorylation of bacterial ribosomal proteins has been known for decades; however, there is still very limited information available on specific locations of the phosphorylation sites in ribosomal proteins and the role they might play in protein synthesis. In this study, we have mapped the specific phosphorylation sites in 24 Escherichia coli ribosomal proteins by tandem mass spectrometry. Detection of phosphorylation was achieved by either phosphorylation specific visualization techniques, ProQ staining, and antibodies for phospho-Ser, Thr, and Tyr; or by mass spectrometry equipped with a capability to detect addition and loss of the phosphate moiety. Enrichment by immobilized metal affinity and/or strong cation exchange chromatography was used to improve the success of detection of the low abundance phosphopeptides. We found the small subunit (30S) proteins S3, S4, S5, S7, S11, S12, S13, S18, and S21 and the large subunit (50S) proteins L1, L2, L3, L5, L6, L7/L12, L13, L14, L16, L18, L19, L21, L22, L28, and L31 to be phosphorylated at one or more residues. Potential roles for each specific site in ribosome function were deduced through careful evaluation of the given phosphorylation sites in 3D-crystal structure models of ribosomes and the previous mutational studies of E. coli ribosomal proteins.
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Affiliation(s)
- George Y Soung
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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2
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Selvam P, Murgesh N, Chandramohan M, De Clercq E, Keyaerts E, Vijgen L, Maes P, Neyts J, Ranst MV. In Vitro Antiviral Activity of some Novel Isatin Derivatives against HCV and SARS-CoV Viruses. Indian J Pharm Sci 2008; 70:91-4. [PMID: 20390088 PMCID: PMC2852069 DOI: 10.4103/0250-474x.40339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 07/23/2007] [Accepted: 01/29/2008] [Indexed: 12/29/2022] Open
Abstract
4-[(1,2-dihydro-2-oxo-3H-indol-3-ylidene)amino]-N(4,6-dimethyl-2-pyrimidiny)benzene sulphonamide and its derivatives were evaluated for antiviral activity against Pathogenic viruses such as Hepatitis C Virus and SARS-CoV in Vero and Huh 5-2 cells, respectively. The 5-fluoro derivative inhibited the HCV RNA synthesis at 6 mug/ml, without toxicity at a concentration up to 42 mug/ml in Huh 5-2 cells. Among the compounds tested SPIII-5F exhibits the 45% maximum protection against replication of SARS-CoV in Vero cells.
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Affiliation(s)
- P. Selvam
- Arulmigu Kalasalingam College of Pharmacy, Krishnankoil - 626 190, India
| | - N. Murgesh
- Institute of Pharmacology, Madurai Medical College, Madurai - 625 020, India
| | - M. Chandramohan
- Bharat Ratna Kamarajar Liver Hospital and Research Center, Madurai - 625 001, Belgium
| | - E. De Clercq
- Raga Institute for Medical Research, Katholieke Universiteit-Leuven, Minder broederstraat 10, LeuvenB-3000, Belgium
| | - E. Keyaerts
- Raga Institute for Medical Research, Katholieke Universiteit-Leuven, Minder broederstraat 10, LeuvenB-3000, Belgium
| | - L. Vijgen
- Raga Institute for Medical Research, Katholieke Universiteit-Leuven, Minder broederstraat 10, LeuvenB-3000, Belgium
| | - P. Maes
- Raga Institute for Medical Research, Katholieke Universiteit-Leuven, Minder broederstraat 10, LeuvenB-3000, Belgium
| | - J. Neyts
- Raga Institute for Medical Research, Katholieke Universiteit-Leuven, Minder broederstraat 10, LeuvenB-3000, Belgium
| | - M. V. Ranst
- Raga Institute for Medical Research, Katholieke Universiteit-Leuven, Minder broederstraat 10, LeuvenB-3000, Belgium
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3
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Grasso DG, Christian BE, Spencer A, Spremulli LL. Overexpression and purification of mammalian mitochondrial translational initiation factor 2 and initiation factor 3. Methods Enzymol 2007; 430:59-78. [PMID: 17913635 DOI: 10.1016/s0076-6879(07)30004-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two mammalian mitochondrial initiation factors have been identified. Initiation factor 2 (IF2(mt)) selects the initiator tRNA (fMet-tRNA) and promotes its binding to the ribosome. Initiation factor 3 (IF3(mt)) promotes the dissociation of the 55S mitochondrial ribosome into subunits and may play additional, less-well-understood, roles in initiation complex formation. Native bovine IF2(mt) was purified from liver a number of years ago. The yield of this factor is very low making biochemical studies difficult. The cDNA for bovine IF2(mt) was expressed in Escherichia coli under the control of the T7 polymerase promoter in a vector that provides a His(6)-tag at the C-terminus of the expressed protein. This factor was expressed in E. coli and purified by chromatography on Ni-NTA resins. The expressed protein has a number of degradation products in partially purified preparations and this factor is then further purified by high-performance liquid chromatography or gravity chromatography on anion exchange resins. IF3(mt) has never been purified from any mammalian system. However, the cDNA for this protein can be identified in the expressed sequence tag (EST) libraries. The portion of the sequence encoding the region of human IF3(mt) predicted to be present in the mitochondrially imported form of this factor was cloned and expressed in E. coli using a vector that provides a C-terminal His(6)-tag. The tagged factor is partially purified on Ni-NTA resins. However, a major proteolytic fragment arising from a defined cleavage of this protein is present in these preparations. This contaminant can be removed by a single step of high-performance liquid chromatography on a cation exchange resin. Alternatively, the mature form of IF3(mt) can be purified by two sequential passes through a gravity S-Sepharose column.
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Affiliation(s)
- Domenick G Grasso
- Department of Chemistry, University of North Carolina at Chapel Hill, USA
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4
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Bhargava K, Spremulli LL. Role of the N- and C-terminal extensions on the activity of mammalian mitochondrial translational initiation factor 3. Nucleic Acids Res 2005; 33:7011-8. [PMID: 16340009 PMCID: PMC1310894 DOI: 10.1093/nar/gki1007] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Mammalian mitochondrial translational initiation factor 3 (IF3mt) promotes initiation complex formation on mitochondrial 55S ribosomes in the presence of IF2mt, fMet-tRNA and poly(A,U,G). The mature form of IF3mt is predicted to be 247 residues. Alignment of IF3mt with bacterial IF3 indicates that it has a central region with 20–30% identity to the bacterial factors. Both the N- and C-termini of IF3mt have extensions of ∼30 residues compared with bacterial IF3. To examine the role of the extensions on IF3mt, deletion constructs were prepared in which the N-terminal extension, the C-terminal extension or both extensions were deleted. These truncated derivatives were slightly more active in promoting initiation complex formation than the mature form of IF3mt. Mitochondrial 28S subunits have the ability to bind fMet-tRNA in the absence of mRNA. IF3mt promotes the dissociation of the fMet-tRNA bound in the absence of mRNA. This activity of IF3mt requires the C-terminal extension of this factor. Mitochondrial 28S subunits also bind mRNA independently of fMet-tRNA or added initiation factors. IF3mt has no effect on the formation of these complexes and cannot dissociate them once formed. These observations have lead to a new model for the function of IF3mt in mitochondrial translational initiation.
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Affiliation(s)
| | - Linda L. Spremulli
- To whom correspondence should be addressed. Tel: +1 919 966 1567; Fax: +1 919 966 3675;
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5
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Spencer AC, Spremulli LL. The interaction of mitochondrial translational initiation factor 2 with the small ribosomal subunit. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 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] [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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6
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Spencer AC, Spremulli LL. Interaction of mitochondrial initiation factor 2 with mitochondrial fMet-tRNA. Nucleic Acids Res 2004; 32:5464-70. [PMID: 15477394 PMCID: PMC524296 DOI: 10.1093/nar/gkh886] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mammalian mitochondrial genome contains a single tRNA(Met) gene that gives rise to the initiator and elongator tRNA(Met). It is generally believed that mitochondrial protein synthesis begins with formylmethionyl-tRNA, which indicates that the formylation of mitochondrial Met-tRNA specifies its participation in initiation through its interaction with initiation factor 2 (IF-2). However, recent studies in yeast mitochondria, suggest that formylation is not required for protein synthesis. In addition, bovine IF-2(mt) could replace yeast IF-2(mt) in strains that lack fMet-tRNA which suggests that this paradigm may extend to mammalian mitochondria. Here, the importance of the formylation of mitochondrial Met-tRNA for the interaction with IF-2(mt) was investigated by measuring the ability of bovine IF-2(mt) to bind mitochondrial fMet-tRNA. In direct binding experiments, bovine IF-2(mt) has a 25-fold greater affinity for mitochondrial fMet-tRNA than Met-tRNA, using either the native mitochondrial tRNA(Met) or an in vitro transcript of bovine mitochondrial tRNA(Met). In addition, IF-2(mt) will not effectively stimulate mitochondrial Met-tRNA binding to mitochondrial ribosomes, exhibiting a 50-fold preference for fMet-tRNA over Met-tRNA in this assay. Finally, the region of IF-2(mt) responsible for the interaction with fMet-tRNA was mapped to the C2 sub-domain of domain VI of this factor.
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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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7
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Koc EC, Spremulli LL. Identification of mammalian mitochondrial translational initiation factor 3 and examination of its role in initiation complex formation with natural mRNAs. J Biol Chem 2002; 277:35541-9. [PMID: 12095986 DOI: 10.1074/jbc.m202498200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human mitochondrial translational initiation factor 3 (IF3(mt)) has been identified from the human expressed sequence tag data base. Using consensus sequences derived from conserved regions of the bacterial IF3, several partially sequenced cDNA clones were identified, and the complete sequence was assembled in silico from overlapping clones. IF3(mt) is 278 amino acid residues in length. MitoProt II predicts a 97% probability that this protein will be localized in mitochondria and further predicts that the mature protein will be 247 residues in length. The cDNA for the predicted mature form of IF3(mt) was cloned, and the protein was expressed in Escherichia coli in a His-tagged form. The mature form of IF3(mt) has short extensions on the N and C termini surrounding a region homologous to bacterial IF3. The region of IF3(mt) homologous to prokaryotic factors ranges between 21-26% identical to the bacterial proteins. Purified IF3(mt) promotes initiation complex formation on mitochondrial 55 S ribosomes in the presence of mitochondrial initiation factor 2 (IF2(mt)), [(35)S]fMet-tRNA, and either poly(A,U,G) or an in vitro transcript of the cytochrome oxidase subunit II gene as mRNA. IF3(mt) shifts the equilibrium between the 55 S mitochondrial ribosome and its subunits toward subunit dissociation. In addition, the ability of E. coli initiation factor 1 to stimulate initiation complex formation on E. coli 70 S and mitochondrial 55 S ribosomes was investigated in the presence of IF2(mt) and IF3(mt).
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Affiliation(s)
- Emine Cavdar Koc
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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8
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Yu NJ, Spremulli LL. Regulation of the activity of chloroplast translational initiation factor 3 by NH2- and COOH-terminal extensions. J Biol Chem 1998; 273:3871-7. [PMID: 9461569 DOI: 10.1074/jbc.273.7.3871] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mature form of the chloroplast translational initiation factor 3 (IF3chl) from Euglena gracilis consists of an internal region homologous to prokaryotic IF3 flanked by long NH2- and COOH-terminal extensions. Sequences in these extensions reduce the activity of the homology domain in promoting initiation complex formation with chloroplast mRNAs and 30 S ribosomal subunits. A series of deletions of the NH2- and COOH-terminal extensions of IF3chl were constructed and tested for their effects on the activity of the homology domain. About half of the inhibitory effect arises from sequences within 9 residues of the junction between the NH2-terminal extension and the homology domain. The remaining inhibitory effect is the result of sequences in the COOH-terminal extension. The equilibrium constant governing the binding of the homology domain of IF3chl to 30 S subunits is estimated to be 1.3 x 10(7) M-1. Sequences close to the junction of the NH2-terminal extension and the homology domain reduce this binding constant about 10-fold. Sequences in the COOH-terminal extension have a similar negative effect. The negative effects of these two regions are cumulative, resulting in a 100-fold reduction of the binding constant. The 9 residues at the NH2-terminal extension effectively prevent the proofreading activity of IF3chl. The entire COOH-terminal extension reduces the proofreading ability by about half. These results are discussed in terms of the proposed three-dimensional structure of the homology domain of IF3chl.
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Affiliation(s)
- N J Yu
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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9
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Woriax VL, Bullard JM, Ma L, Yokogawa T, Spremulli LL. Mechanistic studies of the translational elongation cycle in mammalian mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1352:91-101. [PMID: 9177487 DOI: 10.1016/s0167-4781(97)00002-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Polyclonal antibodies have been prepared against both components of the bovine liver mitochondrial translational elongation factor Tu and Ts complex (EF-Tu x Ts(mt)). The antibodies against EF-Tu(mt) cross-react somewhat with Escherichia coli EF-Tu and wheat germ EF-1alpha. The antibodies against EF-Ts(mt) cross-react little, if at all, with E. coli EF-Ts or with EF-Ts from Euglena gracilis chloroplasts. These polyclonal antibodies have been used to investigate the relative amounts of EF-Tu(mt) and EF-Ts(mt) in bovine liver mitochondria and in cultured cells. The results of this analysis suggest that there is a 1:1 ratio of EF-Tu(mt) to EF-Ts(mt) in mammalian mitochondria. Intermediate complexes formed during the elongation cycle of protein synthesis in bovine liver mitochondria have also been investigated. The EF-Tu x Ts(mt) complex is quite resistant to dissociation by guanine nucleotides. This complex will, however, dissociate in the presence of GTP and Phe-tRNA resulting in the formation of a ternary complex comparable to that observed in prokaryotes. Kinetic data suggest that the use of the ternary complex in chain elongation increases the rate of Phe-tRNA binding to ribosomes, suggesting that it is a true intermediate in the elongation cycle. Sucrose gradient analysis indicates that the binding of EF-Tu(mt) to ribosomes can be detected in the presence of Phe-tRNA and a non-hydrolyzable analog of GTP. These results suggest that, in contrast to previous thinking, the basic features of the elongation cycle in mammalian mitochondria are quite similar to those in prokaryotes.
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Affiliation(s)
- V L Woriax
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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10
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Xin H, Leanza K, Spremulli LL. Expression of bovine mitochondrial elongation factor Ts in Escherichia coli and characterization of the heterologous complex formed with prokaryotic elongation factor Tu. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1352:102-12. [PMID: 9177488 DOI: 10.1016/s0167-4781(97)00003-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
When bovine mitochondrial elongation factor Ts (EF-Ts(mt)) is expressed in Escherichia coli, it forms a tightly associated complex with E. coli EF-Tu (EF-Tu(Eco) x Ts(mt)). This complex is active in poly(U)-directed polymerization and this activity is inhibited by kirromycin. The EF-Tu(Eco) x Ts(mt) complex does not bind guanine nucleotides detectably and is not dissociated to a significant extent by either GDP or GTP. A portion of the EF-Tu(Eco) x Ts(mt) complex can be dissociated by aa-tRNA in the presence of GTP. The heterologous complex cannot be dissociated completely in the presence of either the 8 M urea or 8 M guanidine hydrochloride, suggesting that EF-Ts(mt) has an unusually tight interaction with E. coli EF-Tu. The EF-Tu(Eco) x Ts(mt) complex can be dissociated by denaturation using 2 M guanidine thiocyanate. Free EF-Ts(mt) can then be purified and renatured. The refolded EF-Ts(mt) is active in stimulating the activity of expressed mitochondrial EF-Tu (EF-Tu(mt)) in poly(U)-directed polymerization. Almost all the EF-Ts(mt) molecules appear to refold into a conformation which can interact with EF-Tu(mt). Protease mapping of EF-Ts(mt) indicates that the first 54 residues fold into an independent domain. Analysis of deletion derivatives of EF-Ts(mt) indicates that extensive regions of this factor are required for its tight interaction with EF-Tu.
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Affiliation(s)
- H Xin
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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11
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Lin Q, Yu NJ, Spremulli LL. Expression and functional analysis of Euglena Gracilis chloroplast initiation factor 3. PLANT MOLECULAR BIOLOGY 1996; 32:937-945. [PMID: 8980544 DOI: 10.1007/bf00020490] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A portion of a cDNA predicted to encode the mature form of Euglena gracilis chloroplast translational initiation factor 3 (IF-3chlM, molecular mass, 46 402) and the portion of this factor homologous to bacterial IF-3 (IF-3chlH, molecular mass 22 829) have been cloned and expressed in Escherichia coli as histidine-tagged proteins. The homology domain can be expressed in reasonable levels in E. coli. However, IF-3chlM is quite toxic and can only be produced in small amounts. Both forms of the chloroplast factor are associated with E. coli ribosomes. Purification procedures have been developed for both IF-3chlM and IF-3chlH using Ni-NTA affinity chromatography followed by ion exchange chromatography. IF-3chlM and IF-3chlH are active in promoting ribosome dissociation and in promoting the binding of fMet-tRNA to E. coli ribosomes. However, IF-3chlH has at least 5-fold more activity than either native IF-3chl or IF-3chlM in promoting initiation complex formation on chloroplast 30S ribosomal subunits in the presence of a mRNA carrying a natural translational initiation signal. This observation suggests that regions of IF-3chl lying outside of the homology domain may down-regulate the activity of this factor.
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Affiliation(s)
- Q Lin
- Department of Chemistry CB 3290, University of North Carolina, Chapel Hill 27599-3290, USA
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12
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Woriax VL, Spremulli GH, Spremulli LL. Nucleotide and aminoacyl-tRNA specificity of the mammalian mitochondrial elongation factor EF-Tu.Ts complex. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1307:66-72. [PMID: 8652669 DOI: 10.1016/0167-4781(95)00240-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The bovine mitochondrial elongation factor Tu.Ts complex (EF-Tu.Tsmt) promotes the binding of aminoacyl-tRNA to ribosomes. In the presence of GTP, this complex functions catalytically. Both dGTP and ddGTP can replace GTP although about 4-fold higher concentrations are required. ATP, CTP and UTP are not active. ITP can replace GTP when used at 10- to 20-fold higher concentrations. The catalytic use of EF-Tu.Tsmt is inhibited by GDP but not by GMP. XDP also inhibits although about 20-fold higher concentrations are required. EF-Tu.Tsmt will promote the binding of Phe-tRNA to either Escherichia coli or mitochondrial ribosomes. Unlike E. coli EF-Tu, EF-Tu.Tsmt will promote the binding of AcPhe-tRNA to ribosomes about 25% as efficiently as Phe-tRNA. EF-Tu.Tsmt is active in catalyzing the binding of E. coli Met-tRNAmmet to ribosomes. EF-Tu.Tsmt has about 30% as much activity with E. coli Met-tRNAimet but has essentially no activity with E. coli fMet-tRNAimet. Neither yeast Met-tRNAimet nor fMet-tRNAimet is recognized by bovine EF-Tu.Tsmt.
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MESH Headings
- Acylation
- Animals
- Cattle
- Mitochondria/chemistry
- Mitochondria/genetics
- Mitochondria/metabolism
- Nucleotides/metabolism
- Peptide Elongation Factor Tu/genetics
- Peptide Elongation Factor Tu/metabolism
- Peptide Elongation Factors/genetics
- Peptide Elongation Factors/metabolism
- RNA, Fungal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Substrate Specificity
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Affiliation(s)
- V L Woriax
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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13
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Koo J, Spremulli L. Analysis of the translational initiation region on the Euglena gracilis chloroplast ribulose-bisphosphate carboxylase/oxygenase (rbcL) messenger RNA. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37313-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Schwartzbach C, Spremulli L. Interaction of animal mitochondrial EF-Tu.EF-Ts with aminoacyl-tRNA, guanine nucleotides, and ribosomes. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)55300-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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Wang CC, Roney WB, Alston RL, Spremulli LL. Initiation complex formation on Euglena chloroplast 30S subunits in the presence of natural mRNAs. Nucleic Acids Res 1989; 17:9735-47. [PMID: 2690007 PMCID: PMC335210 DOI: 10.1093/nar/17.23.9735] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An in vitro system has been developed that allows the formation of translation initiation complexes with Euglena chloroplast 30S ribosomal subunits and natural mRNAs. For these experiments two regions of the Euglena chloroplast genome have been cloned behind the T7 transcriptional promoter and the corresponding RNAs synthesized in vitro. These mRNAs are capable of forming initiation complexes with chloroplast 30S subunits in the presence of fMet-tRNA and E. coli initiation factors. Deletion of the normal translation start site results in a message that is no longer recognized by the chloroplast subunits suggesting that the correct AUG initiation codon on the mRNA is being selected by the small ribosomal subunit. Initiation complex formation with the chloroplast 30S subunits is specific for chloroplast mRNAs and mRNA from the phage MS2 is not active in this system.
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Affiliation(s)
- C C Wang
- Department of Biology, University of North Carolina, Chapel Hill 27599
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16
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17
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McGarvey P, Helling RB. Processing of chloroplast ribosomal RNA transcripts in Euglena gracilis bacillaris. Curr Genet 1989; 15:363-70. [PMID: 2507176 DOI: 10.1007/bf00419917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The ribosomal RNA operons (rrn operons) of Euglena gracilis chloroplasts contain genes for (in order) 16S rRNA, tRNA(Ile), tRNA(Ala),23S rRNA and 5S rRNA. Major sites of cleavage of the primary rrn transcript were identified by Northern blot hybridization and S1-mapping. The presumptive termini of all of the mature products have now been identified. During initial processing in the chloroplast, the primary transcript is cleaved between the two tRNAs and between the 23S and 5S rRNAs so as to separate the sequences found in the different mature rRNAs. Subsequently the tRNAs are separated from the rRNAs, further trimming provides the remaining proper ends, and the 3'-ends of the tRNAs are added.
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MESH Headings
- Animals
- Base Sequence
- Blotting, Northern
- Chloroplasts/metabolism
- DNA, Ribosomal/genetics
- Euglena gracilis/genetics
- Molecular Sequence Data
- Operon
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- Restriction Mapping
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
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Affiliation(s)
- P McGarvey
- Department of Biology, University of Michigan, Ann Arbor 48109
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18
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McGarvey P, Helling RB, Lee JY, Engelke DR, el-Gewely MR. Initiation of rrn transcription in chloroplasts of Euglena gracilis bacillaris. Curr Genet 1988; 14:493-500. [PMID: 2852069 DOI: 10.1007/bf00521275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The site of initiation of chloroplast rRNA synthesis was determined by S1-mapping and by sequencing primary rRNA transcripts specifically labeled at their 5'-end. Transcription initiates at a single site 53 nucleotides upstream of the 5'-end of the mature 16S rRNA under all growth conditions examined. The initiation site is within a DNA sequence that is highly homologous to and probably derived from a tRNA gene-region located elsewhere in the chloroplast genome. A nearly identical sequence (102 of 103 nucleotides) is present near the replication origin. The near identity of the two sequences suggests a common mode for control of transcription of the rRNA genes and initiation of chloroplast DNA replication. The related sequence in the tRNA gene-region does not appear to serve as a transcript initiation site.
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Affiliation(s)
- P McGarvey
- Department of Biology, University of Michigan, Ann Arbor 48109
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Eberly SL, Spremulli LL. Purification and characterization of the mitochondrial translocase from Euglena gracilis. Arch Biochem Biophys 1985; 243:246-53. [PMID: 3933427 DOI: 10.1016/0003-9861(85)90793-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Euglena gracilis mitochondrial protein biosynthetic elongation factor G (EF-Gmt) has been purified in four steps to greater than 50% homogeneity by use of a fusidic acid affinity procedure and conventional chromatographic techniques. The purification scheme results in 1100-fold purification with about 3% recovery of the total EF-G activity present in the postribosomal supernatant prepared from whole cell extracts. E. gracilis EF-Gmt has an approximate molecular weight of 76,000, comparable to that observed for procaryotic translocases. As is the case for other translocases which have been examined, pretreatment of E. gracilis EF-Gmt with N-ethylmaleimide results in a loss of polymerization activity, indicating a role for an essential cysteine residue in catalytic activity. GDP partially protects EF-Gmt from N-ethylmaleimide inactivation. E. gracilis EF-Gmt functions well on both Escherichia coli and E. gracilis chloroplast ribosomes, but has negligible activity on wheat germ cytoplasmic ribosomes. In this respect, it differs significantly from the mitochondrial translocase of yeast which has very little activity on chloroplast ribosomes. When assayed on E. coli ribosomes, E. gracilis EF-Gmt is sensitive to the steroid antibiotic, fusidic acid, at levels similar to that required for inactivation of E. coli EF-G. It is less sensitive than E. gracilis chloroplast EF-G, and is more sensitive than Bacillus subtilis EF-G. When assayed on E. gracilis chloroplast ribosomes, the same trends in sensitivities are observed, although the exact level of fusidic acid required for inactivation is slightly altered.
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Eberly SL, Locklear V, Spremulli LL. Bovine mitochondrial ribosomes. Elongation factor specificity. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39410-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Sreedharan SP, Beck CM, Spremulli LL. Euglena gracilis chloroplast elongation factor Tu. Purification and initial characterization. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89481-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Van Buul CP, Hamersma M, Visser W, Van Knippenberg PH. Partial methylation of two adjacent adenosines in ribosomes from Euglena gracilis chloroplasts suggests evolutionary loss of an intermediate stage in the methyl-transfer reaction. Nucleic Acids Res 1984; 12:9205-8. [PMID: 6440121 PMCID: PMC320449 DOI: 10.1093/nar/12.23.9205] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Bacterial, cytoplasmic and organellar ribosomes from a wide phylogenetic spectrum of organisms have a characteristic m6(2)Am6(2)A structure near the 3' end of the RNA of the small ribosomal subunit (SSU). We have studied one of the few exceptions to this extremely conserved post-transcriptionally modified sequence, i.e. dimethylation of only one of the two A's in chloroplasts from Euglena gracilis. It was established that only the A closest to the 5' end is dimethylated, the other one being unmodified. The methylation reaction was studied in vitro using ribosomes from a kasugamycin resistant mutant (ksgA) of Escherichia coli and purified methyl-transferase. Using limited amounts of the methyl donor S-adenosylmethionine (SAM) a partial level of methylation (50% of control) was attained. It is shown that in this case the 3' proximal A is dimethylated while the other is not. This suggests that dimethylation takes place in two successive stages. Apparently in E. gracilis chloroplasts the first stage of methylation does not occur.
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Structural differences between ribosomes of various eukaryotes: stability, density, mass, size and structure in solution of cytoplasmic ribosomes from Tetrahumena, Artemia and Euglena. Int J Biol Macromol 1983. [DOI: 10.1016/0141-8130(83)90061-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Graves MC, Spremulli LL. Activity of Euglena gracilis chloroplast ribosomes with procaryotic and eucaryotic initiation factors. Arch Biochem Biophys 1983; 222:192-9. [PMID: 6404223 DOI: 10.1016/0003-9861(83)90516-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A method that permits the preparation of Euglena gracilis chloroplast 30 S ribosomal subunits that are largely free of endogenous initiation factors and that are active in the binding of fMet-tRNA in response to poly(A, U, G), has been developed. These 30 S subunits have been tested for activity in initiation complex formation with initiation factors from both procaryotes and eucaryotes. We have observed that Escherichia coli IF-2 binds fMet-tRNA nearly as well to Euglena chloroplast ribosomal subunits as it does to its homologous subunits. Neither wheat germ eIF-2 nor Euglena eIF-2A can bind fMet-tRNA efficiently to Euglena chloroplast or E. coli 30 S subunits although both are active with wheat germ 40 S ribosomal subunits. Euglena chloroplast 68 S ribosomes will also bind the initiator tRNA. Both E. coli IF-2 and E. coli IF-3 stimulate this reaction on chloroplast ribosomes with approximately the same efficiency as they do on their homologous ribosomes. E. coli IF-1 enhances the binding of fMet-tRNA to the chloroplast 68 S ribosomes when either IF-2 or IF-3 is limiting. The chloroplast ribosomes unlike E. coli ribosomes show considerable activity over a broad range of Mg2+ ion concentrations.
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Steege DA, Graves MC, Spremulli LL. Euglena gracilis chloroplast small subunit rRNA. Sequence and base pairing potential of the 3' terminus, cleavage by colicin E3. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34037-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Beck CM, Spremulli LL. Purification of Euglena EF-1l: a cytoplasmic factor that also functions on procaryotic and organellar ribosomes. Arch Biochem Biophys 1982; 215:414-24. [PMID: 6920262 DOI: 10.1016/0003-9861(82)90101-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Spremulli LL. Chloroplast elongation factor Tu: evidence that it is the product of a chloroplast gene in Euglena. Arch Biochem Biophys 1982; 214:734-41. [PMID: 6807200 DOI: 10.1016/0003-9861(82)90080-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Slobin LI. The inhibition of eucaryotic protein synthesis by procaryotic elongation factor Tu. Biochem Biophys Res Commun 1981; 101:1388-95. [PMID: 7030339 DOI: 10.1016/0006-291x(81)91601-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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