1
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Takada H, Fujiwara K, Atkinson GC, Chiba S, Hauryliuk V. Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT. Nucleic Acids Res 2024:gkae556. [PMID: 38943426 DOI: 10.1093/nar/gkae556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024] Open
Abstract
Efficiency of protein synthesis on the ribosome is strongly affected by the amino acid composition of the assembled amino acid chain. Challenging sequences include proline-rich motifs as well as highly positively and negatively charged amino acid stretches. Members of the F subfamily of ABC ATPases (ABCFs) have been long hypothesised to promote translation of such problematic motifs. In this study we have applied genetics and reporter-based assays to characterise the four housekeeping ABCF ATPases of Bacillus subtilis: YdiF, YfmM, YfmR/Uup and YkpA/YbiT. We show that YfmR cooperates with the translation factor EF-P that promotes translation of Pro-rich motifs. Simultaneous loss of both YfmR and EF-P results in a dramatic growth defect. Surprisingly, this growth defect can be largely suppressed though overexpression of an EF-P variant lacking the otherwise crucial 5-amino-pentanolylated residue K32. Using in vivo reporter assays, we show that overexpression of YfmR can alleviate ribosomal stalling on Asp-Pro motifs. Finally, we demonstrate that YkpA/YbiT promotes translation of positively and negatively charged motifs but is inactive in resolving ribosomal stalls on proline-rich stretches. Collectively, our results provide insights into the function of ABCF translation factors in modulating protein synthesis in B. subtilis.
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Affiliation(s)
- Hiraku Takada
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
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2
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Yang W, Ramadan S, Zu Y, Sun M, Huang X, Yu B. Chemical synthesis and functional evaluation of glycopeptides and glycoproteins containing rare glycosyl amino acid linkages. Nat Prod Rep 2024. [PMID: 38888170 DOI: 10.1039/d4np00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Covering: 1987 to 2023Naturally existing glycoproteins through post-translational protein glycosylation are highly heterogeneous, which not only impedes the structure-function studies, but also hinders the development of their potential medical usage. Chemical synthesis represents one of the most powerful tools to provide the structurally well-defined glycoforms. Being the key step of glycoprotein synthesis, glycosylation usually takes place at serine, threonine, and asparagine residues, leading to the predominant formation of the O- and N-glycans, respectively. However, other amino acid residues containing oxygen, nitrogen, sulfur, and nucleophilic carbon atoms have also been found to be glycosylated. These diverse glycoprotein linkages, occurring from microorganisms to plants and animals, play also pivotal biological roles, such as in cell-cell recognition and communication. The availability of these homogenous rare glycopeptides and glycoproteins can help decipher the glyco-code for developing therapeutic agents. This review highlights the chemical approaches for assembly of the functional glycopeptides and glycoproteins bearing these "rare" carbohydrate-amino acid linkages between saccharide and canonical amino acid residues and their derivatives.
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Affiliation(s)
- Weizhun Yang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Sherif Ramadan
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA.
| | - Yan Zu
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Mengxia Sun
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA.
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA.
| | - Biao Yu
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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3
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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4
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Hong HR, Prince CR, Tetreault DD, Wu L, Feaga HA. YfmR is a translation factor that prevents ribosome stalling and cell death in the absence of EF-P. Proc Natl Acad Sci U S A 2024; 121:e2314437121. [PMID: 38349882 PMCID: PMC10895253 DOI: 10.1073/pnas.2314437121] [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: 08/21/2023] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, such as polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. Here we identify YfmR as a translation factor that is essential in the absence of EF-P in Bacillus subtilis. YfmR is an ABCF ATPase that is closely related to both Uup and EttA, ABCFs that bind the ribosomal E-site and are conserved in more than 50% of bacterial genomes. We show that YfmR associates with actively translating ribosomes and that depleting YfmR from Δefp cells causes severe ribosome stalling at a polyproline tract in vivo. YfmR depletion from Δefp cells was lethal and caused reduced levels of actively translating ribosomes. Our results therefore identify YfmR as an important translation factor that is essential in B. subtilis in the absence of EF-P.
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Affiliation(s)
- Hye-Rim Hong
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | | | | | - Letian Wu
- Department of Microbiology, Cornell University, Ithaca, NY14853
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5
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Hong HR, Prince CR, Tetreault DD, Wu L, Feaga HA. YfmR is a translation factor that prevents ribosome stalling and cell death in the absence of EF-P. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552005. [PMID: 37577462 PMCID: PMC10418254 DOI: 10.1101/2023.08.04.552005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Protein synthesis is performed by the ribosome and a host of highly conserved elongation factors. Elongation factor P (EF-P) prevents ribosome stalling at difficult-to-translate sequences, particularly polyproline tracts. In bacteria, phenotypes associated with efp deletion range from modest to lethal, suggesting that some species encode an additional translation factor that has similar function to EF-P. Here we identify YfmR as a translation factor that is essential in the absence of EF-P in B. subtilis. YfmR is an ABCF ATPase that is closely related to both Uup and EttA, ABCFs that bind the ribosomal E-site and are conserved in more than 50% of bacterial genomes. We show that YfmR associates with actively translating ribosomes and that depleting YfmR from Δefp cells causes severe ribosome stalling at a polyproline tract in vivo. YfmR depletion from Δefp cells was lethal, and caused reduced levels of actively translating ribosomes. Our results therefore identify YfmR as an important translation factor that is essential in B. subtilis in the absence of EF-P.
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Affiliation(s)
- Hye-Rim Hong
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | | | | | - Letian Wu
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Heather A. Feaga
- Department of Microbiology, Cornell University, Ithaca, NY 14853
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6
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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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7
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Elongation factor P modulates Acinetobacter baumannii physiology and virulence as a cyclic dimeric guanosine monophosphate effector. Proc Natl Acad Sci U S A 2022; 119:e2209838119. [PMID: 36191190 PMCID: PMC9564936 DOI: 10.1073/pnas.2209838119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclic diguanosine monophosphate (c-di-GMP) is widely used by bacteria to control biological functions in response to diverse signals or cues. A previous study showed that potential c-di-GMP metabolic enzymes play a role in the regulation of biofilm formation and motility in Acinetobacter baumannii. However, it was unclear whether and how A. baumannii cells use c-di-GMP signaling to modulate biological functions. Here, we report that c-di-GMP is an important intracellular signal in the modulation of biofilm formation, motility, and virulence in A. baumannii. The intracellular level of c-di-GMP is principally controlled by the diguanylate cyclases (DGCs) A1S_1695, A1S_2506, and A1S_3296 and the phosphodiesterase (PDE) A1S_1254. Intriguingly, we revealed that A1S_2419 (an elongation factor P [EF-P]), is a novel c-di-GMP effector in A. baumannii. Response to a c-di-GMP signal boosted A1S_2419 activity to rescue ribosomes from stalling during synthesis of proteins containing consecutive prolines and thus regulate A. baumannii physiology and pathogenesis. Our study presents a unique and widely conserved effector that controls bacterial physiology and virulence by sensing the second messenger c-di-GMP.
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8
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Li S, Chen F, Li Y, Wang L, Li H, Gu G, Li E. Rhamnose-Containing Compounds: Biosynthesis and Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165315. [PMID: 36014553 PMCID: PMC9415975 DOI: 10.3390/molecules27165315] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Rhamnose-associated molecules are attracting attention because they are present in bacteria but not mammals, making them potentially useful as antibacterial agents. Additionally, they are also valuable for tumor immunotherapy. Thus, studies on the functions and biosynthetic pathways of rhamnose-containing compounds are in progress. In this paper, studies on the biosynthetic pathways of three rhamnose donors, i.e., deoxythymidinediphosphate-L-rhamnose (dTDP-Rha), uridine diphosphate-rhamnose (UDP-Rha), and guanosine diphosphate rhamnose (GDP-Rha), are firstly reviewed, together with the functions and crystal structures of those associated enzymes. Among them, dTDP-Rha is the most common rhamnose donor, and four enzymes, including glucose-1-phosphate thymidylyltransferase RmlA, dTDP-Glc-4,6-dehydratase RmlB, dTDP-4-keto-6-deoxy-Glc-3,5-epimerase RmlC, and dTDP-4-keto-Rha reductase RmlD, are involved in its biosynthesis. Secondly, several known rhamnosyltransferases from Geobacillus stearothermophilus, Saccharopolyspora spinosa, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Streptococcus pneumoniae are discussed. In these studies, however, the functions of rhamnosyltransferases were verified by employing gene knockout and radiolabeled substrates, which were almost impossible to obtain and characterize the products of enzymatic reactions. Finally, the application of rhamnose-containing compounds in disease treatments is briefly described.
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Affiliation(s)
- Siqiang Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Fujia Chen
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Yun Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Lizhen Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, China
| | - Hongyan Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
- Correspondence: (G.G.); (E.L.)
| | - Enzhong Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
- Correspondence: (G.G.); (E.L.)
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9
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Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria. THE ISME JOURNAL 2022; 16:1065-1073. [PMID: 34824398 DOI: 10.1038/s41396-021-01154-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022]
Abstract
Rapid bacterial growth depends on the speed at which ribosomes can translate mRNA into proteins. mRNAs that encode successive stretches of proline can cause ribosomes to stall, substantially reducing translation speed. Such stalling is especially detrimental for species that must grow and divide rapidly. Here, we focus on di-prolyl motifs (XXPPX) and ask whether their prevalence varies with growth rate. To find out we conducted a broad survey of such motifs in >3000 bacterial genomes across 35 phyla. Indeed, fast-growing species encode fewer motifs than slow-growing species, especially in highly expressed proteins. We also found many di-prolyl motifs within thermophiles, where prolines can help maintain proteome stability. Moreover, bacteria with complex, multicellular lifecycles also encode many di-prolyl motifs. This is especially evident in the slow-growing phylum Myxococcota. Bacteria in this phylum encode many serine-threonine kinases, and many di-prolyl motifs at potential phosphorylation sites within these kinases. Serine-threonine kinases are involved in cell signaling and help regulate developmental processes linked to multicellularity in the Myxococcota. Altogether, our observations suggest that weakened selection on translational rate, whether due to slow or thermophilic growth, may allow di-prolyl motifs to take on new roles in biological processes that are unrelated to translational rate.
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10
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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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11
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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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12
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Wagstaff BA, Zorzoli A, Dorfmueller HC. NDP-rhamnose biosynthesis and rhamnosyltransferases: building diverse glycoconjugates in nature. Biochem J 2021; 478:685-701. [PMID: 33599745 DOI: 10.1042/bcj20200505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/17/2022]
Abstract
Rhamnose is an important 6-deoxy sugar present in many natural products, glycoproteins, and structural polysaccharides. Whilst predominantly found as the l-enantiomer, instances of d-rhamnose are also found in nature, particularly in the Pseudomonads bacteria. Interestingly, rhamnose is notably absent from humans and other animals, which poses unique opportunities for drug discovery targeted towards rhamnose utilizing enzymes from pathogenic bacteria. Whilst the biosynthesis of nucleotide-activated rhamnose (NDP-rhamnose) is well studied, the study of rhamnosyltransferases that synthesize rhamnose-containing glycoconjugates is the current focus amongst the scientific community. In this review, we describe where rhamnose has been found in nature, as well as what is known about TDP-β-l-rhamnose, UDP-β-l-rhamnose, and GDP-α-d-rhamnose biosynthesis. We then focus on examples of rhamnosyltransferases that have been characterized using both in vivo and in vitro approaches from plants and bacteria, highlighting enzymes where 3D structures have been obtained. The ongoing study of rhamnose and rhamnosyltransferases, in particular in pathogenic organisms, is important to inform future drug discovery projects and vaccine development.
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Affiliation(s)
- Ben A Wagstaff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, U.K
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Azul Zorzoli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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13
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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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14
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Yakovlieva L, Wood TM, Kemmink J, Kotsogianni I, Koller F, Lassak J, Martin NI, Walvoort MTC. A β-hairpin epitope as novel structural requirement for protein arginine rhamnosylation. Chem Sci 2020; 12:1560-1567. [PMID: 34163919 PMCID: PMC8179230 DOI: 10.1039/d0sc05823h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
For canonical asparagine glycosylation, the primary amino acid sequence that directs glycosylation at specific asparagine residues is well-established. Here we reveal that a recently discovered bacterial enzyme EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the in vitro rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P, the enzyme readily glycosylates the same sequence in a cyclized β-hairpin mimic. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to guide future identifications of rhamnosylation sites in other protein substrates.
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Affiliation(s)
- Liubov Yakovlieva
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Thomas M Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands .,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University Utrecht The Netherlands
| | - Johan Kemmink
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands
| | - Franziska Koller
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München Planegg/Martinsried Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München Planegg/Martinsried Germany
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands
| | - Marthe T C Walvoort
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
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15
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Gast D, Koller F, Krafczyk R, Bauer L, Wunder S, Lassak J, Hoffmann-Röder A. A set of rhamnosylation-specific antibodies enables detection of novel protein glycosylations in bacteria. Org Biomol Chem 2020; 18:6823-6828. [PMID: 32936181 DOI: 10.1039/d0ob01289k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite its potential importance for bacterial virulence, protein rhamnosylation has not yet been sufficiently studied. Specific anti-SerRha, anti-ThrRha and anti-AsnRha antibodies allowed the identification of previously unknown monorhamnosylated proteins in cytosol and membrane fractions of bacterial cell lysates. Mapping of the complete rhamnoproteome in pathogens should facilitate development of targeted therapies against bacterial infections.
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Affiliation(s)
- Daniel Gast
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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16
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Pan X, Luo J, Li S. Bacteria-Catalyzed Arginine Glycosylation in Pathogens and Host. Front Cell Infect Microbiol 2020; 10:185. [PMID: 32411621 PMCID: PMC7199390 DOI: 10.3389/fcimb.2020.00185] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/07/2020] [Indexed: 01/25/2023] Open
Abstract
In recent years, protein glycosylation in pathogenic bacteria has attracted more and more attention, and accumulating evidence indicated that this type of posttranslational modification is involved in many physiological processes. The NleB from several enteropathogenic bacteria species as well as SseK from Salmonella enterica are type III secretion system effectors, which have an atypical N-acetylglucosamine (N-GlcNAc) transferase activity that specifically modified a conserved arginine in TRADD, FADD, and RIPK1. NleB/SseKs GlcNAcylation of death domain proteins abrogates homotypic and heterotypic death receptors/adaptors interactions, thereby blocking an important antimicrobial host response. Interestingly, NleB/SseKs could also GlcNAcylate themselves, and self-GlcNAcylation of NleB, SseK1, and SseK3 are crucial for their biological activity during infection. In addition, EarP (EF-P specific arginine rhamnosyl transferase for Posttranslational activation) catalyzes arginine rhamnosylation of translation elongation factor P (EF-P). Importantly, this kind of N-linked protein glycosylation is not only important for EF-P dependent rescue of polyproline stalled ribosomes but also for pathogenicity in Pseudomonas aeruginosa and other clinically relevant bacteria. Glycosylation of arginine is unique because the guanidine group of arginine has a high acid dissociation constant value and representing an extremely poor nucleophile. Recently, the crystal structures of NleB, SseKs, EarP, arginine GlcNAcylated death domain-containing proteins, NleB/FADD-DD, and EarP/EF-P/dTDP-β-L-rhamnose were solved by our group and other groups, revealing the unique catalytic mechanisms. In this review, we provide detailed information about the currently known arginine glycosyltransferases and their potential catalytic mechanisms.
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Affiliation(s)
- Xing Pan
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jie Luo
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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17
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Nothaft H, Szymanski CM. New discoveries in bacterial N-glycosylation to expand the synthetic biology toolbox. Curr Opin Chem Biol 2019; 53:16-24. [DOI: 10.1016/j.cbpa.2019.05.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022]
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18
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Lassak J, Koller F, Krafczyk R, Volkwein W. Exceptionally versatile – arginine in bacterial post-translational protein modifications. Biol Chem 2019; 400:1397-1427. [DOI: 10.1515/hsz-2019-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/01/2019] [Indexed: 12/24/2022]
Abstract
Abstract
Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.
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Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Franziska Koller
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Wolfram Volkwein
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
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19
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Hummels KR, Kearns DB. Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P. PLoS Genet 2019; 15:e1008179. [PMID: 31237868 PMCID: PMC6613710 DOI: 10.1371/journal.pgen.1008179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/08/2019] [Accepted: 05/07/2019] [Indexed: 11/19/2022] Open
Abstract
Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues, and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviates ribosome pausing at sequences encoding tandem prolines and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.
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Affiliation(s)
- Katherine R. Hummels
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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20
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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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21
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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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22
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Elongation factor P is required to maintain proteome homeostasis at high growth rate. Proc Natl Acad Sci U S A 2018; 115:11072-11077. [PMID: 30297417 DOI: 10.1073/pnas.1812025115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Elongation factor P (EF-P) is a universally conserved translation factor that alleviates ribosome pausing at polyproline (PPX) motifs by facilitating peptide bond formation. In the absence of EF-P, PPX peptide bond formation can limit translation rate, leading to pleotropic phenotypes including slowed growth, increased antibiotic sensitivity, and loss of virulence. In this study, we observe that many of these phenotypes are dependent on growth rate. Limiting growth rate suppresses a variety of detrimental phenotypes associated with ribosome pausing at PPX motifs in the absence of EF-P. Polysome levels are also similar to wild-type under slow growth conditions, consistent with global changes in ribosome queuing in cells without EF-P when growth rate is decreased. Inversely, under high protein synthesis demands, we observe that Escherichia coli lacking EF-P have reduced fitness. Our data demonstrate that EF-P-mediated relief of ribosome queuing is required to maintain proteome homeostasis under conditions of high translational demands.
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23
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Klee SM, Mostafa I, Chen S, Dufresne C, Lehman BL, Sinn JP, Peter KA, McNellis TW. An Erwinia amylovora yjeK mutant exhibits reduced virulence, increased chemical sensitivity and numerous environmentally dependent proteomic alterations. MOLECULAR PLANT PATHOLOGY 2018; 19:1667-1678. [PMID: 29232043 PMCID: PMC6638024 DOI: 10.1111/mpp.12650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 05/02/2023]
Abstract
The Gram-negative bacterium Erwinia amylovora causes fire blight, an economically important disease of apples and pears. Elongation factor P (EF-P) is a highly conserved protein that stimulates the formation of the first peptide bond of certain proteins and facilitates the translation of certain proteins, including those with polyproline motifs. YjeK and YjeA are two enzymes involved in the essential post-translational β-lysylation of EF-P at a conserved lysine residue, K34. EF-P, YjeA and YjeK have been shown to be essential for the full virulence of Escherichia coli, Salmonella species and Agrobacterium tumefaciens, with efp, yjeA and yjeK mutants having highly similar phenotypes. Here, we identified an E. amylovora yjeK::Tn5 transposon mutant with decreased virulence in apple fruit and trees. The yjeK::Tn5 mutant also showed pleiotropic phenotypes, including reduced growth in rich medium, lower extracellular polysaccharide production, reduced swimming motility and increased chemical sensitivity compared with the wild-type, whilst maintaining wild-type level growth in minimal medium. All yjeK::Tn5 mutant phenotypes were complemented in trans with a plasmid bearing a wild-type copy of yjeK. Comprehensive, quantitative proteomics analyses revealed numerous, environmentally dependent changes in the prevalence of a wide range of proteins, in higher abundance and lower abundance, in yjeK::Tn5 compared with the wild-type, and many of these alterations could be linked to yjeK::Tn5 mutant phenotypes. The environmental dependence of the yjeK::Tn5 mutant proteomic alterations suggests that YjeK could be required for aspects of the environmentally dependent regulation of protein translation. YjeK activity may be critical to overcoming stress, including the challenging host environment faced by invading pathogenic bacteria.
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Affiliation(s)
- Sara M. Klee
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
- Graduate Program in Plant PathologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
| | - Islam Mostafa
- Department of BiologyUniversity of FloridaGainesvilleFL 32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFL 32611USA
- Department of Pharmacognosy, Faculty of PharmacyZagazig UniversityZagazig 44519Egypt
| | - Sixue Chen
- Department of BiologyUniversity of FloridaGainesvilleFL 32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFL 32611USA
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFL 32611USA
- Interdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFL 32611USA
| | | | - brian L. Lehman
- The Pennsylvania State University Fruit Research and Extension CenterBiglervillePA 17307USA
| | - Judith P. Sinn
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
| | - Kari A. Peter
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
- The Pennsylvania State University Fruit Research and Extension CenterBiglervillePA 17307USA
| | - Timothy W. McNellis
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
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24
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EF-P Posttranslational Modification Has Variable Impact on Polyproline Translation in Bacillus subtilis. mBio 2018; 9:mBio.00306-18. [PMID: 29615499 PMCID: PMC5885033 DOI: 10.1128/mbio.00306-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Elongation factor P (EF-P) is a ubiquitous translation factor that facilitates translation of polyproline motifs. In order to perform this function, EF-P generally requires posttranslational modification (PTM) on a conserved residue. Although the position of the modification is highly conserved, the structure can vary widely between organisms. In Bacillus subtilis, EF-P is modified at Lys32 with a 5-aminopentanol moiety. Here, we use a forward genetic screen to identify genes involved in 5-aminopentanolylation. Tandem mass spectrometry analysis of the PTM mutant strains indicated that ynbB, gsaB, and ymfI are required for modification and that yaaO, yfkA, and ywlG influence the level of modification. Structural analyses also showed that EF-P can retain unique intermediate modifications, suggesting that 5-aminopentanol is likely directly assembled on EF-P through a novel modification pathway. Phenotypic characterization of these PTM mutants showed that each mutant does not strictly phenocopy the efp mutant, as has previously been observed in other organisms. Rather, each mutant displays phenotypic characteristics consistent with those of either the efp mutant or wild-type B. subtilis depending on the growth condition. In vivo polyproline reporter data indicate that the observed phenotypic differences result from variation in both the severity of polyproline translation defects and altered EF-P context dependence in each mutant. Together, these findings establish a new EF-P PTM pathway and also highlight a unique relationship between EF-P modification and polyproline context dependence. Despite the high level of conservation of EF-P, the posttranslational modification pathway that activates EF-P is highly divergent between species. Here, we have identified and characterized in B. subtilis a novel posttranslational modification pathway. This pathway not only broadens the scope of potential EF-P modification strategies, but it also indicates that EF-P modifications can be assembled directly on EF-P. Furthermore, characterization of these PTM mutants has established that an altered modification state can impact both the severity of polyproline translational defects and context dependence.
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25
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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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26
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Qi F, Motz M, Jung K, Lassak J, Frishman D. Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation. PLoS Comput Biol 2018; 14:e1005987. [PMID: 29389943 PMCID: PMC5811046 DOI: 10.1371/journal.pcbi.1005987] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/13/2018] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Translation of consecutive prolines causes ribosome stalling, which is alleviated but cannot be fully compensated by the elongation factor P. However, the presence of polyproline motifs in about one third of the E. coli proteins underlines their potential functional importance, which remains largely unexplored. We conducted an evolutionary analysis of polyproline motifs in the proteomes of 43 E. coli strains and found evidence of evolutionary selection against translational stalling, which is especially pronounced in proteins with high translational efficiency. Against the overall trend of polyproline motif loss in evolution, we observed their enrichment in the vicinity of translational start sites, in the inter-domain regions of multi-domain proteins, and downstream of transmembrane helices. Our analysis demonstrates that the time gain caused by ribosome pausing at polyproline motifs might be advantageous in protein regions bracketing domains and transmembrane helices. Polyproline motifs might therefore be crucial for co-translational folding and membrane insertion. Polyproline motifs induce ribosome stalling during translation, but the functional significance of this effect remains unclear. Our evolutionary analysis of polyproline motifs reveals that they are disfavored in E. coli proteomes as a consequence of the reduced translation efficiency, supporting the conjecture that translation efficiency-based evolutionary pressure shapes protein sequences. Enrichment of polyproline motifs in the protein regions bracketing structural domains and transmembrane helices indicates their regulatory role in co-translational protein folding and transmembrane helix insertion. Polyproline motifs could thus serve as protein-level cis-acting elements, which directly regulate the rate of translation elongation.
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Affiliation(s)
- Fei Qi
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Magdalena Motz
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jürgen Lassak
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany.,St Petersburg State Polytechnic University, St Petersburg, Russia
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27
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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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28
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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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29
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Abstract
Bacterial elongation factor P (EF-P) plays a pivotal role in the translation of polyproline motifs. To stimulate peptide bond formation, EF-P must enter the ribosome via an empty E-site. Using fluorescence-based single-molecule tracking, Mohapatra et al. (S. Mohapatra, H. Choi, X. Ge, S. Sanyal, and J. C. Weisshaar, mBio 8:e00300-17, 2017, https://doi.org/10.1128/mBio.00300-17) monitored the cellular distribution of EF-P and quantified the frequency of association between EF-P and the ribosome under various conditions. Findings from the study showed that EF-P has a localization pattern that is strikingly similar to that of ribosomes. Intriguingly, EF-P was seen to bind ribosomes more frequently than the estimated number of pausing events, indicating that E-site vacancies occur even when ribosomes are not paused. The study provides new insights into the mechanism of EF-P-dependent peptide bond formation and the intricacies of translation elongation.
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30
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Wang S, Corcilius L, Sharp PP, Payne RJ. Synthesis of a GlcNAcylated arginine building block for the solid phase synthesis of death domain glycopeptide fragments. Bioorg Med Chem 2017; 25:2895-2900. [PMID: 28320614 DOI: 10.1016/j.bmc.2017.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/28/2017] [Accepted: 03/05/2017] [Indexed: 11/26/2022]
Abstract
Herein we describe the synthesis of glycopeptide fragments from the death domains of TRADD and FADD bearing the recently discovered Nω-GlcNAc-β-arginine post-translational modification. TRADD and FADD glycopeptides were accessed through the use of a suitably protected synthetic glycosylamino acid 'cassette' that could be directly incorporated into conventional solid phase peptide synthesis (SPPS) protocols.
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Affiliation(s)
- Siyao Wang
- School of Chemistry, The University of Sydney, Sydney 2006, Australia
| | - Leo Corcilius
- School of Chemistry, The University of Sydney, Sydney 2006, Australia
| | - Phillip P Sharp
- ACRF Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, VIC 3052, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney 2006, Australia.
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31
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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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32
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Van Ostrand R, Jacobsen C, Delahunty A, Stringer C, Noorbehesht R, Ahmed H, Awad AM. Synthesis and antibacterial activity of 5'-tetrachlorophthalimido and 5'-azido 5'-deoxyribonucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:181-197. [PMID: 28045593 DOI: 10.1080/15257770.2016.1250906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Reported is an efficient synthesis of adenyl and uridyl 5'-tetrachlorophthalimido-5'-deoxyribonucleosides, and guanylyl 5'-azido-5'-deoxyribonucleosides, which are useful in solid-phase synthesis of phosphoramidate and ribonucleic guanidine oligonucleotides. Replacement of 5'-hydroxyl with tetrachlorophthalimido group was performed via Mitsunobu reaction for adenosine and uridine. An alternative method was applied for guanosine which replaced the 5'-hydroxyl with an azido group. The resulting compounds were converted to 5'-amino-5'-deoxyribonucleosides for oligonucleotide synthesis. Synthetic intermediates were tested as antimicrobials against six bacterial strains. All analogs containing the 2',3'-O-isopropylidine protecting group demonstrated antibacterial activity against Neisseria meningitidis, and among those analogs with 5'-tetrachlorophthalimido and 5'-azido demonstrated increased antibacterial effect.
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Affiliation(s)
- Robert Van Ostrand
- a Chemistry Program, California State University Channel Islands , Camarillo , CA , USA
| | - Casey Jacobsen
- a Chemistry Program, California State University Channel Islands , Camarillo , CA , USA
| | - Alicia Delahunty
- a Chemistry Program, California State University Channel Islands , Camarillo , CA , USA
| | - Carley Stringer
- a Chemistry Program, California State University Channel Islands , Camarillo , CA , USA
| | - Ryan Noorbehesht
- a Chemistry Program, California State University Channel Islands , Camarillo , CA , USA
| | - Haidi Ahmed
- a Chemistry Program, California State University Channel Islands , Camarillo , CA , USA
| | - Ahmed M Awad
- a Chemistry Program, California State University Channel Islands , Camarillo , CA , USA
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33
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Wang S, Corcilius L, Sharp PP, Rajkovic A, Ibba M, Parker BL, Payne RJ. Synthesis of rhamnosylated arginine glycopeptides and determination of the glycosidic linkage in bacterial elongation factor P. Chem Sci 2016; 8:2296-2302. [PMID: 28451332 PMCID: PMC5363394 DOI: 10.1039/c6sc03847f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 12/09/2016] [Indexed: 12/27/2022] Open
Abstract
We describe the synthesis and incorporation of α- and β-configured rhamnosyl arginine cassettes into Pseudomonas aeruginosa elongation factor P-derived glycopeptides. These were used to unequivocally determine the native anomeric configuration of the rhamnose moiety in EF-P.
A new class of N-linked protein glycosylation – arginine rhamnosylation – has recently been discovered as a critical modification for the function of bacterial elongation factor P (EF-P). Herein, we describe the synthesis of suitably protected α- and β-rhamnosylated arginine amino acid “cassettes” that can be directly installed into rhamnosylated peptides. Preparation of a proteolytic fragment of Pseudomonas aeruginosa EF-P bearing both α- and β-rhamnosylated arginine enabled the unequivocal determination of the native glycosidic linkage to be α through 2D NMR and nano-UHPLC-tandem mass spectrometry studies.
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Affiliation(s)
- Siyao Wang
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia .
| | - Leo Corcilius
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia .
| | - Phillip P Sharp
- ACRF Chemical Biology Division , Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade , VIC3052 , Australia
| | - Andrei Rajkovic
- Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Michael Ibba
- Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Benjamin L Parker
- Charles Perkins Centre , The University of Sydney , NSW 2006 , Australia
| | - Richard J Payne
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia .
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34
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Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:7316725. [PMID: 28053595 PMCID: PMC5178350 DOI: 10.1155/2016/7316725] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/27/2016] [Accepted: 11/06/2016] [Indexed: 11/17/2022]
Abstract
Translation initiation factor 5A (IF5A) is essential and highly conserved in Eukarya (eIF5A) and Archaea (aIF5A). The activity of IF5A requires hypusine, a posttranslational modification synthesized in Eukarya from the polyamine precursor spermidine. Intracellular polyamine analyses revealed that agmatine and cadaverine were the main polyamines produced in Haloferax volcanii in minimal medium, raising the question of how hypusine is synthesized in this halophilic Archaea. Metabolic reconstruction led to a tentative picture of polyamine metabolism and aIF5A modification in Hfx. volcanii that was experimentally tested. Analysis of aIF5A from Hfx. volcanii by LC-MS/MS revealed it was exclusively deoxyhypusinylated. Genetic studies confirmed the role of the predicted arginine decarboxylase gene (HVO_1958) in agmatine synthesis. The agmatinase-like gene (HVO_2299) was found to be essential, consistent with a role in aIF5A modification predicted by physical clustering evidence. Recombinant deoxyhypusine synthase (DHS) from S. cerevisiae was shown to transfer 4-aminobutyl moiety from spermidine to aIF5A from Hfx. volcanii in vitro. However, at least under conditions tested, this transfer was not observed with the Hfx. volcanii DHS. Furthermore, the growth of Hfx. volcanii was not inhibited by the classical DHS inhibitor GC7. We propose a model of deoxyhypusine synthesis in Hfx. volcanii that differs from the canonical eukaryotic pathway, paving the way for further studies.
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35
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Li X, Krafczyk R, Macošek J, Li YL, Zou Y, Simon B, Pan X, Wu QY, Yan F, Li S, Hennig J, Jung K, Lassak J, Hu HG. Resolving the α-glycosidic linkage of arginine-rhamnosylated translation elongation factor P triggers generation of the first Arg Rha specific antibody. Chem Sci 2016; 7:6995-7001. [PMID: 28451135 PMCID: PMC5363779 DOI: 10.1039/c6sc02889f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/20/2016] [Indexed: 12/23/2022] Open
Abstract
A previously discovered posttranslational modification strategy - arginine rhamnosylation - is essential for elongation factor P (EF-P) dependent rescue of polyproline stalled ribosomes in clinically relevant species such as Pseudomonas aeruginosa and Neisseria meningitidis. However, almost nothing is known about this new type of N-linked glycosylation. In the present study we used NMR spectroscopy to show for the first time that the α anomer of rhamnose is attached to Arg32 of EF-P, demonstrating that the corresponding glycosyltransferase EarP inverts the sugar of its cognate substrate dTDP-β-l-rhamnose. Based on this finding we describe the synthesis of an α-rhamnosylated arginine containing peptide antigen in order to raise the first anti-rhamnosyl arginine specific antibody (anti-ArgRha). Using ELISA and Western Blot analyses we demonstrated both its high affinity and specificity without any cross-reactivity to other N-glycosylated proteins. Having the anti-ArgRha at hand we were able to visualize endogenously produced rhamnosylated EF-P. Thus, we expect the antibody to be not only important to monitor EF-P rhamnosylation in diverse bacteria but also to identify further rhamnosyl arginine containing proteins. As EF-P rhamnosylation is essential for pathogenicity, our antibody might also be a powerful tool in drug discovery.
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Affiliation(s)
- Xiang Li
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Ralph Krafczyk
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Jakub Macošek
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Yu-Lei Li
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China . .,School of Pharmacy , Wei Fang Medical University , Shandong 261053 , China
| | - Yan Zou
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Bernd Simon
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Xing Pan
- Institute of Infection and Immunity , Taihe Hospital , Hubei University of Medicine , Shiyan , Hubei 442000 , China
| | - Qiu-Ye Wu
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
| | - Fang Yan
- School of Pharmacy , Wei Fang Medical University , Shandong 261053 , China
| | - Shan Li
- Institute of Infection and Immunity , Taihe Hospital , Hubei University of Medicine , Shiyan , Hubei 442000 , China
| | - Janosch Hennig
- Structural and Computational Biology Unit , EMBL Heidelberg , Heidelberg 69117 , Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Jürgen Lassak
- Department of Biology I, Microbiology , Ludwig Maximilians-Universität München , Munich , Germany.,Center for Integrated Protein Science Munich , Ludwig-Maximilians-Universität München , Munich , Germany .
| | - Hong-Gang Hu
- Department of Organic Chemistry , School of Pharmacy , Second Military Medical University , Shanghai 200433 , China .
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