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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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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: 35] [Impact Index Per Article: 4.4] [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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