1
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Tomasiunaite U, Kielkowski P, Krafczyk R, Forné I, Imhof A, Jung K. Decrypting the functional design of unmodified translation elongation factor P. Cell Rep 2024; 43:114063. [PMID: 38635400 DOI: 10.1016/j.celrep.2024.114063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/17/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Bacteria overcome ribosome stalling by employing translation elongation factor P (EF-P), which requires post-translational modification (PTM) for its full activity. However, EF-Ps of the PGKGP subfamily are unmodified. The mechanism behind the ability to avoid PTM while retaining active EF-P requires further examination. Here, we investigate the design principles governing the functionality of unmodified EF-Ps in Escherichia coli. We screen for naturally unmodified EF-Ps with activity in E. coli and discover that the EF-P from Rhodomicrobium vannielii rescues growth defects of a mutant lacking the modification enzyme EF-P-(R)-β-lysine ligase. We identify amino acids in unmodified EF-P that modulate its activity. Ultimately, we find that substitution of these amino acids in other marginally active EF-Ps of the PGKGP subfamily leads to fully functional variants in E. coli. These results provide strategies to improve heterologous expression of proteins with polyproline motifs in E. coli and give insights into cellular adaptations to optimize protein synthesis.
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Affiliation(s)
- Urte Tomasiunaite
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Institut für Chemische Epigenetik (ICEM), Ludwig-Maximilians-Universität München, 81375 Munich, Germany
| | - Ralph Krafczyk
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Ignasi Forné
- Zentrallabor für Proteinanalytik, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, Biomedical Center Munich, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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2
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Zheng X, Sun X, Xiang W, Ni H, Zou L, Long ZE. Expression of Staphylococcus aureus translation elongation factor P is regulated by a stress-inducible promotor. Antonie Van Leeuwenhoek 2024; 117:54. [PMID: 38489110 DOI: 10.1007/s10482-024-01954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Translation elongation factor P, expressed by the efp gene, is a conserved protein closely related to bacterial virulence and environmental stress regulation responses, however, little is known about the efp gene expression regulations. Here, the strain of Staphylococcus aureus subsp. aureus NCTC 8325 was taken as the research object and cultured under different conditions, including different culture temperatures, pH, and antibiotics, to study the expression of the efp gene in S. aureus by qRT-PCR, the results showed that the expression of the efp gene is upregulated under high temperature (40 °C), acidic (pH 5.4) or alkaline (pH 9.4) culture conditions, but upregulated early and downregulated later under the conditions of 0.5 MIC antibiotics (chloramphenicol at the final concentration of 2 μg/mL and vancomycin at the final concentration of 0.25 μg/mL), indicating that the efp promoter in S. aureus is inducible. The efp promoter sequence and structure in S. aureus were predicted by bioinformatics methods, and the predicted promoter was validated by constructing a promoter-probe vector and a series of promoter mutants, the results showed that the efp promoter sequence in S. aureus, named Pro, located in 1,548,179-1,548,250 of the S. aureus genome (NC_007795.1), and the sequence of - 10 element is CCTTATAGT, - 35 element is TTTACT. The results above could lay a foundation for screening transcription factors involved in the expression of the efp gene and then exploring the transcriptional regulation mechanism of EF-P in S. aureus.
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Affiliation(s)
- Xingxing Zheng
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiuhui Sun
- Chongren County Center for Disease Prevention and Control, Chongren, 344203, China
| | - Weiwei Xiang
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Haiyan Ni
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Long Zou
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhong-Er Long
- Nanchang Key Laboratory of Microbial Resources Exploitation and Utilization From Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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3
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Hijikata A, Oshima T, Yura K, Bessho Y. ThermusQ: Toward the cell simulation platform for Thermus thermophilus. J GEN APPL MICROBIOL 2023; 69:59-67. [PMID: 37460312 DOI: 10.2323/jgam.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
ThermusQ is a website (https://www.thermusq.net/) that aims to gather all the molecular information on Thermus thermophilus and to provide a platform to easily access the whole view of the bacterium. ThermusQ comprises the genome sequences of 22 strains from T. thermophilus and T. oshimai strains, plus the sequences of known Thermus phages. ThermusQ also contains information and map diagrams of pathways unique to Thermus strains. The website provides tools to retrieve sequence data in different ways. By gathering the whole data of T. thermophilus strains, the strainspecific characteristics was found. This bird's-eye view of the whole data will lead the research community to identify missing important data and the integration will provide a platform to conduct future biochemical simulations of the bacterium.
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Affiliation(s)
- Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co., Ltd
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- Graduate School of Advanced Science and Engineering, Waseda University
| | - Yoshitaka Bessho
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- RIKEN SPring-8 Center, Harima Institute
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4
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Daskalova SM, Dedkova LM, Maini R, Talukder P, Bai X, Chowdhury SR, Zhang C, Nangreave RC, Hecht SM. Elongation Factor P Modulates the Incorporation of Structurally Diverse Noncanonical Amino Acids into Escherichia coli Dihydrofolate Reductase. J Am Chem Soc 2023; 145:23600-23608. [PMID: 37871253 PMCID: PMC10762953 DOI: 10.1021/jacs.3c07524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The introduction of noncanonical amino acids into proteins and peptides has been of great interest for many years and has facilitated the detailed study of peptide/protein structure and mechanism. In addition to numerous nonproteinogenic α-l-amino acids, bacterial ribosome modification has provided the wherewithal to enable the synthesis of peptides and proteins with a much greater range of structural diversity, as has the use of endogenous bacterial proteins in reconstituted protein synthesizing systems. In a recent report, elongation factor P (EF-P), putatively essential for enabling the incorporation of contiguous proline residues into proteins, was shown to facilitate the introduction of an N-methylated amino acid in addition to proline. This finding prompted us to investigate the properties of this protein factor with a broad variety of structurally diverse amino acid analogues using an optimized suppressor tRNAPro that we designed. While these analogues can generally be incorporated into proteins only in systems containing modified ribosomes specifically selected for their incorporation, we found that EF-P could significantly enhance their incorporation into model protein dihydrofolate reductase using wild-type ribosomes. Plausibly, the increased yields observed in the presence of structurally diverse amino acid analogues may result from the formation of a stabilized ribosomal complex in the presence of EF-P that provides more favorable conditions for peptide bond formation. This finding should enable the facile incorporation of a much broader structural variety of amino acid analogues into proteins and peptides using native ribosomes.
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Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chao Zhang
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C Nangreave
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for Bioenergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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5
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Mudryi V, Peske F, Rodnina M. Translation Factor Accelerating Peptide Bond Formation on the Ribosome: EF-P and eIF5A as Entropic Catalysts and a Potential Drug Targets. BBA ADVANCES 2023; 3:100074. [PMID: 37082265 PMCID: PMC10074943 DOI: 10.1016/j.bbadva.2023.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Elongation factor P (EF-P) and its eukaryotic homolog eIF5A are auxiliary translation factors that facilitate peptide bond formation when several sequential proline (Pro) residues are incorporated into the nascent chain. EF-P and eIF5A bind to the exit (E) site of the ribosome and contribute to favorable entropy of the reaction by stabilizing tRNA binding in the peptidyl transferase center of the ribosome. In most organisms, EF-P and eIF5A carry a posttranslational modification that is crucial for catalysis. The chemical nature of the modification varies between different groups of bacteria and between pro- and eukaryotes, making the EF-P-modification enzymes promising targets for antibiotic development. In this review, we summarize our knowledge of the structure and function of EF-P and eIF5A, describe their modification enzymes, and present an approach for potential drug screening aimed at EarP, an enzyme that is essential for EF-P modification in several pathogenic bacteria.
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6
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McDonnell CM, Ghanim M, Mike Southern J, Kelly VP, Connon SJ. De-novo designed β-lysine derivatives can both augment and diminish the proliferation rates of E. coli through the action of Elongation Factor P. Bioorg Med Chem Lett 2022; 59:128545. [PMID: 35032607 DOI: 10.1016/j.bmcl.2022.128545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
An investigation into the effect of modified β -lysines on the growth rates of eubacterial cells is reported. It is shown that the effects observed are due to the post translational modification of Elongation Factor P (EFP) with these compounds catalysed by PoxA. PoxA was found to be remarkably promiscuous, which allowed the activity of a wide range of exogenous β -lysines to be examined. Two chain-elongated β -lysine derivatives which differ in aminoalkyl chain length by only 2 carbon units exhibited opposing biological activities - one promoting growth and the other retarding it. Both compounds were shown to operate through modification of EFP.
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Affiliation(s)
- Ciara M McDonnell
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland
| | - Magda Ghanim
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland
| | - J Mike Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse Street, Dublin 2, Ireland.
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7
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Pinheiro B, Scheidler CM, Kielkowski P, Schmid M, Forné I, Ye S, Reiling N, Takano E, Imhof A, Sieber SA, Schneider S, Jung K. Structure and Function of an Elongation Factor P Subfamily in Actinobacteria. Cell Rep 2021; 30:4332-4342.e5. [PMID: 32234471 DOI: 10.1016/j.celrep.2020.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/06/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022] Open
Abstract
Translation of consecutive proline motifs causes ribosome stalling and requires rescue via the action of a specific translation elongation factor, EF-P in bacteria and archaeal/eukaryotic a/eIF5A. In Eukarya, Archaea, and all bacteria investigated so far, the functionality of this translation elongation factor depends on specific and rather unusual post-translational modifications. The phylum Actinobacteria, which includes the genera Corynebacterium, Mycobacterium, and Streptomyces, is of both medical and economic significance. Here, we report that EF-P is required in these bacteria in particular for the translation of proteins involved in amino acid and secondary metabolite production. Notably, EF-P of Actinobacteria species does not need any post-translational modification for activation. While the function and overall 3D structure of this EF-P type is conserved, the loop containing the conserved lysine is flanked by two essential prolines that rigidify it. Actinobacteria's EF-P represents a unique subfamily that works without any modification.
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Affiliation(s)
- Bruno Pinheiro
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | | | - Pavel Kielkowski
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Marina Schmid
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Suhui Ye
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Axel Imhof
- Biomedical Center Munich, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Stephan A Sieber
- Department of Chemistry, Technische Universität München, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
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8
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TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS. J CHEM-NY 2021. [DOI: 10.1155/2021/8876986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shewanella putrefaciens is a specific spoilage bacterium for fish during cold storage. To better understand the molecular mechanisms of cold stress adaptation of S. putrefaciens, tandem mass tag- (TMT-) based quantitative proteomic analysis was performed to detect the effects of cold stress on protein expression profiles in S. putrefaciens which had been cultivated at 4°C and 30°C, respectively. A total of 266670 peptide spectrum matching numbers were quantified proteins after data analysis. Of the 2292 proteins quantitatively analyzed, a total of 274 were found to be differentially expressed (DE) under cold stress compared with the nonstress control. By integrating the results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, 9 common KEGG terms were found notable for the cold-responsive proteins. Generally, the DE proteins involved in carbohydrate, amino acid, and fatty acid biosynthesis and metabolism were significantly upregulated, leading to a specific energy conservation survival mode. The DE proteins related to DNA repair, transcription, and translation were upregulated, implicating change of gene expression and more protein biosynthesis needed in response to cold stress.
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9
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Hummels KR, Kearns DB. Translation elongation factor P (EF-P). FEMS Microbiol Rev 2020; 44:208-218. [PMID: 32011712 DOI: 10.1093/femsre/fuaa003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/30/2020] [Indexed: 01/01/2023] Open
Abstract
Translation elongation factor P (EF-P) is conserved in all three domains of life (called eIF5A and aIF5A in eukaryotes and archaea, respectively) and functions to alleviate ribosome pausing during the translation of specific sequences, including consecutive proline residues. EF-P was identified in 1975 as a factor that stimulated the peptidyltransferase reaction in vitro but its involvement in the translation of tandem proline residues was not uncovered until 2013. Throughout the four decades of EF-P research, perceptions of EF-P function have changed dramatically. In particular, while EF-P was thought to potentiate the formation of the first peptide bond in a protein, it is now broadly accepted to act throughout translation elongation. Further, EF-P was initially reported to be essential, but recent work has shown that the requirement of EF-P for growth is conditional. Finally, it is thought that post-translational modification of EF-P is strictly required for its function but recent studies suggest that EF-P modification may play a more nuanced role in EF-P activity. Here, we review the history of EF-P research, with an emphasis on its initial isolation and characterization as well as the discoveries that altered our perceptions of its function.
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Affiliation(s)
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN USA
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10
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Beyer HM, Virtanen SI, Aranko AS, Mikula KM, Lountos GT, Wlodawer A, Ollila OHS, Iwaï H. The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms. Int J Mol Sci 2020; 21:ijms21218367. [PMID: 33171880 PMCID: PMC7664689 DOI: 10.3390/ijms21218367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022] Open
Abstract
Protein splicing catalyzed by inteins utilizes many different combinations of amino-acid types at active sites. Inteins have been classified into three classes based on their characteristic sequences. We investigated the structural basis of the protein splicing mechanism of class 3 inteins by determining crystal structures of variants of a class 3 intein from Mycobacterium chimaera and molecular dynamics simulations, which suggested that the class 3 intein utilizes a different splicing mechanism from that of class 1 and 2 inteins. The class 3 intein uses a bond cleavage strategy reminiscent of proteases but share the same Hedgehog/INTein (HINT) fold of other intein classes. Engineering of class 3 inteins from a class 1 intein indicated that a class 3 intein would unlikely evolve directly from a class 1 or 2 intein. The HINT fold appears as structural and functional solution for trans-peptidyl and trans-esterification reactions commonly exploited by diverse mechanisms using different combinations of amino-acid types for the active-site residues.
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Affiliation(s)
- Hannes M. Beyer
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - Salla I. Virtanen
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - A. Sesilja Aranko
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - Kornelia M. Mikula
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA;
| | - O. H. Samuli Ollila
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
- Correspondence: ; Tel.: +358-2941-59752
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11
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Zhao R, Wang M, Chen J, Tong Y, Wei GW. The de Rham-Hodge Analysis and Modeling of Biomolecules. Bull Math Biol 2020; 82:108. [PMID: 32770408 PMCID: PMC8137271 DOI: 10.1007/s11538-020-00783-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Biological macromolecules have intricate structures that underpin their biological functions. Understanding their structure-function relationships remains a challenge due to their structural complexity and functional variability. Although de Rham-Hodge theory, a landmark of twentieth-century mathematics, has had a tremendous impact on mathematics and physics, it has not been devised for macromolecular modeling and analysis. In this work, we introduce de Rham-Hodge theory as a unified paradigm for analyzing the geometry, topology, flexibility, and Hodge mode analysis of biological macromolecules. Geometric characteristics and topological invariants are obtained either from the Helmholtz-Hodge decomposition of the scalar, vector, and/or tensor fields of a macromolecule or from the spectral analysis of various Laplace-de Rham operators defined on the molecular manifolds. We propose Laplace-de Rham spectral-based models for predicting macromolecular flexibility. We further construct a Laplace-de Rham-Helfrich operator for revealing cryo-EM natural frequencies. Extensive experiments are carried out to demonstrate that the proposed de Rham-Hodge paradigm is one of the most versatile tools for the multiscale modeling and analysis of biological macromolecules and subcellular organelles. Accurate, reliable, and topological structure-preserving algorithms for implementing discrete exterior calculus (DEC) have been developed to facilitate the aforementioned modeling and analysis of biological macromolecules. The proposed de Rham-Hodge paradigm has potential applications to subcellular organelles and the structure construction from medium- or low-resolution cryo-EM maps, and functional predictions from massive biomolecular datasets.
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Affiliation(s)
- Rundong Zhao
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Menglun Wang
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA
| | - Yiying Tong
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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12
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Abe T, Nagai R, Shimazaki S, Kondo S, Nishimura S, Sakaguchi Y, Suzuki T, Imataka H, Tomita K, Takeuchi-Tomita N. In vitro yeast reconstituted translation system reveals function of eIF5A for synthesis of long polypeptide. J Biochem 2020; 167:451-462. [PMID: 32053170 DOI: 10.1093/jb/mvaa022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
We have recently developed an in vitro yeast reconstituted translation system, which is capable of synthesizing long polypeptides. Utilizing the system, we examined the role of eIF5A and its hypusine modification in translating polyproline sequence within long open reading frames. We found that polyproline motif inserted at the internal position of the protein arrests translation exclusively at low Mg2+ concentrations, and peptidylpolyproline-tRNA intrinsically destabilizes 80S ribosomes. We demonstrate that unmodified eIF5A essentially resolves such ribosome stalling; however, the hypusine modification drastically stimulates ability of eIF5A to rescue polyproline-mediated ribosome stalling and is particularly important for the efficient translation of the N-terminal or long internal polyproline motifs.
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Affiliation(s)
- Taisho Abe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Riku Nagai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shunta Shimazaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Shunta Kondo
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Satoshi Nishimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Imataka
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Nono Takeuchi-Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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13
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Ousalem F, Singh S, Chesneau O, Hunt JF, Boël G. ABC-F proteins in mRNA translation and antibiotic resistance. Res Microbiol 2019; 170:435-447. [PMID: 31563533 DOI: 10.1016/j.resmic.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/01/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022]
Abstract
The ATP binding cassette protein superfamily comprises ATPase enzymes which are, for the most part, involved in transmembrane transport. Within this superfamily however, some protein families have other functions unrelated to transport. One example is the ABC-F family, which comprises an extremely diverse set of cytoplasmic proteins. All of the proteins in the ABC-F family characterized to date act on the ribosome and are translation factors. Their common function is ATP-dependent modulation of the stereochemistry of the peptidyl transferase center (PTC) in the ribosome coupled to changes in its global conformation and P-site tRNA binding geometry. In this review, we give an overview of the function, structure, and theories for the mechanisms-of-action of microbial proteins in the ABC-F family, including those involved in mediating resistance to ribosome-binding antibiotics.
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Affiliation(s)
- Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Shikha Singh
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 75724, Paris Cedex 15, France.
| | - John F Hunt
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States.
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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14
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Golubev AA, Validov SZ, Usachev KS, Yusupov MM. Elongation Factor P: New Mechanisms of Function and an Evolutionary Diversity of Translation Regulation. Mol Biol 2019. [DOI: 10.1134/s0026893319040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Complex Structure of Pseudomonas aeruginosa Arginine Rhamnosyltransferase EarP with Its Acceptor Elongation Factor P. J Bacteriol 2019; 201:JB.00128-19. [PMID: 31010899 DOI: 10.1128/jb.00128-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 03/28/2019] [Indexed: 01/10/2023] Open
Abstract
A bacterial inverting glycosyltransferase EarP transfers rhamnose from dTDP-β-l-rhamnose (TDP-Rha) to Arg32 of translation elongation factor P (EF-P) to activate its function. We report here the structural and biochemical characterization of Pseudomonas aeruginosa EarP. In contrast to recently reported Neisseria meningitidis EarP, P. aeruginosa EarP exhibits differential conformational changes upon TDP-Rha and EF-P binding. Sugar donor binding enhances acceptor binding to EarP, as revealed by structural comparison between the apo-, TDP-Rha-, and TDP/EF-P-bound forms and isothermal titration calorimetry experiments. In vitro EF-P rhamnosylation combined with active-site geometry indicates that Asp16 corresponding to Asp20 of N. meningitidis EarP is the catalytic base, whereas Glu272 is another putative catalytic residue. Our study should provide the basis for EarP-targeted inhibitor design against infections from P. aeruginosa and other clinically relevant species.IMPORTANCE Posttranslational rhamnosylation of EF-P plays a key role in Pseudomonas aeruginosa, establishing virulence and antibiotic resistance, as well as survival. The detailed structural and biochemical characterization of the EF-P-specific rhamnosyltransferase EarP from P. aeruginosa not only demonstrates that sugar donor TDP-Rha binding enhances acceptor EF-P binding to EarP but also should provide valuable information for the structure-guided development of its inhibitors against infections from P. aeruginosa and other EarP-containing pathogens.
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16
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Volkwein W, Krafczyk R, Jagtap PKA, Parr M, Mankina E, Macošek J, Guo Z, Fürst MJLJ, Pfab M, Frishman D, Hennig J, Jung K, Lassak J. Switching the Post-translational Modification of Translation Elongation Factor EF-P. Front Microbiol 2019; 10:1148. [PMID: 31178848 PMCID: PMC6544042 DOI: 10.3389/fmicb.2019.01148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
Tripeptides with two consecutive prolines are the shortest and most frequent sequences causing ribosome stalling. The bacterial translation elongation factor P (EF-P) relieves this arrest, allowing protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function and modified at its tip by lysylation of lysine or rhamnosylation of arginine. Phylogenetic analyses unveiled an invariant proline in the -2 position of the modification site in EF-Ps that utilize lysine modifications such as Escherichia coli. Bacteria with the arginine modification like Pseudomonas putida on the contrary have selected against it. Focusing on the EF-Ps from these two model organisms we demonstrate the importance of the β3/β4 loop composition for functionalization by chemically distinct modifications. Ultimately, we show that only two amino acid changes in E. coli EF-P are needed for switching the modification strategy from lysylation to rhamnosylation.
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Affiliation(s)
- Wolfram Volkwein
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.,St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Elena Mankina
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Heidelberg, Germany
| | - Zhenghuan Guo
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian Josef Ludwig Johannes Fürst
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
| | - Miriam Pfab
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.,St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jürgen Lassak
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
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17
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Structural dynamics of a spinlabeled ribosome elongation factor P (EF-P) from Staphylococcus aureus by EPR spectroscopy. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0468-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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18
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Park MH, Wolff EC. Hypusine, a polyamine-derived amino acid critical for eukaryotic translation. J Biol Chem 2018; 293:18710-18718. [PMID: 30257869 DOI: 10.1074/jbc.tm118.003341] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The natural amino acid hypusine (N ϵ-4-amino-2-hydroxybutyl(lysine)) is derived from the polyamine spermidine, and occurs only in a single family of cellular proteins, eukaryotic translation factor 5A (eIF5A) isoforms. Hypusine is formed by conjugation of the aminobutyl moiety of spermidine to a specific lysine residue of this protein. The posttranslational synthesis of hypusine involves two enzymatic steps, catalyzed by deoxyhypusine synthase (DHPS) and deoxyhypusine hydroxylase (DOHH). Hypusine is essential for eIF5A activity. Inactivation of either the eIF5A or the DHPS gene is lethal in yeast and mouse, underscoring the vital role of eIF5A hypusination in eukaryotic cell growth and animal development. The long and basic side chain of the hypusine residue promotes eIF5A-mediated translation elongation by facilitating peptide bond formation at polyproline stretches and at many other ribosome-pausing sites. It also enhances translation termination by stimulating peptide release. By promoting translation, the hypusine modification of eIF5A provides a key link between polyamines and cell growth regulation. eIF5A has been implicated in several human pathological conditions. Recent genetic data suggest that eIF5A haploinsufficiency or impaired deoxyhypusine synthase activity is associated with neurodevelopmental disorders in humans.
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Affiliation(s)
- Myung Hee Park
- From the NIDCR, National Institutes of Health, Bethesda, Maryland 20892
| | - Edith C Wolff
- From the NIDCR, National Institutes of Health, Bethesda, Maryland 20892
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19
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Sengoku T, Suzuki T, Dohmae N, Watanabe C, Honma T, Hikida Y, Yamaguchi Y, Takahashi H, Yokoyama S, Yanagisawa T. Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP. Nat Chem Biol 2018; 14:368-374. [PMID: 29440735 DOI: 10.1038/s41589-018-0002-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022]
Abstract
Protein glycosylation regulates many cellular processes. Numerous glycosyltransferases with broad substrate specificities have been structurally characterized. A novel inverting glycosyltransferase, EarP, specifically transfers rhamnose from dTDP-β-L-rhamnose to Arg32 of bacterial translation elongation factor P (EF-P) to activate its function. Here we report a crystallographic study of Neisseria meningitidis EarP. The EarP structure contains two tandem Rossmann-fold domains, which classifies EarP in glycosyltransferase superfamily B. In contrast to other structurally characterized protein glycosyltransferases, EarP binds the entire β-sheet structure of EF-P domain I through numerous interactions that specifically recognize its conserved residues. Thus Arg32 is properly located at the active site, and causes structural change in a conserved dTDP-β-L-rhamnose-binding loop of EarP. Rhamnosylation by EarP should occur via an SN2 reaction, with Asp20 as the general base. The Arg32 binding and accompanying structural change of EarP may induce a change in the rhamnose-ring conformation suitable for the reaction.
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Affiliation(s)
- Toru Sengoku
- RIKEN Structural Biology Laboratory, Yokohama, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Chiduru Watanabe
- Structure-Based Molecular Design Team, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Teruki Honma
- Structure-Based Molecular Design Team, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | | | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Japan
| | - Hideyuki Takahashi
- Department of Bacteriology, National Institute of Infectious Disease, Tokyo, Japan
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20
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Huter P, Arenz S, Bock LV, Graf M, Frister JO, Heuer A, Peil L, Starosta AL, Wohlgemuth I, Peske F, Nováček J, Berninghausen O, Grubmüller H, Tenson T, Beckmann R, Rodnina MV, Vaiana AC, Wilson DN. Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Mol Cell 2017; 68:515-527.e6. [PMID: 29100052 DOI: 10.1016/j.molcel.2017.10.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022]
Abstract
Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.
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Affiliation(s)
- Paul Huter
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Stefan Arenz
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Michael Graf
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Jan Ole Frister
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andre Heuer
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Lauri Peil
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Agata L Starosta
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Otto Berninghausen
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Roland Beckmann
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea C Vaiana
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
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21
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Abstract
Glycosylation is a universal strategy to posttranslationally modify proteins. The recently discovered arginine rhamnosylation activates the polyproline-specific bacterial translation elongation factor EF-P. EF-P is rhamnosylated on arginine 32 by the glycosyltransferase EarP. However, the enzymatic mechanism remains elusive. In the present study, we solved the crystal structure of EarP from Pseudomonas putida. The enzyme is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B). While dTDP-β-l-rhamnose is located within a highly conserved pocket of the C-domain, EarP recognizes the KOW-like N-domain of EF-P. Based on our data, we propose a structural model for arginine glycosylation by EarP. As EarP is essential for pathogenicity in P. aeruginosa, our study provides the basis for targeted inhibitor design. The structural and biochemical characterization of the EF-P-specific rhamnosyltransferase EarP not only provides the first molecular insights into arginine glycosylation but also lays the basis for targeted-inhibitor design against Pseudomonas aeruginosa infection.
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22
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Hummels KR, Witzky A, Rajkovic A, Tollerson R, Jones LA, Ibba M, Kearns DB. Carbonyl reduction by YmfI in Bacillus subtilis prevents accumulation of an inhibitory EF-P modification state. Mol Microbiol 2017; 106:236-251. [PMID: 28787546 DOI: 10.1111/mmi.13760] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2017] [Indexed: 12/29/2022]
Abstract
Translation elongation factor P (EF-P) in Bacillus subtilis is required for a form of surface migration called swarming motility. Furthermore, B. subtilis EF-P is post-translationally modified with a 5-aminopentanol group but the pathway necessary for the synthesis and ligation of the modification is unknown. Here we determine that the protein YmfI catalyzes the reduction of EF-P-5 aminopentanone to EF-P-5 aminopentanol. In the absence of YmfI, accumulation of 5-aminopentanonated EF-P is inhibitory to swarming motility. Suppressor mutations that enhanced swarming in the absence of YmfI were found at two positions on EF-P, including one that changed the conserved modification site (Lys 32) and abolished post-translational modification. Thus, while modification of EF-P is thought to be essential for EF-P activity, here we show that in some cases it can be dispensable. YmfI is the first protein identified in the pathway leading to EF-P modification in B. subtilis, and B. subtilis encodes the first EF-P ortholog that retains function in the absence of modification.
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Affiliation(s)
| | - Anne Witzky
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Andrei Rajkovic
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Rodney Tollerson
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Lisa A Jones
- Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Michael Ibba
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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23
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Abstract
In vitro assays find that ribosomes form peptide bonds to proline (Pro) residues more slowly than to other residues. Ribosome profiling shows that stalling at Pro-Pro-X triplets is especially severe but is largely alleviated in Escherichia coli by the action of elongation factor EF-P. EF-P and its eukaryotic/archaeal homolog IF5A enhance the peptidyl transfer step of elongation. Here, a superresolution fluorescence localization and tracking study of EF-P–mEos2 in live E. coli provides the first in vivo information about the spatial distribution and on-off binding kinetics of EF-P. Fast imaging at 2 ms/frame helps to distinguish ribosome-bound (slowly diffusing) EF-P from free (rapidly diffusing) EF-P. Wild-type EF-P exhibits a three-peaked axial spatial distribution similar to that of ribosomes, indicating substantial binding. The mutant EF-PK34A exhibits a homogeneous distribution, indicating little or no binding. Some 30% of EF-P copies are bound to ribosomes at a given time. Two-state modeling and copy number estimates indicate that EF-P binds to 70S ribosomes during 25 to 100% of translation cycles. The timescale of the typical diffusive search by free EF-P for a ribosome-binding site is τfree ≈ 16 ms. The typical residence time of an EF-P on the ribosome is very short, τbound ≈ 7 ms. Evidently, EF-P binds to ribosomes during many or most elongation cycles, much more often than the frequency of Pro-Pro motifs. Emptying of the E site during part of the cycle is consistent with recent in vitro experiments indicating dissociation of the deacylated tRNA upon translocation. Ribosomes translate the codon sequence within mRNA into the corresponding sequence of amino acids within the nascent polypeptide chain, which in turn ultimately folds into functional protein. At each codon, bacterial ribosomes are assisted by two well-known elongation factors: EF-Tu, which aids binding of the correct aminoacyl-tRNA to the ribosome, and EF-G, which promotes tRNA translocation after formation of the new peptide bond. A third factor, EF-P, has been shown to alleviate ribosomal pausing at rare Pro-Pro motifs, which are translated very slowly without EF-P. Here, we use superresolution fluorescence imaging to study the spatial distribution and ribosome-binding dynamics of EF-P in live E. coli cells. We were surprised to learn that EF-P binds to and unbinds from translating ribosomes during at least 25% of all elongation events; it may bind during every elongation cycle.
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24
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Nakashima M, Yamagami R, Tomikawa C, Ochi Y, Moriya T, Asahara H, Fourmy D, Yoshizawa S, Oshima T, Hori H. Long and branched polyamines are required for maintenance of the ribosome, tRNAHisand tRNATyrinThermus thermophiluscells at high temperatures. Genes Cells 2017; 22:628-645. [DOI: 10.1111/gtc.12502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Misa Nakashima
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Yuki Ochi
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 Japan
| | - Haruichi Asahara
- New England Biolabs, Inc; 240 County Road Ipswich Massachusetts 01938 USA
| | - Dominique Fourmy
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Satoko Yoshizawa
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Tairo Oshima
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
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25
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Abstract
Elongation factor P (EF-P) binds to ribosomes requiring assistance with the formation of oligo-prolines. In order for EF-P to associate with paused ribosomes, certain tRNAs with specific d-arm residues must be present in the peptidyl site, e.g., tRNAPro. Once EF-P is accommodated into the ribosome and bound to Pro-tRNAPro, productive synthesis of the peptide bond occurs. The underlying mechanism by which EF-P facilitates this reaction seems to have entropic origins. Maximal activity of EF-P requires a posttranslational modification in Escherichia coli, Pseudomonas aeruginosa, and Bacillus subtilis. Each of these modifications is distinct and ligated onto its respective EF-P through entirely convergent means. Here we review the facets of translation elongation that are controlled by EF-P, with a particular focus on the purpose behind the many different modifications of EF-P.
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Affiliation(s)
- Andrei Rajkovic
- Molecular, Cellular and Developmental Biology Program and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210;
| | - Michael Ibba
- Molecular, Cellular and Developmental Biology Program and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210; .,Department of Microbiology, Ohio State University, Columbus, Ohio 43210
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26
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Self-Referential Encoding on Modules of Anticodon Pairs-Roots of the Biological Flow System. Life (Basel) 2017; 7:life7020016. [PMID: 28383509 PMCID: PMC5492138 DOI: 10.3390/life7020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 12/22/2022] Open
Abstract
The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes-structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process-anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.
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27
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Katz A, Elgamal S, Rajkovic A, Ibba M. Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology. Mol Microbiol 2016; 101:545-58. [PMID: 27169680 DOI: 10.1111/mmi.13419] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 12/27/2022]
Abstract
Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl-tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl-tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond translation include synthetic, regulatory and information functions within the cell. Here we provide an overview of the non-canonical roles of tRNAs and their mimics in bacteria, and discuss some of the common themes that arise when comparing these different functions.
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Affiliation(s)
- Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Andrei Rajkovic
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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Doerfel LK, Rodnina MV. Elongation factor P: Function and effects on bacterial fitness. Biopolymers 2016; 99:837-45. [PMID: 23828669 DOI: 10.1002/bip.22341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 06/19/2013] [Indexed: 12/22/2022]
Abstract
The elongation phase of translation is promoted by three universal elongation factors, EF-Tu, EF-Ts, and EF-G in bacteria and their homologs in archaea and eukaryotes. Recent findings demonstrate that the translation of a subset of mRNAs requires a fourth elongation factor, EF-P in bacteria or the homologs factors a/eIF5A in other kingdoms of life. EF-P prevents the ribosome from stalling during the synthesis of proteins containing consecutive Pro residues, such as PPG, PPP, or longer Pro clusters. The efficient and coordinated synthesis of such proteins is required for bacterial growth, motility, virulence, and stress response. EF-P carries a unique post-translational modification, which contributes to its catalytic proficiency. The modification enzymes, which are lacking in higher eukaryotes, provide attractive new targets for the development of new, highly specific antimicrobials.
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Affiliation(s)
- Lili K Doerfel
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Goettingen, Germany
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Yanagisawa T, Takahashi H, Suzuki T, Masuda A, Dohmae N, Yokoyama S. Neisseria meningitidis Translation Elongation Factor P and Its Active-Site Arginine Residue Are Essential for Cell Viability. PLoS One 2016; 11:e0147907. [PMID: 26840407 PMCID: PMC4739656 DOI: 10.1371/journal.pone.0147907] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 01/10/2016] [Indexed: 12/16/2022] Open
Abstract
Translation elongation factor P (EF-P), a ubiquitous protein over the entire range of bacterial species, rescues ribosomal stalling at consecutive prolines in proteins. In Escherichia coli and Salmonella enterica, the post-translational β-lysyl modification of Lys34 of EF-P is important for the EF-P activity. The β-lysyl EF-P modification pathway is conserved among only 26–28% of bacteria. Recently, it was found that the Shewanella oneidensis and Pseudomonas aeruginosa EF-P proteins, containing an Arg residue at position 32, are modified with rhamnose, which is a novel post-translational modification. In these bacteria, EF-P and its Arg modification are both dispensable for cell viability, similar to the E. coli and S. enterica EF-P proteins and their Lys34 modification. However, in the present study, we found that EF-P and Arg32 are essential for the viability of the human pathogen, Neisseria meningitidis. We therefore analyzed the modification of Arg32 in the N. meningitidis EF-P protein, and identified the same rhamnosyl modification as in the S. oneidensis and P. aeruginosa EF-P proteins. N. meningitidis also has the orthologue of the rhamnosyl modification enzyme (EarP) from S. oneidensis and P. aeruginosa. Therefore, EarP should be a promising target for antibacterial drug development specifically against N. meningitidis. The pair of genes encoding N. meningitidis EF-P and EarP suppressed the slow-growth phenotype of the EF-P-deficient mutant of E. coli, indicating that the activity of N. meningitidis rhamnosyl–EF-P for rescuing the stalled ribosomes at proline stretches is similar to that of E. coli β-lysyl–EF-P. The possible reasons for the unique requirement of rhamnosyl–EF-P for N. meningitidis cells are that more proline stretch-containing proteins are essential and/or the basal ribosomal activity to synthesize proline stretch-containing proteins in the absence of EF-P is lower in this bacterium than in others.
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Affiliation(s)
- Tatsuo Yanagisawa
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230–0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230–0045, Japan
- * E-mail: (TY); (SY)
| | - Hideyuki Takahashi
- National Institute of Infectious Disease, Department of Bacteriology, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162–8640, Japan
| | - Takehiro Suzuki
- RIKEN Center for Sustainable Resource Science (CSRS), 2–1 Hirosawa, Wako, Saitama 351–0198, Japan
| | - Akiko Masuda
- RIKEN Center for Sustainable Resource Science (CSRS), 2–1 Hirosawa, Wako, Saitama 351–0198, Japan
- National Maritime Research Institute, 6-38-1 Shinkawa, Mitaka, Tokyo 181–0004, Japan
| | - Naoshi Dohmae
- RIKEN Center for Sustainable Resource Science (CSRS), 2–1 Hirosawa, Wako, Saitama 351–0198, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230–0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230–0045, Japan
- * E-mail: (TY); (SY)
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Lassak J, Wilson DN, Jung K. Stall no more at polyproline stretches with the translation elongation factors EF-P and IF-5A. Mol Microbiol 2015; 99:219-35. [PMID: 26416626 DOI: 10.1111/mmi.13233] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2015] [Indexed: 01/18/2023]
Abstract
Synthesis of polyproline proteins leads to translation arrest. To overcome this ribosome stalling effect, bacteria depend on a specialized translation elongation factor P (EF-P), being orthologous and functionally identical to eukaryotic/archaeal elongation factor e/aIF-5A (recently renamed 'EF5'). EF-P binds to the stalled ribosome between the peptidyl-tRNA binding and tRNA-exiting sites, and stimulates peptidyl-transferase activity, thus allowing translation to resume. In their active form, both EF-P and e/aIF-5A are post-translationally modified at a positively charged residue, which protrudes toward the peptidyl-transferase center when bound to the ribosome. While archaeal and eukaryotic IF-5A strictly depend on (deoxy-) hypusination (hypusinylation) of a conserved lysine, bacteria have evolved diverse analogous modification strategies to activate EF-P. In Escherichia coli and Salmonella enterica a lysine is extended by β-lysinylation and subsequently hydroxylated, whereas in Pseudomonas aeruginosa and Shewanella oneidensis an arginine in the equivalent position is rhamnosylated. Inactivation of EF-P, or the corresponding modification systems, reduces not only bacterial fitness, but also impairs virulence. Here, we review the function of EF-P and IF-5A and their unusual posttranslational protein modifications.
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Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, D-81377, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, D-82152, Martinsried, Germany
| | - Daniel N Wilson
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, D-81377, Munich, Germany.,Gene Center, Department for Biochemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, D-81377, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, D-82152, Martinsried, Germany
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32
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Arginine-rhamnosylation as new strategy to activate translation elongation factor P. Nat Chem Biol 2015; 11:266-70. [PMID: 25686373 DOI: 10.1038/nchembio.1751] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/22/2014] [Indexed: 12/26/2022]
Abstract
Ribosome stalling at polyproline stretches is common and fundamental. In bacteria, translation elongation factor P (EF-P) rescues such stalled ribosomes, but only when it is post-translationally activated. In Escherichia coli, activation of EF-P is achieved by (R)-β-lysinylation and hydroxylation of a conserved lysine. Here we have unveiled a markedly different modification strategy in which a conserved arginine of EF-P is rhamnosylated by a glycosyltransferase (EarP) using dTDP-L-rhamnose as a substrate. This is to our knowledge the first report of N-linked protein glycosylation on arginine in bacteria and the first example in which a glycosylated side chain of a translation elongation factor is essential for function. Arginine-rhamnosylation of EF-P also occurs in clinically relevant bacteria such as Pseudomonas aeruginosa. We demonstrate that the modification is needed to develop pathogenicity, making EarP and dTDP-L-rhamnose-biosynthesizing enzymes ideal targets for antibiotic development.
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Mandal A, Mandal S, Park MH. Genome-wide analyses and functional classification of proline repeat-rich proteins: potential role of eIF5A in eukaryotic evolution. PLoS One 2014; 9:e111800. [PMID: 25364902 PMCID: PMC4218817 DOI: 10.1371/journal.pone.0111800] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/06/2014] [Indexed: 12/16/2022] Open
Abstract
The eukaryotic translation factor, eIF5A has been recently reported as a sequence-specific elongation factor that facilitates peptide bond formation at consecutive prolines in Saccharomyces cerevisiae, as its ortholog elongation factor P (EF-P) does in bacteria. We have searched the genome databases of 35 representative organisms from six kingdoms of life for PPP (Pro-Pro-Pro) and/or PPG (Pro-Pro-Gly)-encoding genes whose expression is expected to depend on eIF5A. We have made detailed analyses of proteome data of 5 selected species, Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, Mus musculus and Homo sapiens. The PPP and PPG motifs are low in the prokaryotic proteomes. However, their frequencies markedly increase with the biological complexity of eukaryotic organisms, and are higher in newly derived proteins than in those orthologous proteins commonly shared in all species. Ontology classifications of S. cerevisiae and human genes encoding the highest level of polyprolines reveal their strong association with several specific biological processes, including actin/cytoskeletal associated functions, RNA splicing/turnover, DNA binding/transcription and cell signaling. Previously reported phenotypic defects in actin polarity and mRNA decay of eIF5A mutant strains are consistent with the proposed role for eIF5A in the translation of the polyproline-containing proteins. Of all the amino acid tandem repeats (≥3 amino acids), only the proline repeat frequency correlates with functional complexity of the five organisms examined. Taken together, these findings suggest the importance of proline repeat-rich proteins and a potential role for eIF5A and its hypusine modification pathway in the course of eukaryotic evolution.
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Affiliation(s)
- Ajeet Mandal
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Swati Mandal
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myung Hee Park
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland, United States of America
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Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O. The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation. Nucleic Acids Res 2014; 42:12295-305. [PMID: 25274739 PMCID: PMC4231759 DOI: 10.1093/nar/gku898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
EF-P is a bacterial tRNA-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. In Escherichia coli, EF-P is post-translationally modified on a conserved lysine residue. The post-translational modification is performed in a two-step reaction involving the addition of a β-lysine moiety and the subsequent hydroxylation, catalyzed by PoxA and YfcM, respectively. The β-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of the hydroxylation is poorly understood. We solved the crystal structure of YfcM and performed functional analyses to determine the hydroxylation mechanism. In addition, YfcM appears to be structurally distinct from any other hydroxylase structures reported so far. The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology. Furthermore, YfcM has a metal ion-coordinating motif, similar to YbeY. The metal ion-coordinating motif of YfcM resembles a 2-His-1-carboxylate motif, which coordinates an Fe(II) ion and forms the catalytic site of non-heme iron enzymes. Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P. Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM.
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Affiliation(s)
- Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Assaf Katz
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Andrei Rajkovic
- Molecular, Cell, and Developmental Biology Program, Ohio State University, Columbus, OH 43210, USA
| | - Ryohei Ishii
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Owen E Branson
- Department of Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael A Freitas
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
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Abstract
In addition to the small and large ribosomal subunits, aminoacyl-tRNAs, and an mRNA, cellular protein synthesis is dependent on translation factors. The eukaryotic translation initiation factor 5A (eIF5A) and its bacterial ortholog elongation factor P (EF-P) were initially characterized based on their ability to stimulate methionyl-puromycin (Met-Pmn) synthesis, a model assay for protein synthesis; however, the function of these factors in cellular protein synthesis has been difficult to resolve. Interestingly, a conserved lysine residue in eIF5A is post-translationally modified to hypusine and the corresponding lysine residue in EF-P from at least some bacteria is modified by the addition of a β-lysine moiety. In this review, we provide a summary of recent data that have identified a novel role for the translation factor eIF5A and its hypusine modification in the elongation phase of protein synthesis and more specifically in stimulating the production of proteins containing runs of consecutive proline residues.
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Affiliation(s)
- Thomas E. Dever
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Erik Gutierrez
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Byung-Sik Shin
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Kobayashi K, Suzuki T, Dohmae N, Ishitani R, Nureki O. Crystallization and preliminary X-ray crystallographic analysis of YfcM: an important factor for EF-P hydroxylation. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:1236-9. [PMID: 25195899 PMCID: PMC4157426 DOI: 10.1107/s2053230x14015726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/05/2014] [Indexed: 11/11/2022]
Abstract
Elongation factor P (EF-P) plays an essential role in the translation of polyproline-containing proteins in bacteria. It becomes functional by the post-translational modification of its highly conserved lysine residue. It is first β-lysylated by PoxA and then hydroxylated by YfcM. In this work, the YfcM protein from Escherichia coli was overexpressed, purified and crystallized. The crystal of YfcM was obtained by the in situ proteolysis crystallization method and diffracted X-rays to 1.45 Å resolution. It belonged to space group C2, with unit-cell parameters a = 124.4, b = 37.0, c = 37.6 Å, β = 101.2°. The calculated Matthews coefficient (VM) of the crystal was 1.91 Å(3) Da(-1), indicating that one YfcM molecule is present in the asymmetric unit with a solvent content of 35.7%.
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Affiliation(s)
- Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiro Suzuki
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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Hersch SJ, Elgamal S, Katz A, Ibba M, Navarre WW. Translation initiation rate determines the impact of ribosome stalling on bacterial protein synthesis. J Biol Chem 2014; 289:28160-71. [PMID: 25148683 DOI: 10.1074/jbc.m114.593277] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ribosome stalling during translation can be caused by a number of characterized mechanisms. However, the impact of elongation stalls on protein levels is variable, and the reasons for this are often unclear. To investigate this relationship, we examined the bacterial translation elongation factor P (EF-P), which plays a critical role in rescuing ribosomes stalled at specific amino acid sequences including polyproline motifs. In previous proteomic analyses of both Salmonella and Escherichia coli efp mutants, it was evident that not all proteins containing a polyproline motif were dependent on EF-P for efficient expression in vivo. The α- and β-subunits of ATP synthase, AtpA and AtpD, are translated from the same mRNA transcript, and both contain a PPG motif; however, proteomic analysis revealed that AtpD levels are strongly dependent on EF-P, whereas AtpA levels are independent of EF-P. Using these model proteins, we systematically determined that EF-P dependence is strongly influenced by elements in the 5'-untranslated region of the mRNA. By mutating either the Shine-Dalgarno sequence or the start codon, we find that EF-P dependence correlates directly with the rate of translation initiation where strongly expressed proteins show the greatest dependence on EF-P. Our findings demonstrate that polyproline-induced stalls exert a net effect on protein levels only if they limit translation significantly more than initiation. This model can be generalized to explain why sequences that induce pauses in translation elongation to, for example, facilitate folding do not necessarily exact a penalty on the overall production of the protein.
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Affiliation(s)
- Steven J Hersch
- From the Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada and
| | - Sara Elgamal
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Assaf Katz
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Michael Ibba
- the Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - William Wiley Navarre
- From the Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada and
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38
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EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genet 2014; 10:e1004553. [PMID: 25144653 PMCID: PMC4140641 DOI: 10.1371/journal.pgen.1004553] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/20/2014] [Indexed: 12/21/2022] Open
Abstract
Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp. To define the particular sequences that trigger ribosome stalling at diprolyl (PPX) motifs, we used ribosome profiling to monitor global ribosome occupancy in Escherichia coli strains lacking EF-P. Only 2.8% of PPX motifs caused significant ribosomal pausing in the Δefp strain, with up to a 45-fold increase in ribosome density observed at the pausing site. The unexpectedly low fraction of PPX motifs that produce a pause in translation led us to investigate the possible role of sequences upstream of PPX. Our data indicate that EF-P dependent pauses are strongly affected by sequences upstream of the PPX pattern. We found that residues as far as 3 codons upstream of the ribosomal peptidyl-tRNA site had a dramatic effect on whether or not a particular PPX motif triggered a ribosomal pause, while internal Shine Dalgarno sequences upstream of the motif had no effect on EF-P dependent translation efficiency. Increased ribosome occupancy at particular stall sites did not reliably correlate with a decrease in total protein levels, suggesting that in many cases other factors compensate for the potentially deleterious effects of stalling on protein synthesis. These findings indicate that the ability of a given PPX motif to initiate an EF-P-alleviated stall is strongly influenced by its local context, and that other indirect post-transcriptional effects determine the influence of such stalls on protein levels within the cell. Elongation factor P (EF-P) is a well-conserved bacterial protein. Although it can enhance protein synthesis in vitro, it is generally regarded as an ancillary factor required for robust translation of transcripts with stretches of consecutive prolines. In this work we performed ribosome profiling to better understand the role of EF-P during translation. Our data confirmed that translational effects due to lack of EF-P are mainly confined to PPX–encoding genes. Wide variations in EF-P dependent translation of these PPXs led us to investigate the effect of sequences upstream of diproline-containing motifs. We found that amino acids encoded upstream of PPX play a key role in EF-P-dependent translation. Finally, comparison of ribosome profiling data to existing proteomic data indicates that although many PPX-containing patterns have increased ribosome occupancies, this does not necessarily lead to altered protein levels. Taken together these data show a direct role for EF-P during synthesis of PPX motifs, and indirect effects on other post-transcriptional regulators of gene expression.
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Bai XH, Chen HJ, Jiang YL, Wen Z, Huang Y, Cheng W, Li Q, Qi L, Zhang JR, Chen Y, Zhou CZ. Structure of pneumococcal peptidoglycan hydrolase LytB reveals insights into the bacterial cell wall remodeling and pathogenesis. J Biol Chem 2014; 289:23403-16. [PMID: 25002590 DOI: 10.1074/jbc.m114.579714] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Streptococcus pneumoniae causes a series of devastating infections in humans. Previous studies have shown that the endo-β-N-acetylglucosaminidase LytB is critical for pneumococcal cell division and nasal colonization, but the biochemical mechanism of LytB action remains unknown. Here we report the 1.65 Å crystal structure of the catalytic domain (residues Lys-375-Asp-658) of LytB (termed LytBCAT), excluding the choline binding domain. LytBCAT consists of three structurally independent modules: SH3b, WW, and GH73. These modules form a "T-shaped" pocket that accommodates a putative tetrasaccharide-pentapeptide substrate of peptidoglycan. Structural comparison and simulation revealed that the GH73 module of LytB harbors the active site, including the catalytic residue Glu-564. In vitro assays of hydrolytic activity indicated that LytB prefers the peptidoglycan from the lytB-deficient pneumococci, suggesting the existence of a specific substrate of LytB in the immature peptidoglycan. Combined with in vitro cell-dispersing and in vivo cell separation assays, we demonstrated that all three modules are necessary for the optimal activity of LytB. Further functional analysis showed that the full catalytic activity of LytB is required for pneumococcal adhesion to and invasion into human lung epithelial cells. Structure-based alignment indicated that the unique modular organization of LytB is highly conserved in its orthologs from Streptococcus mitis group and Gemella species. These findings provided structural insights into the pneumococcal cell wall remodeling and novel hints for the rational design of therapeutic agents against pneumococcal growth and thereby the related diseases.
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Affiliation(s)
- Xiao-Hui Bai
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Hui-Jie Chen
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Yong-Liang Jiang
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Zhensong Wen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yubin Huang
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Wang Cheng
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Qiong Li
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Lei Qi
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuxing Chen
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Cong-Zhao Zhou
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
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40
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Rossi D, Kuroshu R, Zanelli CF, Valentini SR. eIF5A and EF-P: two unique translation factors are now traveling the same road. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:209-22. [PMID: 24402910 DOI: 10.1002/wrna.1211] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/01/2013] [Accepted: 11/06/2013] [Indexed: 11/09/2022]
Abstract
Translational control is extremely important in all organisms, and some of its aspects are highly conserved among all primary kingdoms, such as those related to the translation elongation step. The previously classified translation initiation factor 5A (eIF5A) and its bacterial homologue elongation factor P (EF-P) were discovered in the late 70's and have recently been the object of many studies. eIF5A and EF-P are the only cellular proteins that undergo hypusination and lysinylation, respectively, both of which are unique posttranslational modifications. Herein, we review all the important discoveries related to the biochemical and functional characterization of these factors, highlighting the implication of eIF5A in translation elongation instead of initiation. The findings that eIF5A and EF-P are important for specific cellular processes and play a role in the relief of ribosome stalling caused by specific amino acid sequences, such as those containing prolines reinforce the hypothesis that these factors are involved in specialized translation. Although there are some divergences between these unique factors, recent studies have clarified that they act similarly during protein synthesis. Further studies may reveal their precise mechanism of ribosome activity modulation as well as the mRNA targets that require eIF5A and EF-P for their proper translation.
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Affiliation(s)
- Danuza Rossi
- Department of Biological Sciences, School of Pharmaceutical Sciences, Univ Estadual Paulista (UNESP), Araraquara, SP, Brazil
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41
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Abstract
Although the ribosome is a very general catalyst, it cannot synthesize all protein sequences equally well. For example, ribosomes stall on the secretion monitor (SecM) leader peptide to regulate expression of a downstream gene. Using a genetic selection in Escherichia coli, we identified additional nascent peptide motifs that stall ribosomes. Kinetic studies show that some nascent peptides dramatically inhibit rates of peptide release by release factors. We find that residues upstream of the minimal stalling motif can either enhance or suppress this effect. In other stalling motifs, peptidyl transfer to certain aminoacyl-tRNAs is inhibited. In particular, three consecutive Pro codons pose a challenge for elongating ribosomes. The translation factor elongation factor P, which alleviates pausing at polyproline sequences, has little or no effect on other stalling peptides. The motifs that we identified are underrepresented in bacterial proteomes and show evidence of stalling on endogenous E. coli proteins.
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42
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Dias CAO, Garcia W, Zanelli CF, Valentini SR. eIF5A dimerizes not only in vitro but also in vivo and its molecular envelope is similar to the EF-P monomer. Amino Acids 2013; 44:631-44. [PMID: 22945904 DOI: 10.1007/s00726-012-1387-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 08/01/2012] [Indexed: 11/28/2022]
Abstract
The protein eukaryotic initiation factor 5A (eIF5A) is highly conserved among archaea and eukaryotes, but not in bacteria. Bacteria have the elongation factor P (EF-P), which is structurally and functionally related to eIF5A. eIF5A is essential for cell viability and the only protein known to contain the amino acid residue hypusine, formed by post-translational modification of a specific lysine residue. Although eIF5A was initially identified as a translation initiation factor, recent studies strongly support a function for eIF5A in the elongation step of translation. However, the mode of action of eIF5A is still unknown. Here, we analyzed the oligomeric state of yeast eIF5A. First, by using size-exclusion chromatography, we showed that this protein exists as a dimer in vitro, independent of the hypusine residue or electrostatic interactions. Protein-protein interaction assays demonstrated that eIF5A can form oligomers in vitro and in vivo, in an RNA-dependent manner, but independent of the hypusine residue or the ribosome. Finally, small-angle X-ray scattering (SAXS) experiments confirmed that eIF5A behaves as a stable dimer in solution. Moreover, the molecular envelope determined from the SAXS data shows that the eIF5A dimer is L-shaped and superimposable on the tRNA(Phe) tertiary structure, analogously to the EF-P monomer.
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Affiliation(s)
- Camila Arnaldo Olhê Dias
- Department of Biological Sciences, School of Pharmaceutical Sciences, UNESP-Univ Estadual Paulista, Rodovia Araraquara-Jaú, km 01, Araraquara, SP 14801-902, Brazil
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43
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Abstract
A protein that associates with the ribosome alleviates stalling and stimulates translation of proline-rich motifs.
[Also see Reports by
Ude
et al.
and
Doerfel
et al.
]
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Affiliation(s)
- Allen R Buskirk
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
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44
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Park JH, Johansson HE, Aoki H, Huang BX, Kim HY, Ganoza MC, Park MH. Post-translational modification by β-lysylation is required for activity of Escherichia coli elongation factor P (EF-P). J Biol Chem 2011; 287:2579-90. [PMID: 22128152 DOI: 10.1074/jbc.m111.309633] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical β-lysyl-lysine. Here we present biochemical evidence for β-lysyl-lysine modification in Escherichia coli EF-P and for its role in EF-P activity by characterizing native and recombinant EF-P proteins for their modification status and activity in vitro. Mass spectrometric analyses confirmed the lysyl modification at lysine 34 in native and recombinant EF-P proteins. The β-lysyl-lysine isopeptide was identified in the exhaustive Pronase digests of native EF-P and recombinant EF-P isolated from E. coli coexpressing EF-P, YjeA, and YjeK but not in the digests of proteins derived from the vectors encoding EF-P alone or EF-P together with YjeA, indicating that both enzymes, YjeA and YjeK, are required for β-lysylation of EF-P. Endogenous EF-P as well as the recombinant EF-P preparation containing β-lysyl-EF-P stimulated N-formyl-methionyl-puromycin synthesis ∼4-fold over the preparations containing unmodified EF-P and/or α-lysyl-EF-P. The mutant lacking the modification site lysine (K34A) was inactive. This is the first report of biochemical evidence for the β-lysylation of EF-P in vivo and the requirement for this modification for the activity of EF-P.
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Affiliation(s)
- Jong-Hwan Park
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland 20892, USA
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45
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Abstract
Elongation factor P (EF-P) is posttranslationally modified at a conserved lysyl residue by the coordinated action of two enzymes, PoxA and YjeK. We have previously established the importance of this modification in Salmonella stress resistance. Here we report that, like poxA and yjeK mutants, Salmonella strains lacking EF-P display increased susceptibility to hypoosmotic conditions, antibiotics, and detergents and enhanced resistance to the compound S-nitrosoglutathione. The susceptibility phenotypes are largely explained by the enhanced membrane permeability of the efp mutant, which exhibits increased uptake of the hydrophobic dye 1-N-phenylnaphthylamine (NPN). Analysis of the membrane proteomes of wild-type and efp mutant Salmonella strains reveals few changes, including the prominent overexpression of a single porin, KdgM, in the efp mutant outer membrane. Removal of KdgM in the efp mutant background ameliorates the detergent, antibiotic, and osmosensitivity phenotypes and restores wild-type permeability to NPN. Our data support a role for EF-P in the translational regulation of a limited number of proteins that, when perturbed, renders the cell susceptible to stress by the adventitious overexpression of an outer membrane porin.
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46
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Proteomics of early and late cold shock stress on thermophilic bacterium, Thermus sp. GH5. J Proteomics 2011; 74:2100-11. [DOI: 10.1016/j.jprot.2011.05.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 05/18/2011] [Accepted: 05/25/2011] [Indexed: 11/19/2022]
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47
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Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011; 75:361-422. [PMID: 21646433 PMCID: PMC3122624 DOI: 10.1128/mmbr.00039-10] [Citation(s) in RCA: 320] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.
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Affiliation(s)
- Beth N. Orcutt
- Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jason B. Sylvan
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Nina J. Knab
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Katrina J. Edwards
- Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
- Department of Earth Sciences, University of Southern California, Los Angeles, California 90089
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Henderson A, Hershey JW. Eukaryotic translation initiation factor (eIF) 5A stimulates protein synthesis in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2011; 108:6415-9. [PMID: 21451136 PMCID: PMC3081013 DOI: 10.1073/pnas.1008150108] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Within the field of eukaryotic protein synthesis, one factor remained putative for decades: eukaryotic translation initiation factor (eIF) 5A. Because eIF5A is an essential protein required for cell proliferation, and one easily targeted by inhibitors, identifying its role in the cell remains important and urgent. Recent reports support early findings that eIF5A stimulates protein synthesis and newly assign the factor a role in elongation rather than initiation. Here we show that eIF5A directly stimulates protein synthesis on native mRNAs, that rapid depletion of eIF5A in vivo immediately leads to a 2-fold inhibition of protein synthesis, and that both the immediate and lasting effects of eIF5A depletion are a reduction in polysome size concomitant with eIF5A depletion. Addition of purified eIF5A to a depleted lysate results in a roughly 2-fold stimulation of protein synthesis in vitro, a result consistent with both older methionyl-puromycin synthesis data and more recently published findings. We find that although eIF5A is not required for protein synthesis, it stimulates the process by about 2- to 3-fold. Our data, along with other published results, reinforce the conclusion that eIF5A stimulates protein synthesis with one important difference: Polysome profiles observed immediately after eIF5A depletion are diagnostic for a role in initiation. This discrepancy is discussed.
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Affiliation(s)
- Allen Henderson
- Department of Microbiology and Immunology, University of California, 513 Parnassus Avenue, Room S-472, San Francisco, CA 94143; and
| | - John W. Hershey
- Department of Biochemistry and Molecular Medicine, University of California, 4408 Tupper Hall, Davis, CA 95616
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49
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Nakamura Y, Ito K. tRNA mimicry in translation termination and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:647-68. [DOI: 10.1002/wrna.81] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Zou SB, Roy H, Ibba M, Navarre WW. Elongation factor P mediates a novel post-transcriptional regulatory pathway critical for bacterial virulence. Virulence 2011; 2:147-51. [PMID: 21317554 DOI: 10.4161/viru.2.2.15039] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bacterial pathogens detect and integrate multiple environmental signals to coordinate appropriate changes in gene expression including the selective expression of virulence factors, changes to metabolism and the activation of stress response systems. Mutations that abolish the ability of the pathogen to respond to external cues are typically attenuating. Here we discuss our recent discovery of a novel post-transcriptional regulatory pathway critical for Salmonella virulence and stress resistance. The enzymes PoxA and YjeK coordinately attach a unique beta-amino acid onto a highly conserved lysine residue in the translation factor elongation factor P (EF-P). Strains in which EF-P is unmodified due to the absence of PoxA or YjeK are attenuated for virulence and display highly pleiotropic phenotypes, including hypersusceptibility to a wide range of unrelated antimicrobial compounds. Work from our laboratory and others now suggests that EF-P, previously thought to be essential, instead plays an ancillary role in translation by regulating the synthesis of a relatively limited subset of proteins. Other observations suggest that the eukaryotic homolog of EF-P, eIF5A, may illicit similar changes in the translation machinery during stress adaptation, indicating that the role of these factors in physiology may be broadly conserved.
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Affiliation(s)
- S Betty Zou
- Department of Molecular Genetics, University of Toronto, ON, Canada
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