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Xiong W, Ye Y, He D, He S, Xiang Y, Xiao J, Feng W, Wu M, Yang Z, Wang D. Deregulation of Ribosome Biogenesis in Nitrite-Oxidizing Bacteria Leads to Nitrite Accumulation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16673-16684. [PMID: 37862695 DOI: 10.1021/acs.est.3c06002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Nitrite (NO2-) accumulation caused by nitrite-oxidizing bacteria (NOB) inhibition in nitrification is a double-edged sword, i.e., a disaster in aquatic environments but a hope for innovating nitrogen removal technology in wastewater treatment. However, little information is available regarding the molecular mechanism of NOB inhibition at the cellular level. Herein, we investigate the response of NOB inhibition on NO2- accumulation established by a side-stream free ammonia treatment unit in a nitrifying reactor using integrated metagenomics and metaproteomics. Results showed that compared with the baseline, the relative abundance and activity of NOB in the experimental stage decreased by 91.64 and 68.66%, respectively, directly resulting in a NO2- accumulation rate of 88%. Moreover, RNA polymerase, translation factors, and aa-tRNA ligase were significantly downregulated, indicating that protein synthesis in NOB was interfered during NO2- accumulation. Further investigations showed that ribosomal proteins and GTPases, responsible for bindings between either ribosomal proteins and rRNA or ribosome subunits, were remarkably downregulated. This suggests that ribosome biogenesis was severely disrupted, which might be the key reason for the inhibited protein synthesis. Our findings fill a knowledge gap regarding the underlying mechanisms of NO2- accumulation, which would be beneficial for regulating the accumulation of NO2- in aquatic environments and engineered systems.
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Affiliation(s)
- Weiping Xiong
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Yuhang Ye
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Dandan He
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Siying He
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Yinping Xiang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Jun Xiao
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Wenyi Feng
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Mengru Wu
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Zhaohui Yang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Dongbo Wang
- College of Environmental Science and Engineering and Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
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2
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Choi E, Hwang J. The GTPase BipA expressed at low temperature in Escherichia coli assists ribosome assembly and has chaperone-like activity. J Biol Chem 2018; 293:18404-18419. [PMID: 30305394 DOI: 10.1074/jbc.ra118.002295] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
BPI-inducible protein A (BipA) is a conserved ribosome-associated GTPase in bacteria that is structurally similar to other GTPases associated with protein translation, including IF2, EF-Tu, and EF-G. Its binding site on the ribosome appears to overlap those of these translational GTPases. Mutations in the bipA gene cause a variety of phenotypes, including cold and antibiotics sensitivities and decreased pathogenicity, implying that BipA may participate in diverse cellular processes by regulating translation. According to recent studies, a bipA-deletion strain of Escherichia coli displays a ribosome assembly defect at low temperature, suggesting that BipA might be involved in ribosome assembly. To further investigate BipA's role in ribosome biogenesis, here, we compared and analyzed the ribosomal protein compositions of MG1655 WT and bipA-deletion strains at 20 °C. Aberrant 50S ribosomal subunits (i.e. 44S particles) accumulated in the bipA-deletion strain at 20 °C, and the ribosomal protein L6 was absent in these 44S particles. Furthermore, bipA expression was significantly stimulated at 20 °C, suggesting that it encodes a cold shock-inducible GTPase. Moreover, the transcriptional regulator cAMP receptor protein (CRP) positively promoted bipA expression only at 20 °C. Importantly, GFP and α-glucosidase refolding assays revealed that BipA has chaperone activity. Our findings indicate that BipA is a cold shock-inducible GTPase that participates in 50S ribosomal subunit assembly by incorporating the L6 ribosomal protein into the 44S particle during the assembly.
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Affiliation(s)
- Eunsil Choi
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea
| | - Jihwan Hwang
- From the Department of Microbiology, Pusan National University, Busan 46241, Korea.
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3
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Zhu P, Liu Y, Zhang F, Bai X, Chen Z, Shangguan F, Zhang B, Zhang L, Chen Q, Xie D, Lan L, Xue X, Liang XJ, Lu B, Wei T, Qin Y. Human Elongation Factor 4 Regulates Cancer Bioenergetics by Acting as a Mitochondrial Translation Switch. Cancer Res 2018; 78:2813-2824. [PMID: 29572227 DOI: 10.1158/0008-5472.can-17-2059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/01/2018] [Accepted: 03/20/2018] [Indexed: 11/16/2022]
Abstract
Mitochondria regulate cellular bioenergetics and redox states and influence multiple signaling pathways required for tumorigenesis. In this study, we determined that the mitochondrial translation elongation factor 4 (EF4) is a critical component of tumor progression. EF4 was ubiquitous in human tissues with localization to the mitochondria (mtEF4) and performed quality control on respiratory chain biogenesis. Knockout of mtEF4 induced respiratory chain complex defects and apoptosis, while its overexpression stimulated cancer development. In multiple cancers, expression of mtEF4 was increased in patient tumor tissues. These findings reveal that mtEF4 expression may promote tumorigenesis via an imbalance in the regulation of mitochondrial activities and subsequent variation of cellular redox. Thus, dysregulated mitochondrial translation may play a vital role in the etiology and development of diverse human cancers.Significance: Dysregulated mitochondrial translation drives tumor development and progression. Cancer Res; 78(11); 2813-24. ©2018 AACR.
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Affiliation(s)
- Ping Zhu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongzhang Liu
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fenglin Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Xiufeng Bai
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zilei Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fugen Shangguan
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Bo Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Lingyun Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Qianqian Chen
- University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Deyao Xie
- Departments of Cardiothoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Linhua Lan
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangdong Xue
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Zhongguancun, Beijing, China
| | - Xing-Jie Liang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Zhongguancun, Beijing, China
| | - Bin Lu
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Taotao Wei
- University of Chinese Academy of Sciences, Beijing, China. .,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China
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4
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Carlson MA, Haddad BG, Weis AJ, Blackwood CS, Shelton CD, Wuerth ME, Walter JD, Spiegel PC. Ribosomal protein L7/L12 is required for GTPase translation factors EF-G, RF3, and IF2 to bind in their GTP state to 70S ribosomes. FEBS J 2017; 284:1631-1643. [PMID: 28342293 DOI: 10.1111/febs.14067] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/06/2017] [Accepted: 03/22/2017] [Indexed: 12/01/2022]
Abstract
Ribosomal protein L7/L12 is associated with translation initiation, elongation, and termination by the 70S ribosome. The guanosine 5' triphosphate hydrolase (GTPase) activity of elongation factor G (EF-G) requires the presence of L7/L12, which is critical for ribosomal translocation. Here, we have developed new methods for the complete depletion of L7/L12 from Escherichia coli 70S ribosomes to analyze the effect of L7/L12 on the activities of the GTPase factors EF-G, RF3, IF2, and LepA. Upon removal of L7/L12 from ribosomes, the GTPase activities of EF-G, RF3, and IF2 decreased to basal levels, while the activity of LepA decreased marginally. Upon reconstitution of ribosomes with recombinant L12, the GTPase activities of all GTPases returned to full activity. Moreover, ribosome binding assays indicated that EF-G, RF3, and IF2 require L7/L12 for stable binding in the GTP state, and LepA retained > 50% binding. Lastly, an EF-G∆G' truncation mutant possessed ribosome-dependent GTPase activity, which was insensitive to L7/L12. Our results indicate that L7/L12 is required for stable binding of ribosome-dependent GTPases that harbor direct interactions to the L7/L12 C-terminal domains, either through a G' domain (EF-G, RF3) or a unique N-terminal domain (IF2). Furthermore, we hypothesize this interaction is concomitant with counterclockwise ribosomal intersubunit rotation, which is required for translocation, initiation, and post-termination.
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Affiliation(s)
- Markus A Carlson
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Bassam G Haddad
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Amanda J Weis
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Colby S Blackwood
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | | | - Michelle E Wuerth
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Justin D Walter
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Paul Clint Spiegel
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
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5
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EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome. Nat Struct Mol Biol 2016; 23:125-31. [PMID: 26809121 DOI: 10.1038/nsmb.3160] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/11/2015] [Indexed: 11/08/2022]
Abstract
EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome.
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6
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Ma XL, Cui WN, Zhao Q, Zhao J, Hou XN, Li DY, Chen ZL, Shen YZ, Huang ZJ. Functional study of a salt-inducible TaSR gene in Triticum aestivum. PHYSIOLOGIA PLANTARUM 2016; 156:40-53. [PMID: 25855206 DOI: 10.1111/ppl.12337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/16/2015] [Accepted: 02/20/2015] [Indexed: 06/04/2023]
Abstract
The gene expression chip of a salt-tolerant wheat mutant under salt stress was used to clone a salt-induced gene with unknown functions. This gene was designated as TaSR (Triticum aestivum salt-response gene) and submitted to GenBank under accession number EF580107. Quantitative polymerase chain reaction (PCR) analysis showed that gene expression was induced by salt stress. Arabidopsis and rice (Oryza sativa) plants expressing TaSR presented higher salt tolerance than the controls, whereas AtSR mutant and RNA interference rice plants were more sensitive to salt. Under salt stress, TaSR reduced Na(+) concentration and improved cellular K(+) and Ca(2+) concentrations; this gene was also localized on the cell membrane. β-Glucuronidase (GUS) staining and GUS fluorescence quantitative determination were conducted through fragmentation cloning of the TaSR promoter. Salt stress-responsive elements were detected at 588-1074 bp upstream of the start codon. GUS quantitative tests of the full-length promoter in different tissues indicated that promoter activity was highest in the leaf under salt stress. Bimolecular fluorescence complementation and yeast two-hybrid screening further showed the correlation of TaSR with TaPRK and TaKPP. In vitro phosphorylation of TaSR and TaPRK2697 showed that TaPRK2697 did not phosphorylate TaSR. This study revealed that the novel TaSR may be used to improve plant tolerance to salt stress.
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Affiliation(s)
- Xiao-Li Ma
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
| | - Wei-Na Cui
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
| | - Qian Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
| | - Jing Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
| | - Xiao-Na Hou
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, People's Republic of China
| | - Dong-Yan Li
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
| | - Zhao-Liang Chen
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
| | - Yin-Zhu Shen
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
| | - Zhan-Jing Huang
- College of Life Science, Hebei Normal University, Shijiazhuang, People's Republic of China
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7
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EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Nat Struct Mol Biol 2014; 21:817-24. [PMID: 25108354 DOI: 10.1038/nsmb.2869] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 07/11/2014] [Indexed: 02/01/2023]
Abstract
During translation, elongation factor G (EF-G) catalyzes the translocation of tRNA2-mRNA inside the ribosome. Translocation is coupled to a cycle of conformational rearrangements of the ribosomal machinery, and how EF-G initiates translocation remains unresolved. Here we performed systematic mutagenesis of Escherichia coli EF-G and analyzed inhibitory single-site mutants of EF-G that preserved pretranslocation (Pre)-state ribosomes with tRNAs in A/P and P/E sites (Pre-EF-G). Our results suggest that the interactions between the decoding center and the codon-anticodon duplex constitute the barrier for translocation. Catalysis of translocation by EF-G involves the factor's highly conserved loops I and II at the tip of domain IV, which disrupt the hydrogen bonds between the decoding center and the duplex to release the latter, hence inducing subsequent translocation events, namely 30S head swiveling and tRNA2-mRNA movement on the 30S subunit.
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8
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Yamamoto H, Qin Y, Achenbach J, Li C, Kijek J, Spahn CMT, Nierhaus KH. EF-G and EF4: translocation and back-translocation on the bacterial ribosome. Nat Rev Microbiol 2013; 12:89-100. [PMID: 24362468 DOI: 10.1038/nrmicro3176] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ribosomes translate the codon sequence of an mRNA into the amino acid sequence of the corresponding protein. One of the most crucial events is the translocation reaction, which involves movement of both the mRNA and the attached tRNAs by one codon length and is catalysed by the GTPase elongation factor G (EF-G). Interestingly, recent studies have identified a structurally related GTPase, EF4, that catalyses movement of the tRNA2-mRNA complex in the opposite direction when the ribosome stalls, which is known as back-translocation. In this Review, we describe recent insights into the mechanistic basis of both translocation and back-translocation.
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Affiliation(s)
- Hiroshi Yamamoto
- 1] Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. [2]
| | - Yan Qin
- 1] Laboratory of noncoding RNA, Institute of Biophysics, Chinese Academy of Science; 15 Datun Road, Beijing 100101, China. [2]
| | - John Achenbach
- 1] NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany. [2]
| | - Chengmin Li
- Laboratory of noncoding RNA, Institute of Biophysics, Chinese Academy of Science; 15 Datun Road, Beijing 100101, China
| | - Jaroslaw Kijek
- Max Planck Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Knud H Nierhaus
- 1] Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. [2] Max Planck Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany
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9
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The paradox of elongation factor 4: highly conserved, yet of no physiological significance? Biochem J 2013; 452:173-81. [DOI: 10.1042/bj20121792] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
LepA [EF4 (elongation factor 4)] is a highly conserved protein found in nearly all known genomes. EF4 triggers back-translocation of the elongating ribosome, causing the translation machinery to move one codon backwards along the mRNA. Knockout of the corresponding gene in various bacteria results in different phenotypes; however, the physiological function of the factor in vivo is unclear. Although functional research on Guf1 (GTPase of unknown function 1), the eukaryotic homologue of EF4, showed that it plays a critical role under suboptimal translation conditions in vivo, its detailed mechanism has yet to be identified. In the present review we briefly cover recent advances in our understanding of EF4, including in vitro structural and biochemical studies, and research on its physiological role in vivo. Lastly, we present a hypothesis for back-translocation and discuss the directions future EF4 research should focus on.
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