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Koc EC, Hunter CA, Koc H. Phosphorylation of mammalian mitochondrial EF-Tu by Fyn and c-Src kinases. Cell Signal 2023; 101:110524. [PMID: 36379377 DOI: 10.1016/j.cellsig.2022.110524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 11/14/2022]
Abstract
Src Family Kinases (SFKs) are tyrosine kinases known to regulate glucose and fatty acid metabolism as well as oxidative phosphorylation (OXPHOS) in mammalian mitochondria. We and others discovered the association of the SFK kinases Fyn and c-Src with mitochondrial translation components. This translational system is responsible for the synthesis of 13 mitochondrial (mt)-encoded subunits of the OXPHOS complexes and is, thus, essential for energy generation. Mitochondrial ribosomal proteins and various translation elongation factors including Tu (EF-Tumt) have been identified as possible Fyn and c-Src kinase targets. However, the phosphorylation of specific residues in EF-Tumt by these kinases and their roles in the regulation of protein synthesis are yet to be explored. In this study, we report the association of EF-Tumt with cSrc kinase and mapping of phosphorylated Tyr (pTyr) residues by these kinases. We determined that a specific Tyr residue in EF-Tumt at position 266 (EF-Tumt-Y266), located in a highly conserved c-Src consensus motif is one of the major phosphorylation sites. The potential role of EF-Tumt-Y266 phosphorylation in regulation of mitochondrial translation investigated by site-directed mutagenesis. Its phosphomimetic to Glu residue (EF-Tumt-E266) inhibited ternary complex (EF-Tumt•GTP•aatRNA) formation and translation in vitro. Our findings along with data mining analysis of the c-Src knock out (KO) mice proteome suggest that the SFKs have possible roles for regulation of mitochondrial protein synthesis and oxidative energy metabolism in animals.
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Affiliation(s)
- Emine C Koc
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, United States of America.
| | - Caroline A Hunter
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, United States of America
| | - Hasan Koc
- Department of Pharmacological Science, School of Pharmacy, Marshall University, Huntington, WV 25755, United States of America.
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2
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Créchet JB, Malosse C, Hountondji C. EF-Tu from the enacyloxin producing Frateuria W-315 strain: Structure/activity relationship and antibiotic resistance. Biochimie 2016; 127:59-69. [PMID: 27126073 DOI: 10.1016/j.biochi.2016.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
In this report, we have demonstrated that the poly(U)-dependent poly(Phe) synthesis activity of elongator factor Tu (EF-Tu) from the enacyloxin producing strain Frateuria sp. W-315 is inhibited by the antibiotic similarly to that of Escherichia coli EF-Tu. The inhibitory effect of enacyloxin observed in a purified system was the same as that obtained with an S30 extract from E. coli or Frateuria sp. W-315, respectively, suggesting that antibiotic resistance of enacyloxin producing Frateuria sp. W-315 is not due neither to EF-Tu nor to other components of the translation machinery but to a still unknown mechanism. The EF-Tu gene, as PCR amplified from Frateuria W-315 genomic DNA and sequenced represented an ORF of 1191 nucleotides corresponding to 396 amino acids. This protein is larger than the product of tufA from E. coli by only two amino acid residues. Alignment of the amino acid sequence of EF-Tu from E. coli with those of Frateuria and Ralstonia solanacearum indicates on average 80% identical amino acid residues and 9.7% conservative replacements between EF-Tu Frateuria and EF-Tu E. coli, on one hand, and 97% identity and 1.7% conservative replacement between EF-Tu Frateuria and EF-Tu Ralstonia solanacearum, on the other hand. These strong primary structure similarities between EF-Tu from different origins are consistent with the fact that this factor is essential for the translation process in all kingdoms of life. Comparison of the effects of antibiotics on EF-Tu Frateuria and EF-Tu E. coli revealed that enacyloxin, kirromycin and pulvomycin exert a stronger stimulation of the GDP dissociation rate on EF-Tu Frateuria, while the effects of the antibiotics on the GDP association rate were comparable for the two EF-Tu species. Different mutants of EF-Tu E. coli were constructed with the help of site directed mutagenesis by changing one or several residues of EF-Tu E. coli by the corresponding residues of EF-Tu Frateuria. The single A45K substitution did not modify the intrinsic GTPase activity of EF-Tu E. coli. In contrast, a 2-3 fold stimulation of the intrinsic GTPase activity was observed with the single A42E, F46Y, Q48E and the double F46Y/Q48E substitution. Finally, up to a 7 fold stimulation was observed with the quadruple substitution (mutant A42E/A45K/F46Y/Q48E.
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Affiliation(s)
| | - Christian Malosse
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, 28 rue du Dr Roux, 75724 PARIS Cedex 15 France
| | - Codjo Hountondji
- Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 4, Place Jussieu, F-75252 Paris Cedex 05, France
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3
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Ahn KY, Lee B, Han KY, Song JA, Lee DS, Lee J. Synthesis of Mycoplasma arginine deiminase in E. coli using stress-responsive proteins. Enzyme Microb Technol 2014; 63:46-9. [DOI: 10.1016/j.enzmictec.2014.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 11/26/2022]
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Hountondji C, Bulygin K, Créchet JB, Woisard A, Tuffery P, Nakayama JI, Frolova L, Nierhaus KH, Karpova G, Baouz S. The CCA-end of P-tRNA Contacts Both the Human RPL36AL and the A-site Bound Translation Termination Factor eRF1 at the Peptidyl Transferase Center of the Human 80S Ribosome. Open Biochem J 2014; 8:52-67. [PMID: 25191528 PMCID: PMC4150381 DOI: 10.2174/1874091x01408010052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/07/2014] [Accepted: 03/09/2014] [Indexed: 11/26/2022] Open
Abstract
We have demonstrated previously that the E-site specific protein RPL36AL present in human ribosomes can be crosslinked with the CCA-end of a P-tRNA in situ. Here we report the following: (i) We modeled RPL36AL into the structure of the archaeal ortholog RPL44E extracted from the known X-ray structure of the 50S subunit of Haloarcula marismortui. Superimposing the obtained RPL36AL structure with that of P/E tRNA observed in eukaryotic 80S ribosomes suggested that RPL36AL might in addition to its CCA neighbourhood interact with the inner site of the tRNA elbow similar to an interaction pattern known from tRNA•synthetase pairs. (ii) Accordingly, we detected that the isolated recombinant protein RPL36AL can form a tight binary complex with deacylated tRNA, and even tRNA fragments truncated at their CCA end showed a high affinity in the nanomolar range supporting a strong interaction outside the CCA end. (iii) We constructed programmed 80S complexes containing the termination factor eRF1 (stop codon UAA at the A-site) and a 2’,3’-dialdehyde tRNA (tRNAox) analog at the P-site. Surprisingly, we observed a crosslinked ternary complex containing the tRNA, eRF1 and RPL36AL crosslinked both to the aldehyde groups of tRNAox at the 2’- and 3’-positions of the ultimate A. We also demonstrated that, upon binding to the ribosomal A-site, eRF1 induces an alternative conformation of the ribosome and/or the tRNA, leading to a novel crosslink of tRNAox to another large-subunit ribosomal protein (namely L37) rather than to RPL36AL, both ribosomal proteins being labeled in a mutually exclusive fashion. Since the human 80S ribosome in complex with P-site bound tRNAox and A-site bound eRF1 corresponds to the post-termination state of the ribosome, the results represent the first biochemical evidence for the positioning of the CCA-arm of the P-tRNA in close proximity to both RPL36AL and eRF1 at the end of the translation process.
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Affiliation(s)
- Codjo Hountondji
- Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 2, Place Jussieu, F-75252 Paris Cedex 05, France
| | - Konstantin Bulygin
- Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 2, Place Jussieu, F-75252 Paris Cedex 05, France ; Institute of Chemical Biology and Fundamental Medecine, Siberian Branch of the Russian Academy of Sciences, pr Lavrentieva, 8, 630090 Novosibirsk, Russia
| | | | - Anne Woisard
- Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 2, Place Jussieu, F-75252 Paris Cedex 05, France
| | - Pierre Tuffery
- Université Denis Diderot-Paris 7, INSERM-UMR-S973 and RPBS, France
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501, Japan
| | - Ludmila Frolova
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| | - Knud H Nierhaus
- Charité, Institut für Medizinische Physik und Biophysic, Charitéplatz 1. D-10117 Berlin, Germany
| | - Galina Karpova
- Institute of Chemical Biology and Fundamental Medecine, Siberian Branch of the Russian Academy of Sciences, pr Lavrentieva, 8, 630090 Novosibirsk, Russia
| | - Soria Baouz
- Sorbonne Universités UPMC Univ Paris 06, Unité de Recherche UPMC UR6 "Enzymologie de l'ARN", 2, Place Jussieu, F-75252 Paris Cedex 05, France
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Gunasekaran K, Bergquist PL, Sunna A. Facile production and rapid purification of functional recombinant Qβ replicase heterotetramer complex. Appl Biochem Biotechnol 2012; 169:651-9. [PMID: 23269632 DOI: 10.1007/s12010-012-0018-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/04/2012] [Indexed: 11/25/2022]
Abstract
We describe an improved method for the production of recombinant Qβ replicase heterotetramer. The successful expression of the soluble Qβ RNA polymerase complex depends on the EF-Ts and EF-Tu subunits being co-expressed prior to β-subunit expression. Efficient co-expression requires two different inducible operons to co-ordinate the expression of the heterotrimer. The complete heterotetramer enzyme complex is achieved by production of the recombinant S1-subunit of Qβ replicase in a separate host. This approach represents a facile way for producing and purifying large amounts of soluble and active recombinant Qβ replicase tetramer without the necessity of a His-tag for purification.
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Affiliation(s)
- Karthikeyan Gunasekaran
- Department of Chemistry and Biomolecular Sciences, and Environmental Biotechnology CRC, Macquarie University, North Ryde, 2109 Sydney, NSW, Australia
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6
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Ceylan S, Yilan G, Akbulut BS, Poli A, Kazan D. Interplay of adaptive capabilities of Halomonas sp. AAD12 under salt stress. J Biosci Bioeng 2012; 114:45-52. [DOI: 10.1016/j.jbiosc.2012.02.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 10/28/2022]
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7
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Cogo K, de Andrade A, Labate CA, Bergamaschi CC, Berto LA, Franco GCN, Gonçalves RB, Groppo FC. Proteomic analysis ofPorphyromonas gingivalisexposed to nicotine and cotinine. J Periodontal Res 2012; 47:766-75. [DOI: 10.1111/j.1600-0765.2012.01494.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Xu C, Wang J, Li J, Fang R. Expression of elongation factor (EF)-Tu is correlated with prognosis of gastric adenocarcinomas. Int J Mol Sci 2011; 12:6645-55. [PMID: 22072909 PMCID: PMC3211000 DOI: 10.3390/ijms12106645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/16/2011] [Accepted: 09/22/2011] [Indexed: 12/21/2022] Open
Abstract
Altered expressions of mitochondria elongation factor Tu (EF-Tu) have been observed in certain types of cancers, including gastric cancer cell lines, but the impact of the alterations in gastric adenocarcinoma remains unclear. The purpose of this study was to investigate the expression of EF-Tu in gastric adenocarcinoma and to assess its clinical significance. A total of 104 paired resected gastric adenocarcinoma and corresponding normal specimens were collected in this study. EF-Tu expression was assessed by immunohistochemical staining. The correlation of EF-Tu expression and patients’ clinicopathological parameters was statically evaluated and the prognostic significance of EF-Tu expression was assessed by univariate and multivariate analyses. Forty-nine out of 104 (47.1%) gastric adenocarcinoma specimens showed high expression of EF-Tu, while the remaining 55 specimens showed weak or negative expression of EF-Tu. In contrast, EF-Tu high expression was detected in 62.5% (65 of 104) normal tissues. Down-regulation of EF-Tu was associated with serosal invasion (P = 0.042) and node involvement (P = 0.005), and down-regulation of EF-Tu was correlated with poor overall survival (P = 0.020). In curative resection (R0) patients, there were also significant differences (P = 0.043). In the multivariate analysis, the EF-Tu expression remained a significant independent prognostic factor (P = 0.038). Our results indicate that EF-Tu is expressed in both gastric adenocarcinoma and corresponding normal tissues. Down-regulation of EF-Tu expression is associated with advanced disease stage and EF-Tu expression maybe served as an independent prognostic factor.
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Affiliation(s)
- Chaoyang Xu
- Department of Breast and Thyroid Surgery, Shaoxing People’s Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang, 312000, China
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-571-86006912; Fax: +86-571-86044817
| | - Jianjun Wang
- Department of Surgical Oncology, The Chunan County First Hospital, Chunan, Zhejiang, 311700, China; E-Mails: (J.W.); (R.F.)
| | - Jiajia Li
- Department of Surgery, Shaoxing People’s Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang, 312000, China; E-Mail: (J.L.)
| | - Rengui Fang
- Department of Surgical Oncology, The Chunan County First Hospital, Chunan, Zhejiang, 311700, China; E-Mails: (J.W.); (R.F.)
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9
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Lery LMS, Hemerly AS, Nogueira EM, von Krüger WMA, Bisch PM. Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:562-576. [PMID: 21190439 DOI: 10.1094/mpmi-08-10-0178] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Gluconacetobacter diazotrophicus is a plant-growth-promoting bacterium that colonizes sugarcane. In order to investigate molecular aspects of the G. diazotrophicus-sugarcane interaction, we performed a quantitative mass spectrometry-based proteomic analysis by (15)N metabolic labeling of bacteria, root samples, and co-cultures. Overall, more than 400 proteins were analyzed and 78 were differentially expressed between the plant-bacterium interaction model and control cultures. A comparative analysis of the G. diazotrophicus in interaction with two distinct genotypes of sugarcane, SP70-1143 and Chunee, revealed proteins with fundamental roles in cellular recognition. G. diazotrophicus presented proteins involved in adaptation to atypical conditions and signaling systems during the interaction with both genotypes. However, SP70-1143 and Chunee, sugarcane genotypes with high and low contribution of biological nitrogen fixation, showed divergent responses in contact with G. diazotrophicus. The SP70-1143 genotype overexpressed proteins from signaling cascades and one from a lipid metabolism pathway, whereas Chunee differentially synthesized proteins involved in chromatin remodeling and protein degradation pathways. In addition, we have identified 30 bacterial proteins in the roots of the plant samples; from those, nine were specifically induced by plant signals. This is the first quantitative proteomic analysis of a bacterium-plant interaction, which generated insights into early signaling of the G. diazotrophicus-sugarcane interaction.
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Affiliation(s)
- Letícia M S Lery
- Unidade Multidisciplinar de Genômica, Instituto de Biofísica Carlos Chagas Filho da Universidade Federal do Rio de Janeiro, Brazil.
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10
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Ceylan S, Akbulut BS, Denizci AA, Kazan D. Proteomic insight into phenolic adaptation of a moderately halophilicHalomonassp. strain AAD12. Can J Microbiol 2011; 57:295-302. [DOI: 10.1139/w11-009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A gram-negative, moderately halophilic bacterium was isolated from Çamaltı Saltern area, located in the Aegean Region of Turkey. Analysis of its 16S rRNA gene sequence and physiological characteristics showed that this strain belonged to the genus Halomonas ; hence, it was designated as Halomonas sp. strain AAD12. The isolate tolerated up to 800 mg⋅L–1phenol; however, at elevated concentrations, phenol severely retarded cell growth. The increase in lag phase with increasing phenol concentrations indicated that the microorganism was undergoing serious adaptative changes. To understand the physiological responses of Halomonas sp. strain AAD12 to phenol, a 2-dimensional electrophoresis approach combined with mass spectrometric analysis was used. This approach showed that the expression of 14 protein spots were altered as phenol concentration increased from 200 to 800 mg⋅L–1. Among the identified proteins were those involved in protein biosynthesis, energy, transport, and stress metabolism. So far, this is the first study on phenolic adaptation of a gram-negative, moderately halophilic bacteria using proteomic tools. The results provided new insights for understanding the general mechanism used by moderately halophilic bacteria to tolerate phenol and suggested the potential for using these microorganisms in bioremediation.
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Affiliation(s)
- Selim Ceylan
- Marmara University, Engineering Faculty, Bioengineering Department, Goztepe Campus, 34722 Istanbul, Turkey
| | - Berna Sarıyar Akbulut
- Marmara University, Engineering Faculty, Bioengineering Department, Goztepe Campus, 34722 Istanbul, Turkey
| | - Aziz Akın Denizci
- TUBİTAK MRC Genetic Engineering and Biotechnology Institute, PK: 21, 41470 Gebze Kocaeli, Turkey
| | - Dilek Kazan
- Marmara University, Engineering Faculty, Bioengineering Department, Goztepe Campus, 34722 Istanbul, Turkey
- TUBİTAK MRC Genetic Engineering and Biotechnology Institute, PK: 21, 41470 Gebze Kocaeli, Turkey
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11
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Mao S, Luo Y, Zhang T, Li J, Bao G, Zhu Y, Chen Z, Zhang Y, Li Y, Ma Y. Proteome Reference Map and Comparative Proteomic Analysis between a Wild Type Clostridium acetobutylicum DSM 1731 and its Mutant with Enhanced Butanol Tolerance and Butanol Yield. J Proteome Res 2010; 9:3046-61. [DOI: 10.1021/pr9012078] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shaoming Mao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Yuanming Luo
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Tianrui Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Jinshan Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Guanhui Bao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Yan Zhu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Zugen Chen
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Yanping Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Yin Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
| | - Yanhe Ma
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, Graduate School of Chinese Academy of Sciences, Beijing, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, and Department of Human Genetics, School of Medicine, University of California, Los Angeles, California 90095
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12
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Han KY, Park JS, Seo HS, Ahn KY, Lee J. Multiple Stressor-Induced Proteome Responses of Escherichia coli BL21(DE3). J Proteome Res 2008; 7:1891-903. [DOI: 10.1021/pr700631c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kyung-Yeon Han
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Jin-Seung Park
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Hyuk-Seong Seo
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Keum-Young Ahn
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-713, South Korea
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13
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Han KY, Song JA, Ahn KY, Park JS, Seo HS, Lee J. Enhanced solubility of heterologous proteins by fusion expression using stress-induced Escherichia coli protein, Tsf. FEMS Microbiol Lett 2007; 274:132-8. [PMID: 17608803 DOI: 10.1111/j.1574-6968.2007.00824.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Through two-dimensional electrophoresis, Escherichia coli proteome response to a protein denaturant, guanidine hydrochloride, was analyzed and elongation factor Ts (Tsf) detected as a stress-induced protein. Many host proteins aggregated, or their synthesis levels decreased significantly under conditions of protein denaturation as 34 out of 699 soluble proteins knocked out and 63 proteins decreased by over 2.5-fold. Interestingly, the expression level of Tsf increased 1.61-fold compared with a nonstress condition. Contrary to direct expression, various heterologous proteins were solubly expressed in E. coli when subjected to N-terminus fusions of Tsf. Owing most likely to an intrinsic high folding efficiency, Tsf seemed to play critical roles in sequestering interactive surfaces of heterologous proteins from nonspecific protein-protein interactions leading to formation of inclusion bodies. It has been also demonstrated that Tsf is effective in aiding the production of a biologically active bacterial cutinase, which could be of interest to biotechnology and commercial applications.
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Affiliation(s)
- Kyung-Yeon Han
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
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14
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Sanderson LE, Uhlenbeck OC. Directed mutagenesis identifies amino acid residues involved in elongation factor Tu binding to yeast Phe-tRNAPhe. J Mol Biol 2007; 368:119-30. [PMID: 17328911 PMCID: PMC2246379 DOI: 10.1016/j.jmb.2007.01.075] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 01/25/2007] [Accepted: 01/28/2007] [Indexed: 11/24/2022]
Abstract
The co-crystal structure of Thermus aquaticus elongation factor Tu.guanosine 5'- [beta,gamma-imido]triphosphate (EF-Tu.GDPNP) bound to yeast Phe-tRNA(Phe) reveals that EF-Tu interacts with the tRNA body primarily through contacts with the phosphodiester backbone. Twenty amino acids in the tRNA binding cleft of Thermus Thermophilus EF-Tu were each mutated to structurally conservative alternatives and the affinities of the mutant proteins to yeast Phe-tRNA(Phe) determined. Eleven of the 20 mutations reduced the binding affinity from fourfold to >100-fold, while the remaining ten had no effect. The thermodynamically important residues were spread over the entire tRNA binding interface, but were concentrated in the region which contacts the tRNA T-stem. Most of the data could be reconciled by considering the crystal structures of both free EF-Tu.GTP and the ternary complex and allowing for small (1.0 A) movements in the amino acid side-chains. Thus, despite the non-physiological crystallization conditions and crystal lattice interactions, the crystal structures reflect the biochemically relevant interaction in solution.
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15
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Jonák J. Bacterial elongation factors EF-Tu, their mutants, chimeric forms, and domains: isolation and purification. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:141-53. [PMID: 17197255 DOI: 10.1016/j.jchromb.2006.11.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 11/14/2006] [Accepted: 11/20/2006] [Indexed: 11/24/2022]
Abstract
Prokaryotic elongation factors EF-Tu form a family of homologous, three-domain molecular switches catalyzing the binding of aminoacyl-tRNAs to ribosomes during the process of mRNA translation. They are GTP-binding proteins, or GTPases. Binding of GTP or GDP regulates their conformation and thus their activity. Because of their particular structure and regulation, various activities (also outside of the translation system) and a relative abundance they represent attractive tools for studies of many basic but still not fully understood mechanisms both of the translation process, the structure-function relationships in EF-Tu molecules themselves and proteins and energy transduction mechanisms in general. The review critically summarizes procedures for the isolation and purification of native and engineered eubacterial elongation factors EF-Tu and their mutants on a large as well as small scale. Current protocols for the purification of both native and polyHis-tagged or glutathione-S-transferase (GST)-tagged EF-Tu proteins and their variants using conventional procedures and the Ni-NTA-Agarose or Glutathione Sepharose are presented.
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Affiliation(s)
- J Jonák
- Department of Gene Expression, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 37 Prague 6, Czech Republic.
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Arena S, D'Ambrosio C, Renzone G, Rullo R, Ledda L, Vitale F, Maglione G, Varcamonti M, Ferrara L, Scaloni A. A study ofStreptococcus thermophilus proteome by integrated analytical procedures and differential expression investigations. Proteomics 2006; 6:181-92. [PMID: 16281183 DOI: 10.1002/pmic.200402109] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Streptococcus thermophilus is a Gram-positive bacterium belonging to the group of lactic acid bacteria, among which several genera play an essential role in manufacture of food products. Recently, a genomic consortium sequenced and annotated its entire genome, which has been demonstrated to contain 1900 coding sequences. In this study, we have revealed the expression products of almost 200 different genes using a proteomic strategy combining 2-DE plus MALDI-TOF PMF and differential 1-DE plus muLC-ESI-IT-MS/MS. Thus, a number of cellular pathways related to important physiological processes were described at the proteomic level. Almost 50 genes were related to multiple electrophoretic species, whose heterogeneity was mainly due to variability in pI values. A 2-DE reference map obtained for lactose-grown cells was compared with those obtained after heat, cold, acid, oxidative and starvation stresses. Protein up/down-regulation measurements demonstrated that adaptation to different environmental challenges may involve the contribution of unique as well as combined physiological mechanisms. Common regulatory sites in the promoter region of genes whose expression was induced after stress were identified. These results provide a better comprehension of biochemical processes related to stress resistance in S. thermophilus, allowing defining the molecular bases of adaptative responses or markers for the identification of strains with potential industrial applications.
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Affiliation(s)
- Simona Arena
- Proteomics & Mass Spectrometry Laboratory, I.S.P.A.A.M., National Research Council, via Argine 1085, 80147 Naples, Italy
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Chiron S, Suleau A, Bonnefoy N. Mitochondrial translation: elongation factor tu is essential in fission yeast and depends on an exchange factor conserved in humans but not in budding yeast. Genetics 2005; 169:1891-901. [PMID: 15695360 PMCID: PMC1449603 DOI: 10.1534/genetics.104.037473] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The translation elongation factor EF-Tu is a GTPase that delivers amino-acylated tRNAs to the ribosome during the elongation step of translation. EF-Tu/GDP is recycled by the guanine nucleotide exchange factor EF-Ts. Whereas EF-Ts is lacking in S. cerevisiae, both translation factors are found in S. pombe and H. sapiens mitochondria, consistent with the known similarity between fission yeast and human cell mitochondrial physiology. We constructed yeast mutants lacking these elongation factors. We show that mitochondrial translation is vital for S. pombe, as it is for human cells. In a genetic background allowing the loss of mitochondrial functions, a block in mitochondrial translation in S. pombe leads to a major depletion of mtDNA. The relationships between EF-Ts and EF-Tu from both yeasts and humans were investigated through functional complementation and coexpression experiments and by a search for suppressors of the absence of the S. pombe EF-Ts. We find that S. cerevisiae EF-Tu is functionally equivalent to the S. pombe EF-Tu/EF-Ts couple. Point mutations in the S. pombe EF-Tu can render it independent of its exchange factor, thereby mimicking the situation in S. cerevisiae.
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Affiliation(s)
- Stéphane Chiron
- Centre de Génétique Moléculaire du CNRS, Gif-sur-Yvette, France
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Len ACL, Harty DWS, Jacques NA. Stress-responsive proteins are upregulated in Streptococcus mutans during acid tolerance. Microbiology (Reading) 2004; 150:1339-1351. [PMID: 15133096 DOI: 10.1099/mic.0.27008-0] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus mutansis an important pathogen in the initiation of dental caries as the bacterium remains metabolically active when the environment becomes acidic. The mechanisms underlying this ability to survive and proliferate at low pH remain an area of intense investigation. Differential two-dimensional electrophoretic proteome analysis ofS. mutansgrown at steady state in continuous culture at pH 7·0 or pH 5·0 enabled the resolution of 199 cellular and extracellular protein spots with altered levels of expression. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry identified 167 of these protein spots. Sixty-one were associated with stress-responsive pathways involved in DNA replication, transcription, translation, protein folding and proteolysis. The 61 protein spots represented isoforms or cleavage products of 30 different proteins, of which 25 were either upregulated or uniquely expressed during acid-tolerant growth at pH 5·0. Among the unique and upregulated proteins were five that have not been previously identified as being associated with acid tolerance inS. mutansand/or which have not been studied in any detail in oral streptococci. These were the single-stranded DNA-binding protein, Ssb, the transcription elongation factor, GreA, the RNA exonuclease, polyribonucleotide nucleotidyltransferase (PnpA), and two proteinases, the ATP-binding subunit, ClpL, of the Clp family of proteinases and a proteinase encoded by thepepgene family with properties similar to the dipeptidase, PepD, ofLactobacillus helveticus. The identification of these and other differentially expressed proteins associated with an acid-tolerant-growth phenotype provides new information on targets for mutagenic studies that will allow the future assessment of their physiological significance in the survival and proliferation ofS. mutansin low pH environments.
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Affiliation(s)
- Alice C L Len
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO BOX 533, Wentworthville, NSW 2145, Australia
| | - Derek W S Harty
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO BOX 533, Wentworthville, NSW 2145, Australia
| | - Nicholas A Jacques
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO BOX 533, Wentworthville, NSW 2145, Australia
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Karring H, Mathu SGJ, van Duin J, Clark BFC, Kraal B, Knudsen CR. Qbeta-phage resistance by deletion of the coiled-coil motif in elongation factor Ts. J Biol Chem 2003; 279:1878-84. [PMID: 14583631 DOI: 10.1074/jbc.m306605200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elongation factor Ts (EF-Ts) is the guanine-nucleotide exchange factor of elongation factor Tu (EF-Tu), which promotes the binding of aminoacyl-tRNA to the mRNA-programmed ribosome in prokaryotes. The EF-Tu.EF-Ts complex, one of the EF-Tu complexes during protein synthesis, is also a component of RNA-dependent RNA polymerases like the polymerase from coliphage Qbeta. The present study shows that the Escherichia coli mutant GRd.tsf lacking the coiled-coil motif of EF-Ts is completely resistant to phage Qbeta and that Qbeta-polymerase complex formation is not observed. GRd.tsf is the first E. coli mutant ever described that is unable to form a Qbeta-polymerase complex while still maintaining an almost normal growth behavior. The phage resistance correlates with an observed instability of the mutant EF-Tu.EF-Ts complex in the presence of guanine nucleotides. Thus, the mutant EF-Tu.EF-Ts is the first EF-Tu.EF-Ts complex ever described that is completely inactive in the Qbeta-polymerase complex despite its almost full activity in protein synthesis. We propose that the role of EF-Ts in the Qbeta-polymerase complex is to control and trap EF-Tu in a stable conformation with affinity for RNA templates while unable to bind aminoacyl-tRNA.
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Affiliation(s)
- Henrik Karring
- Department of Molecular Biology, Gustav Wieds Vej 10c, University of Aarhus, DK-8000 Aarhus C, Denmark
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Mathu SGJ, Knudsen CR, van Duin J, Kraal B. Isolation of Qbeta polymerase complexes containing mutant species of elongation factor Tu. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 786:279-86. [PMID: 12651024 DOI: 10.1016/s1570-0232(02)00811-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA genome of coliphage Qbeta is replicated by a complex of four proteins, one of them being the translation elongation factor Tu. The role of EF-Tu in this RNA polymerase complex is still unclear, but the obligate presence of translationally functional EF-Tu in the cell hampers the use of conventional mutational analysis. Therefore, we designed a system based on affinity chromatography and could separate two types of complexes by placing an affinity tag on mutated EF-Tu species. Thus, we were able to show a direct link between the vital tRNA binding property of EF-Tu and polymerase activity.
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Affiliation(s)
- Sander G J Mathu
- Department of Biochemistry, LIC, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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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] [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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Krab IM, Parmeggiani A. Mechanisms of EF-Tu, a pioneer GTPase. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2003; 71:513-51. [PMID: 12102560 DOI: 10.1016/s0079-6603(02)71050-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This review considers several aspects of the function of EF-Tu, a protein that has greatly contributed to the advancement of our knowledge of both protein biosynthesis and GTP-binding proteins in general. A number of topics are described with emphasis on the function-structure relationships, in particular of EF-Tu's domains, the nucleotide-binding site, and the magnesium-binding network. Aspects related to the interaction with macromolecular ligands and antibiotics and to folding and GTPase activity are also presented and discussed. Comments and criticism are offered to draw attention to remaining discrepancies and problems.
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Affiliation(s)
- Ivo M Krab
- Laboratory of Biophysics, Ecole Polytechnique, Palaiseau, France
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Ohtsuki T, Sakurai M, Sato A, Watanabe K. Characterization of the interaction between the nucleotide exchange factor EF-Ts from nematode mitochondria and elongation factor Tu. Nucleic Acids Res 2002; 30:5444-51. [PMID: 12490713 PMCID: PMC140056 DOI: 10.1093/nar/gkf679] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Caenorhabditis elegans mitochondria have two elongation factor (EF)-Tu species, denoted EF-Tu1 and EF-Tu2. Recombinant nematode EF-Ts purified from Escherichia coli bound both of these molecules and also stimulated the translational activity of EF-Tu, indicating that the nematode EF-Ts homolog is a functional EF-Ts protein of mitochondria. Complexes formed by the interaction of nematode EF-Ts with EF-Tu1 and EF-Tu2 could be detected by native gel electrophoresis and purified by gel filtration. Although the nematode mitochondrial (mt) EF-Tu molecules are extremely unstable and easily form aggregates, native gel electrophoresis and gel filtration analysis revealed that EF-Tu.EF-Ts complexes are significantly more soluble. This indicates that nematode EF-Ts can be used to stabilize homologous EF-Tu molecules for experimental purposes. The EF-Ts bound to two eubacterial EF-Tu species (E.coli and Thermus thermophilus). Although the EF-Ts did not bind to bovine mt EF-Tu, it could bind to a chimeric nematode-bovine EF-Tu molecule containing domains 1 and 2 from bovine mt EF-Tu. Thus, the nematode EF-Ts appears to have a broad specificity for EF-Tu molecules from different species.
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Affiliation(s)
- Takashi Ohtsuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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