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Vaňková Hausnerová V, Shoman M, Kumar D, Schwarz M, Modrák M, Jirát Matějčková J, Mikesková E, Neva S, Herrmannová A, Šiková M, Halada P, Novotná I, Pajer P, Valášek LS, Převorovský M, Krásný L, Hnilicová J. RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria. Nucleic Acids Res 2024; 52:4604-4626. [PMID: 38348908 PMCID: PMC11077062 DOI: 10.1093/nar/gkae081] [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: 07/21/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/09/2024] Open
Abstract
Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far-6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.
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Affiliation(s)
- Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Mahmoud Shoman
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Dilip Kumar
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Marek Schwarz
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Martin Modrák
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Department of Bioinformatics, Second Faculty of Medicine, Charles University, Prague150 06, Czech Republic
| | - Jitka Jirát Matějčková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Eliška Mikesková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Silvia Neva
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Michaela Šiková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Petr Halada
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Vestec252 50, Czech Republic
| | - Iva Novotná
- Military Health Institute, Military Medical Agency, Prague169 02, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Prague169 02, Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague128 00, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
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2
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Seely SM, Basu RS, Gagnon MG. Mechanistic insights into the alternative ribosome recycling by HflXr. Nucleic Acids Res 2024; 52:4053-4066. [PMID: 38407413 DOI: 10.1093/nar/gkae128] [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: 11/06/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024] Open
Abstract
During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ritwika S Basu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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3
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Beardslee PC, Schmitz KR. Toxin-based screening of C-terminal tags in Escherichia coli reveals the exceptional potency of ssrA-like degrons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.576913. [PMID: 38352471 PMCID: PMC10862746 DOI: 10.1101/2024.01.29.576913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
All bacteria possess ATP-dependent proteases that destroy cytosolic proteins. These enzymes help cells mitigate proteotoxic stress, adapt to changing nutrient availability, regulate virulence phenotypes, and transition to pathogenic lifestyles. Moreover, ATP-dependent proteases have emerged as promising antibacterial and antivirulence targets in a variety of pathogens. The physiological roles of these proteases are largely defined by the complement of proteins that they degrade. Substrates are typically recognized in a highly selective manner, often via short unstructured sequences termed degrons. While a few degrons have been identified and rigorously characterized, we lack a systematic understanding of how proteases select valid degrons from the vast complexity of protein sequence space. Here, we describe a novel high-throughput screening approach in Escherichia coli that couples proteolysis of a protein toxin to cell survival. We used this method to screen a combinatorial library of C-terminal pentapeptide sequences for functionality as proteolytic degrons in wild type E. coli, and in strains lacking components of the ClpXP and ClpAP proteases. By examining the competitive enrichment of sequences over time, we found that about one percent of pentapeptide tags lead to toxin proteolysis. Interestingly, the most enriched degrons were ClpXP-dependent and highly similar to the ssrA tag, one of the most extensively characterized degrons in bacteria. Among ssrA-like sequences, we observed that specific upstream residues correlate with successful recognition. The lack of diversity among strongly enriched sequences suggests that ssrA-like tags comprise a uniquely potent class of short C-terminal degron in E. coli. Efficient proteolysis of substrates lacking such degrons likely requires adaptors or multivalent interactions. These findings broaden our understanding of the constraints that shape the bacterial proteolytic landscape. Our screening approach may be broadly applicable to probing aspects of proteolytic substrate selection in other bacterial systems.
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Affiliation(s)
- Patrick C. Beardslee
- Department of Chemistry & Biochemistry, University of Delaware, Newark DE, 19716
| | - Karl R. Schmitz
- Department of Chemistry & Biochemistry, University of Delaware, Newark DE, 19716
- Department of Biological Sciences, University of Delaware, Newark DE, 19716
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4
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Venkataraman P, Nagendra P, Ahlawat N, Brajesh RG, Saini S. Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence. Front Mol Biosci 2024; 11:1286824. [PMID: 38660375 PMCID: PMC11039892 DOI: 10.3389/fmolb.2024.1286824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/15/2024] [Indexed: 04/26/2024] Open
Abstract
Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However, pleiotropic behaviour was observed in several environmental contexts, including other carbon environments. Genome sequencing reveals that mutations in global regulators rpoB and rpoC cause this pleiotropy. We report three new alleles of the rpoB gene, and one new allele of the rpoC gene. The novel rpoB alleles confer resistance to Rifampicin, and alter motility. Our results show how single nucleotide changes in the process of adaptation in minimal media can lead to wide-scale pleiotropy, resulting in changes in traits that are not under direct selection.
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Affiliation(s)
| | | | | | | | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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5
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Sanyal S, Kouznetsova A, Ström L, Björkegren C. A system for inducible mitochondria-specific protein degradation in vivo. Nat Commun 2024; 15:1454. [PMID: 38365818 PMCID: PMC10873288 DOI: 10.1038/s41467-024-45819-6] [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: 02/24/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Targeted protein degradation systems developed for eukaryotes employ cytoplasmic machineries to perform proteolysis. This has prevented mitochondria-specific analysis of proteins that localize to multiple locations, for example, the mitochondria and the nucleus. Here, we present an inducible mitochondria-specific protein degradation system in Saccharomyces cerevisiae based on the Mesoplasma florum Lon (mf-Lon) protease and its corresponding ssrA tag (called PDT). We show that mitochondrially targeted mf-Lon protease efficiently and selectively degrades a PDT-tagged reporter protein localized to the mitochondrial matrix. The degradation can be induced by depleting adenine from the medium, and tuned by altering the promoter strength of the MF-LON gene. We furthermore demonstrate that mf-Lon specifically degrades endogenous, PDT-tagged mitochondrial proteins. Finally, we show that mf-Lon-dependent PDT degradation can also be achieved in human mitochondria. In summary, this system provides an efficient tool to selectively analyze the mitochondrial function of dually localized proteins.
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Affiliation(s)
- Swastika Sanyal
- Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83, Huddinge, Sweden.
| | - Anna Kouznetsova
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77, Stockholm, Sweden
| | - Lena Ström
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77, Stockholm, Sweden
| | - Camilla Björkegren
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77, Stockholm, Sweden.
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6
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Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H. Structural basis of ribosomal 30S subunit degradation by RNase R. Nature 2024; 626:1133-1140. [PMID: 38326618 PMCID: PMC10901742 DOI: 10.1038/s41586-024-07027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
Protein synthesis is a major energy-consuming process of the cell that requires the controlled production1-3 and turnover4,5 of ribosomes. Although the past few years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3' to 5' exonuclease ribonuclease R (RNase R). The structures reveal that RNase R binds at first to the 30S platform to facilitate the degradation of the functionally important anti-Shine-Dalgarno sequence and the decoding-site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S subunit, and this is overcome by a major structural rearrangement of the 30S head, involving the loss of ribosomal proteins. RNase R parallels this movement and relocates to the decoding site by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also indicate that the enzyme alone is sufficient for complete degradation of 30S subunits. Collectively, our results provide a mechanistic basis for the degradation of 30S mediated by RNase R, and reveal that RNase R targets orphaned 30S subunits using a dynamic mechanism involving an anchored switching of binding sites.
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Affiliation(s)
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Sander Granneman
- Centre for Engineering Biology (SynthSys), University of Edinburgh, Edinburgh, UK
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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7
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Dos Santos OAL, Carneiro RL, Requião RD, Ribeiro-Alves M, Domitrovic T, Palhano FL. Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells. Sci Rep 2024; 14:1439. [PMID: 38228636 PMCID: PMC10792078 DOI: 10.1038/s41598-023-50811-z] [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: 08/30/2023] [Accepted: 12/26/2023] [Indexed: 01/18/2024] Open
Abstract
During protein synthesis, organisms detect translation defects that induce ribosome stalling and result in protein aggregation. The Ribosome-associated Quality Control (RQC) complex, comprising TCF25, LTN1, and NEMF, is responsible for identifying incomplete protein products from unproductive translation events, targeting them for degradation. Although RQC disruption causes adverse effects on vertebrate neurons, data regarding mRNA/protein expression and regulation across tissues are lacking. Employing high-throughput methods, we analyzed public datasets to explore RQC gene expression and phenotypes. Our findings revealed widespread expression of RQC components in human tissues; however, silencing of RQC yielded only mild negative effects on cell growth. Notably, TCF25 exhibited elevated mRNA levels that were not reflected in the protein content. We experimentally demonstrated that this disparity arose from post-translational protein degradation by the proteasome. Additionally, we observed that cellular aging marginally influenced RQC expression, leading to reduced mRNA levels in specific tissues. Our results suggest the necessity of RQC expression in all mammalian tissues. Nevertheless, when RQC falters, alternative mechanisms seem to compensate, ensuring cell survival under nonstress conditions.
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Affiliation(s)
- Otávio Augusto Leitão Dos Santos
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodolfo L Carneiro
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodrigo D Requião
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, 21040-900, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Fernando L Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
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8
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Ghanbarpour A, Cohen SE, Fei X, Kinman LF, Bell TA, Zhang JJ, Baker TA, Davis JH, Sauer RT. A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation. Nat Commun 2023; 14:7281. [PMID: 37949857 PMCID: PMC10638403 DOI: 10.1038/s41467-023-43145-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
AAA+ proteases degrade intracellular proteins in a highly specific manner. E. coli ClpXP, for example, relies on a C-terminal ssrA tag or other terminal degron sequences to recognize proteins, which are then unfolded by ClpX and subsequently translocated through its axial channel and into the degradation chamber of ClpP for proteolysis. Prior cryo-EM structures reveal that the ssrA tag initially binds to a ClpX conformation in which the axial channel is closed by a pore-2 loop. Here, we show that substrate-free ClpXP has a nearly identical closed-channel conformation. We destabilize this closed-channel conformation by deleting residues from the ClpX pore-2 loop. Strikingly, open-channel ClpXP variants degrade non-native proteins lacking degrons faster than the parental enzymes in vitro but degraded GFP-ssrA more slowly. When expressed in E. coli, these open channel variants behave similarly to the wild-type enzyme in assays of filamentation and phage-Mu plating but resulted in reduced growth phenotypes at elevated temperatures or when cells were exposed to sub-lethal antibiotic concentrations. Thus, channel closure is an important determinant of ClpXP degradation specificity.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Steven E Cohen
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Xue Fei
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Laurel F Kinman
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Tristan A Bell
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Jia Jia Zhang
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Tania A Baker
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA
| | - Joseph H Davis
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA.
| | - Robert T Sauer
- Department of Biology Massachusetts Institute of Technology Cambridge, Cambridge, MA, 02139, USA.
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9
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Patil PR, Burroughs AM, Misra M, Cerullo F, Costas-Insua C, Hung HC, Dikic I, Aravind L, Joazeiro CAP. Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10. Cell Rep 2023; 42:113100. [PMID: 37676773 PMCID: PMC10591846 DOI: 10.1016/j.celrep.2023.113100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/11/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
In ribosome-associated quality control (RQC), nascent polypeptides produced by interrupted translation are modified with C-terminal polyalanine tails ("Ala-tails") that function outside ribosomes to induce ubiquitylation by E3 ligases Pirh2 (p53-induced RING-H2 domain-containing) or CRL2 (Cullin-2 RING ligase2)-KLHDC10. Here, we investigate the molecular basis of Ala-tail function using biochemical and in silico approaches. We show that Pirh2 and KLHDC10 directly bind to Ala-tails and that structural predictions identify candidate Ala-tail-binding sites, which we experimentally validate. The degron-binding pockets and specific pocket residues implicated in Ala-tail recognition are conserved among Pirh2 and KLHDC10 homologs, suggesting that an important function of these ligases across eukaryotes is in targeting Ala-tailed substrates. Moreover, we establish that the two Ala-tail-binding pockets have convergently evolved, either from an ancient module of bacterial provenance (Pirh2) or via tinkering of a widespread C-degron-recognition element (KLHDC10). These results shed light on the recognition of a simple degron sequence and the evolution of Ala-tail proteolytic signaling.
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Affiliation(s)
- Pratik Rajendra Patil
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mohit Misra
- Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Federico Cerullo
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - Carlos Costas-Insua
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - Hao-Chih Hung
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, USA.
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10
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Morra R, Pratama F, Butterfield T, Tomazetto G, Young K, Lopez R, Dixon N. arfA antisense RNA regulates MscL excretory activity. Life Sci Alliance 2023; 6:e202301954. [PMID: 37012050 PMCID: PMC10070815 DOI: 10.26508/lsa.202301954] [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: 01/27/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Excretion of cytoplasmic protein (ECP) is a commonly observed phenomenon in bacteria, and this partial extracellular localisation of the intracellular proteome has been implicated in a variety of stress response mechanisms. In response to hypoosmotic shock and ribosome stalling in Escherichia coli, ECP is dependent upon the presence of the large-conductance mechanosensitive channel and the alternative ribosome-rescue factor A gene products. However, it is not known if a mechanistic link exists between the corresponding genes and the respective stress response pathways. Here, we report that the corresponding mscL and arfA genes are commonly co-located on the genomes of Gammaproteobacteria and display overlap in their respective 3' UTR and 3' CDS. We show this unusual genomic arrangement permits an antisense RNA-mediated regulatory control between mscL and arfA, and this modulates MscL excretory activity in E. coli These findings highlight a mechanistic link between osmotic, translational stress responses and ECP in E. coli, further elucidating the previously unknown regulatory function of arfA sRNA.
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Affiliation(s)
- Rosa Morra
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Fenryco Pratama
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Institut Teknologi Bandung, Bandung, Indonesia
| | - Thomas Butterfield
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Geizecler Tomazetto
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Kate Young
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Ruth Lopez
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Neil Dixon
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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11
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Patil PR, Burroughs AM, Misra M, Cerullo F, Dikic I, Aravind L, Joazeiro CAP. Mechanism and evolutionary origins of Alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539038. [PMID: 37205381 PMCID: PMC10187211 DOI: 10.1101/2023.05.03.539038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In Ribosome-associated Quality Control (RQC), nascent-polypeptides produced by interrupted translation are modified with C-terminal polyalanine tails ('Ala-tails') that function outside ribosomes to induce ubiquitylation by Pirh2 or CRL2-KLHDC10 E3 ligases. Here we investigate the molecular basis of Ala-tail function using biochemical and in silico approaches. We show that Pirh2 and KLHDC10 directly bind to Ala-tails, and structural predictions identify candidate Ala-tail binding sites, which we experimentally validate. The degron-binding pockets and specific pocket residues implicated in Ala-tail recognition are conserved among Pirh2 and KLHDC10 homologs, suggesting that an important function of these ligases across eukaryotes is in targeting Ala-tailed substrates. Moreover, we establish that the two Ala-tail binding pockets have convergently evolved, either from an ancient module of bacterial provenance (Pirh2) or via tinkering of a widespread C-degron recognition element (KLHDC10). These results shed light on the recognition of a simple degron sequence and the evolution of Ala-tail proteolytic signaling.
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12
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Wang X, Li Y, Yan X, Yang Q, Zhang B, Zhang Y, Yuan X, Jiang C, Chen D, Liu Q, Liu T, Mi W, Yu Y, Dong C. Recognition of an Ala-rich C-degron by the E3 ligase Pirh2. Nat Commun 2023; 14:2474. [PMID: 37120596 PMCID: PMC10148881 DOI: 10.1038/s41467-023-38173-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
The ribosome-associated quality-control (RQC) pathway degrades aberrant nascent polypeptides arising from ribosome stalling during translation. In mammals, the E3 ligase Pirh2 mediates the degradation of aberrant nascent polypeptides by targeting the C-terminal polyalanine degrons (polyAla/C-degrons). Here, we present the crystal structure of Pirh2 bound to the polyAla/C-degron, which shows that the N-terminal domain and the RING domain of Pirh2 form a narrow groove encapsulating the alanine residues of the polyAla/C-degron. Affinity measurements in vitro and global protein stability assays in cells further demonstrate that Pirh2 recognizes a C-terminal A/S-X-A-A motif for substrate degradation. Taken together, our study provides the molecular basis underlying polyAla/C-degron recognition by Pirh2 and expands the substrate recognition spectrum of Pirh2.
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Affiliation(s)
- Xiaolu Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Tianjin Medical University, 300070, Tianjin, China
| | - Yao Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Xiaojie Yan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Qing Yang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Bing Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Ying Zhang
- Department of Immunology, Tianjin Institute of Immunology, Tianjin Medical University, 300070, Tianjin, China
| | - Xinxin Yuan
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Chenhao Jiang
- Department of Immunology, Tianjin Institute of Immunology, Tianjin Medical University, 300070, Tianjin, China
| | - Dongxing Chen
- Department of Medicinal Chemistry, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, 300070, Tianjin, China
| | - Quanyan Liu
- Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Tong Liu
- Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, 300211, Tianjin, China
| | - Wenyi Mi
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Immunology, Tianjin Institute of Immunology, Tianjin Medical University, 300070, Tianjin, China
| | - Ying Yu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Tianjin Medical University, 300070, Tianjin, China.
| | - Cheng Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China.
- Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital, 300052, Tianjin, China.
- Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, 300211, Tianjin, China.
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13
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D'Urso G, Guyomar C, Chat S, Giudice E, Gillet R. Insights into the ribosomal trans-translation rescue system: lessons from recent structural studies. FEBS J 2023; 290:1461-1472. [PMID: 35015931 DOI: 10.1111/febs.16349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/27/2021] [Accepted: 01/10/2022] [Indexed: 11/29/2022]
Abstract
The arrest of protein synthesis caused when ribosomes stall on an mRNA lacking a stop codon is a deadly risk for all cells. In bacteria, this situation is remedied by the trans-translation quality control system. Trans-translation occurs because of the synergistic action of two main partners, transfer-messenger RNA (tmRNA) and small protein B (SmpB). These act in complex to monitor protein synthesis, intervening when necessary to rescue stalled ribosomes. During this process, incomplete nascent peptides are tagged for destruction, problematic mRNAs are degraded and the previously stalled ribosomes are recycled. In this 'Structural Snapshot' article, we describe the mechanism at the molecular level, a view updated after the most recent structural studies using cryo-electron microscopy.
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Affiliation(s)
- Gaetano D'Urso
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Charlotte Guyomar
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Sophie Chat
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Emmanuel Giudice
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Reynald Gillet
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
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14
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Davies MR, Keller N, Brouwer S, Jespersen MG, Cork AJ, Hayes AJ, Pitt ME, De Oliveira DMP, Harbison-Price N, Bertolla OM, Mediati DG, Curren BF, Taiaroa G, Lacey JA, Smith HV, Fang NX, Coin LJM, Stevens K, Tong SYC, Sanderson-Smith M, Tree JJ, Irwin AD, Grimwood K, Howden BP, Jennison AV, Walker MJ. Detection of Streptococcus pyogenes M1 UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA. Nat Commun 2023; 14:1051. [PMID: 36828918 PMCID: PMC9951164 DOI: 10.1038/s41467-023-36717-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
A new variant of Streptococcus pyogenes serotype M1 (designated 'M1UK') has been reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase in invasive infections, and exhibiting enhanced expression of the superantigen SpeA. The progenitor S. pyogenes 'M1global' and M1UK clones can be differentiated by 27 SNPs and 4 indels, yet the mechanism for speA upregulation is unknown. Here we investigate the previously unappreciated expansion of M1UK in Australia, now isolated from the majority of serious infections caused by serotype M1 S. pyogenes. M1UK sub-lineages circulating in Australia also contain a novel toxin repertoire associated with epidemic scarlet fever causing S. pyogenes in Asia. A single SNP in the 5' transcriptional leader sequence of the transfer-messenger RNA gene ssrA drives enhanced SpeA superantigen expression as a result of ssrA terminator read-through in the M1UK lineage. This represents a previously unappreciated mechanism of toxin expression and urges enhanced international surveillance.
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Affiliation(s)
- Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Nadia Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miranda E Pitt
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Olivia M Bertolla
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bodie F Curren
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen V Smith
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Ning-Xia Fang
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martina Sanderson-Smith
- Illawarra Health and Medical Research Institute and Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Adam D Irwin
- University of Queensland Centre for Clinical Research, Brisbane, QLD, Australia.,Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, QLD, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Amy V Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Queensland Health, Coopers Plains, QLD, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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15
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Zabolotskii AI, Kozlovskiy SV, Katrukha AG. The Influence of the Nucleotide Composition of Genes and Gene Regulatory Elements on the Efficiency of Protein Expression in Escherichia coli. BIOCHEMISTRY (MOSCOW) 2023; 88:S176-S191. [PMID: 37069120 DOI: 10.1134/s0006297923140109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Recombinant proteins expressed in Escherichia coli are widely used in biochemical research and industrial processes. At the same time, achieving higher protein expression levels and correct protein folding still remains the key problem, since optimization of nutrient media, growth conditions, and methods for induction of protein synthesis do not always lead to the desired result. Often, low protein expression is determined by the sequences of the expressed genes and their regulatory regions. The genetic code is degenerated; 18 out of 20 amino acids are encoded by more than one codon. Choosing between synonymous codons in the coding sequence can significantly affect the level of protein expression and protein folding due to the influence of the gene nucleotide composition on the probability of formation of secondary mRNA structures that affect the ribosome binding at the translation initiation phase, as well as the ribosome movement along the mRNA during elongation, which, in turn, influences the mRNA degradation and the folding of the nascent protein. The nucleotide composition of the mRNA untranslated regions, in particular the promoter and Shine-Dalgarno sequences, also affects the efficiency of mRNA transcription, translation, and degradation. In this review, we describe the genetic principles that determine the efficiency of protein production in Escherichia coli.
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Affiliation(s)
- Artur I Zabolotskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | - Alexey G Katrukha
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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16
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Jadhav P, Chen Y, Butzin N, Buceta J, Urchueguía A. Bacterial degrons in synthetic circuits. Open Biol 2022; 12:220180. [PMID: 35975648 PMCID: PMC9382460 DOI: 10.1098/rsob.220180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial proteases are a promising post-translational regulation strategy in synthetic circuits because they recognize specific amino acid degradation tags (degrons) that can be fine-tuned to modulate the degradation levels of tagged proteins. For this reason, recent efforts have been made in the search for new degrons. Here we review the up-to-date applications of degradation tags for circuit engineering in bacteria. In particular, we pay special attention to the effects of degradation bottlenecks in synthetic oscillators and introduce mathematical approaches to study queueing that enable the quantitative modelling of proteolytic queues.
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Affiliation(s)
- Prajakta Jadhav
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
| | - Arantxa Urchueguía
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
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17
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Shimohata N, Harada Y, Hayano T. Proteomic analysis of nascent polypeptide chains that potentially induce translational pausing during elongation. Biosci Biotechnol Biochem 2022; 86:1262-1269. [PMID: 35749475 DOI: 10.1093/bbb/zbac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022]
Abstract
Currently, proteins equipped with "ribosomal arrest peptides" (RAPs) that regulate the expression of downstream genes and their own activity by pausing their own translation during elongation are extensively studied. However, studies focusing on RAP have been conducted primarily in prokaryotic cells; studies on eukaryotic cells, especially mammalian cells, are limited. In the present study, we comprehensively examined translationally arrested nascent polypeptides to gain novel insights into RAPs in mammalian cells. Cetyltrimethylammonium bromide was used to obtain nascent polypeptide chains that were translationally arrested during translation elongation. After proteomic analysis, additional screening by discriminating according to amino acid residues at the C-terminal end revealed several novel RAP candidates. Our method can be applied for comprehensive RAP studies in mammalian cells.
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Affiliation(s)
- Nobuyuki Shimohata
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan.,Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan
| | - Yudai Harada
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan
| | - Toshiya Hayano
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan
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18
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Filbeck S, Cerullo F, Pfeffer S, Joazeiro CAP. Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell 2022; 82:1451-1466. [PMID: 35452614 PMCID: PMC9034055 DOI: 10.1016/j.molcel.2022.03.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
Ribosome-associated quality-control (RQC) surveys incomplete nascent polypeptides produced by interrupted translation. Central players in RQC are the human ribosome- and tRNA-binding protein, NEMF, and its orthologs, yeast Rqc2 and bacterial RqcH, which sense large ribosomal subunits obstructed with nascent chains and then promote nascent-chain proteolysis. In canonical eukaryotic RQC, NEMF stabilizes the LTN1/Listerin E3 ligase binding to obstructed ribosomal subunits for nascent-chain ubiquitylation. Furthermore, NEMF orthologs across evolution modify nascent chains by mediating C-terminal, untemplated polypeptide elongation. In eukaryotes, this process exposes ribosome-buried nascent-chain lysines, the ubiquitin acceptor sites, to LTN1. Remarkably, in both bacteria and eukaryotes, C-terminal tails also have an extra-ribosomal function as degrons. Here, we discuss recent findings on RQC mechanisms and briefly review how ribosomal stalling is sensed upstream of RQC, including via ribosome collisions, from an evolutionary perspective. Because RQC defects impair cellular fitness and cause neurodegeneration, this knowledge provides a framework for pathway-related biology and disease studies.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Florida, Jupiter, FL 33458, USA.
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19
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Sauer RT, Fei X, Bell TA, Baker TA. Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis. Crit Rev Biochem Mol Biol 2022; 57:188-204. [PMID: 34923891 PMCID: PMC9871882 DOI: 10.1080/10409238.2021.1979461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ClpXP is an archetypical AAA+ protease, consisting of ClpX and ClpP. ClpX is an ATP-dependent protein unfoldase and polypeptide translocase, whereas ClpP is a self-compartmentalized peptidase. ClpXP is currently the only AAA+ protease for which high-resolution structures exist, the molecular basis of recognition for a protein substrate is understood, extensive biochemical and genetic analysis have been performed, and single-molecule optical trapping has allowed direct visualization of the kinetics of substrate unfolding and translocation. In this review, we discuss our current understanding of ClpXP structure and function, evaluate competing sequential and probabilistic mechanisms of ATP hydrolysis, and highlight open questions for future exploration.
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Affiliation(s)
- Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xue Fei
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan A. Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tania A. Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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20
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Matavacas J, von Wachenfeldt C. Update on the Protein Homeostasis Network in Bacillus subtilis. Front Microbiol 2022; 13:865141. [PMID: 35350626 PMCID: PMC8957991 DOI: 10.3389/fmicb.2022.865141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Protein homeostasis is fundamental to cell function and survival. It relies on an interconnected network of processes involving protein synthesis, folding, post-translational modification and degradation as well as regulators of these processes. Here we provide an update on the roles, regulation and subcellular localization of the protein homeostasis machinery in the Gram-positive model organism Bacillus subtilis. We discuss emerging ideas and current research gaps in the field that, if tackled, increase our understanding of how Gram-positive bacteria, including several human pathogens, maintain protein homeostasis and cope with stressful conditions that challenge their survival.
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21
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Szydlo K, Ignatova Z, Gorochowski TE. Improving the Robustness of Engineered Bacteria to Nutrient Stress Using Programmed Proteolysis. ACS Synth Biol 2022; 11:1049-1059. [PMID: 35174698 PMCID: PMC9097571 DOI: 10.1021/acssynbio.1c00490] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 11/30/2022]
Abstract
The use of short peptide tags in synthetic genetic circuits allows for the tuning of gene expression dynamics and release of amino acid resources through targeted protein degradation. Here, we use elements of the Escherichia coli and Mesoplasma florum transfer-mRNA (tmRNA) ribosome rescue systems to compare endogenous and foreign proteolysis systems in E. coli. We characterize the performance and burden of each and show that, while both greatly shorten the half-life of a tagged protein, the endogenous system is approximately 10 times more efficient. On the basis of these results we then demonstrate using mathematical modeling and experiments how proteolysis can improve cellular robustness through targeted degradation of a reporter protein in auxotrophic strains, providing a limited secondary source of essential amino acids that help partially restore growth when nutrients become scarce. These findings provide avenues for controlling the functional lifetime of engineered cells once deployed and increasing their tolerance to fluctuations in nutrient availability.
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Affiliation(s)
- Klara Szydlo
- Institute
of Biochemistry and Molecular Biology, University
of Hamburg, 20146, Hamburg, Germany
| | - Zoya Ignatova
- Institute
of Biochemistry and Molecular Biology, University
of Hamburg, 20146, Hamburg, Germany
| | - Thomas E. Gorochowski
- School
of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, United Kingdom
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22
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Thakur M, Breger JC, Susumu K, Oh E, Spangler JR, Medintz IL, Walper SA, Ellis GA. Self-assembled nanoparticle-enzyme aggregates enhance functional protein production in pure transcription-translation systems. PLoS One 2022; 17:e0265274. [PMID: 35298538 PMCID: PMC8929567 DOI: 10.1371/journal.pone.0265274] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/27/2022] [Indexed: 11/19/2022] Open
Abstract
Cell-free protein synthesis systems (CFPS) utilize cellular transcription and translation (TX-TL) machinery to synthesize proteins in vitro. These systems are useful for multiple applications including production of difficult proteins, as high-throughput tools for genetic circuit screening, and as systems for biosensor development. Though rapidly evolving, CFPS suffer from some disadvantages such as limited reaction rates due to longer diffusion times, significant cost per assay when using commercially sourced materials, and reduced reagent stability over prolonged periods. To address some of these challenges, we conducted a series of proof-of-concept experiments to demonstrate enhancement of CFPS productivity via nanoparticle assembly driven nanoaggregation of its constituent proteins. We combined a commercially available CFPS that utilizes purified polyhistidine-tagged (His-tag) TX-TL machinery with CdSe/CdS/ZnS core/shell/shell quantum dots (QDs) known to readily coordinate His-tagged proteins in an oriented fashion. We show that nanoparticle scaffolding of the CFPS cross-links the QDs into nanoaggregate structures while enhancing the production of functional recombinant super-folder green fluorescent protein and phosphotriesterase, an organophosphate hydrolase; the latter by up to 12-fold. This enhancement, which occurs by an undetermined mechanism, has the potential to improve CFPS in general and specifically CFPS-based biosensors (faster response time) while also enabling rapid detoxification/bioremediation through point-of-concern synthesis of similar catalytic enzymes. We further show that such nanoaggregates improve production in diluted CFPS reactions, which can help to save money and extend the amount of these costly reagents. The results are discussed in the context of what may contribute mechanistically to the enhancement and how this can be applied to other CFPS application scenarios.
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Affiliation(s)
- Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- College of Science, George Mason University, Fairfax, Virginia, United States of America
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- Jacobs Corporation, Dallas, Texas, United States of America
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Joseph R. Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
| | - Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia, United States of America
- * E-mail:
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23
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Cerullo F, Filbeck S, Patil PR, Hung HC, Xu H, Vornberger J, Hofer FW, Schmitt J, Kramer G, Bukau B, Hofmann K, Pfeffer S, Joazeiro CAP. Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. Nature 2022; 603:509-514. [PMID: 35264791 DOI: 10.1038/s41586-022-04487-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/28/2022] [Indexed: 12/12/2022]
Abstract
Ribosome stalling during translation is detrimental to cellular fitness, but how this is sensed and elicits recycling of ribosomal subunits and quality control of associated mRNA and incomplete nascent chains is poorly understood1,2. Here we uncover Bacillus subtilis MutS2, a member of the conserved MutS family of ATPases that function in DNA mismatch repair3, as an unexpected ribosome-binding protein with an essential function in translational quality control. Cryo-electron microscopy analysis of affinity-purified native complexes shows that MutS2 functions in sensing collisions between stalled and translating ribosomes and suggests how ribosome collisions can serve as platforms to deploy downstream processes: MutS2 has an RNA endonuclease small MutS-related (SMR) domain, as well as an ATPase/clamp domain that is properly positioned to promote ribosomal subunit dissociation, which is a requirement both for ribosome recycling and for initiation of ribosome-associated protein quality control (RQC). Accordingly, MutS2 promotes nascent chain modification with alanine-tail degrons-an early step in RQC-in an ATPase domain-dependent manner. The relevance of these observations is underscored by evidence of strong co-occurrence of MutS2 and RQC genes across bacterial phyla. Overall, the findings demonstrate a deeply conserved role for ribosome collisions in mounting a complex response to the interruption of translation within open reading frames.
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Affiliation(s)
- Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Pratik Rajendra Patil
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hao-Chih Hung
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Haifei Xu
- Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Julia Vornberger
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florian W Hofer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jaro Schmitt
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Guenter Kramer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Bernd Bukau
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany. .,Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA.
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Muto A, Goto S, Kurita D, Ushida C, Soma A, Himeno H. A leaderless mRNA including tRNA-like sequence encodes a small peptide that regulates the expression of GcvB small RNA in Escherichia coli. J Biochem 2022; 171:459-465. [PMID: 35081614 DOI: 10.1093/jb/mvac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 11/14/2022] Open
Abstract
A tRNA-like sequence conserved in the genomes of all Escherichia coli strains was found. The sequence resembles arginine-tRNA, which is present in E. coli pathogenic islands and phages. Expression experiments revealed that this sequence is a part of a leaderless mRNA encoding a short peptide (60 amino acids: XtpA). A deletion mutant of this gene is more sensitive than wild-type cell to several aminoglycoside antibiotics at low concentrations. Further analyses indicated that XtpA positively regulates the expression of GcvB small RNA, which is involved in the intrinsic resistance to aminoblycosides in E. coli.
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Affiliation(s)
- Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Chisato Ushida
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Akiko Soma
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
| | - Hyota Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Bioscience, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
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25
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Campos-Silva R, D’Urso G, Delalande O, Giudice E, Macedo AJ, Gillet R. Trans-Translation Is an Appealing Target for the Development of New Antimicrobial Compounds. Microorganisms 2021; 10:3. [PMID: 35056452 PMCID: PMC8778911 DOI: 10.3390/microorganisms10010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 01/06/2023] Open
Abstract
Because of the ever-increasing multidrug resistance in microorganisms, it is crucial that we find and develop new antibiotics, especially molecules with different targets and mechanisms of action than those of the antibiotics in use today. Translation is a fundamental process that uses a large portion of the cell's energy, and the ribosome is already the target of more than half of the antibiotics in clinical use. However, this process is highly regulated, and its quality control machinery is actively studied as a possible target for new inhibitors. In bacteria, ribosomal stalling is a frequent event that jeopardizes bacterial wellness, and the most severe form occurs when ribosomes stall at the 3'-end of mRNA molecules devoid of a stop codon. Trans-translation is the principal and most sophisticated quality control mechanism for solving this problem, which would otherwise result in inefficient or even toxic protein synthesis. It is based on the complex made by tmRNA and SmpB, and because trans-translation is absent in eukaryotes, but necessary for bacterial fitness or survival, it is an exciting and realistic target for new antibiotics. Here, we describe the current and future prospects for developing what we hope will be a novel generation of trans-translation inhibitors.
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Affiliation(s)
- Rodrigo Campos-Silva
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil;
| | - Gaetano D’Urso
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Olivier Delalande
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Emmanuel Giudice
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Alexandre José Macedo
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil;
| | - Reynald Gillet
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
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26
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Harwood CR, Kikuchi Y. The ins and outs of Bacillus proteases: activities, functions and commercial significance. FEMS Microbiol Rev 2021; 46:6354784. [PMID: 34410368 PMCID: PMC8767453 DOI: 10.1093/femsre/fuab046] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
Because the majority of bacterial species divide by binary fission, and do not have distinguishable somatic and germline cells, they could be considered to be immortal. However, bacteria ‘age’ due to damage to vital cell components such as DNA and proteins. DNA damage can often be repaired using efficient DNA repair mechanisms. However, many proteins have a functional ‘shelf life’; some are short lived, while others are relatively stable. Specific degradation processes are built into the life span of proteins whose activities are required to fulfil a specific function during a prescribed period of time (e.g. cell cycle, differentiation process, stress response). In addition, proteins that are irreparably damaged or that have come to the end of their functional life span need to be removed by quality control proteases. Other proteases are involved in performing a variety of specific functions that can be broadly divided into three categories: processing, regulation and feeding. This review presents a systematic account of the proteases of Bacillus subtilis and their activities. It reviews the proteases found in, or associated with, the cytoplasm, the cell membrane, the cell wall and the external milieu. Where known, the impacts of the deletion of particular proteases are discussed, particularly in relation to industrial applications.
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Affiliation(s)
- Colin R Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University NE2 4AX, Newcastle upon Tyne, UK
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, JAPAN
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Multi-omics Study of Planobispora rosea, Producer of the Thiopeptide Antibiotic GE2270A. mSystems 2021; 6:e0034121. [PMID: 34156292 PMCID: PMC8269224 DOI: 10.1128/msystems.00341-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Planobispora rosea is the natural producer of the potent thiopeptide antibiotic GE2270A. Here, we present the results of a metabolomics and transcriptomics analysis of P. rosea during production of GE2270A. The data generated provides useful insights into the biology of this genetically intractable bacterium. We characterize the details of the shutdown of protein biosynthesis and the respiratory chain associated with the end of the exponential growth phase. We also provide the first description of the phosphate regulon in P. rosea. Based on the transcriptomics data, we show that both phosphate and iron are limiting P. rosea growth in our experimental conditions. Additionally, we identified and validated a new biosynthetic gene cluster associated with the production of the siderophores benarthin and dibenarthin in P. rosea. Together, the metabolomics and transcriptomics data are used to inform and refine the very first genome-scale metabolic model for P. rosea, which will be a valuable framework for the interpretation of future studies of the biology of this interesting but poorly characterized species. IMPORTANCEPlanobispora rosea is a genetically intractable bacterium used for the production of GE2270A on an industrial scale. GE2270A is a potent thiopeptide antibiotic currently used as a precursor for the synthesis of two compounds under clinical studies for the treatment of Clostridium difficile infection and acne. Here, we present the very first systematic multi-omics investigation of this important bacterium, which provides a much-needed detailed picture of the dynamics of metabolism of P. rosea while producing GE2270A. Author Video: An author video summary of this article is available.
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28
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Wu S, Li X, Wang G. tRNA-like structures and their functions. FEBS J 2021; 289:5089-5099. [PMID: 34117728 DOI: 10.1111/febs.16070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 06/10/2021] [Indexed: 11/27/2022]
Abstract
tRNA-like structures (TLSs) were first identified in the RNA genomes of turnip yellow mosaic virus. Since then, TLSs have been found in many other species including mammals, and the RNAs harboring these structures range from viral genomic RNAs to mRNAs and noncoding RNAs. Some progress has also been made on understanding their functions that include regulation of RNA replication, translation enhancement, RNA-protein interaction, and more. In this review, we summarize the current knowledge about the regulations and functions of these TLSs. Possible future directions of the field are also briefly discussed.
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Affiliation(s)
- Sipeng Wu
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Xiang Li
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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29
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Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
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Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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30
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Abstract
C-terminal tailing is an ancient and conserved form of peptide synthesis that protects cells from incomplete and potentially toxic translation products. Filbeck et al. (2020) and Crowe-McAuliffe et al. (2020) use structural, genetic, and biochemical approaches to elucidate the mechanisms driving C-terminal tailing.
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Affiliation(s)
- Onn Brandman
- Department of Biochemistry, Stanford University, Palo Alto, CA 94305, USA.
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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31
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Filbeck S, Cerullo F, Paternoga H, Tsaprailis G, Joazeiro CAP, Pfeffer S. Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Mol Cell 2020; 81:104-114.e6. [PMID: 33259811 DOI: 10.1016/j.molcel.2020.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved RQC factor, senses the obstruction and recruits tRNAAla(UGC) to modify nascent-chain C termini with a polyalanine degron. However, how RqcH and its eukaryotic homologs (Rqc2 and NEMF), despite their relatively simple architecture, synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained unknown. Here, we present cryoelectron microscopy (cryo-EM) structures of Bacillus subtilis RQC complexes representing different Ala tail synthesis steps. The structures explain how tRNAAla is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNAAla into a hybrid A/P-state associated with peptidyl-transfer. Finally, we provide structural, biochemical, and molecular genetic evidence identifying the Hsp15 homolog (encoded by rqcP) as a novel RQC component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Helge Paternoga
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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32
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Abstract
Ro60 ribonucleoproteins (RNPs), composed of the ring-shaped Ro 60-kDa (Ro60) protein and noncoding RNAs called Y RNAs, are present in all three domains of life. Ro60 was first described as an autoantigen in patients with rheumatic disease, and Ro60 orthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla. Their functions have been characterized primarily in Deinococcus radiodurans, the first sequenced bacterium with a recognizable ortholog. In D. radiodurans, the Ro60 ortholog enhances the ability of 3'-to-5' exoribonucleases to degrade structured RNA during several forms of environmental stress. Y RNAs are regulators that inhibit or allow the interactions of Ro60 with other proteins and RNAs. Studies of Ro60 RNPs in other bacteria hint at additional functions, since the most conserved Y RNA contains a domain that is a close tRNA mimic and Ro60 RNPs are often encoded adjacent to components of RNA repair systems.
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Affiliation(s)
- Soyeong Sim
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Kevin Hughes
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA; , , ,
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33
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The ClpX and ClpP2 Orthologs of Chlamydia trachomatis Perform Discrete and Essential Functions in Organism Growth and Development. mBio 2020; 11:mBio.02016-20. [PMID: 32873765 PMCID: PMC7468207 DOI: 10.1128/mbio.02016-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chlamydia trachomatis is the leading cause of infectious blindness globally and the most reported bacterial sexually transmitted infection both domestically and internationally. Given the economic burden, the lack of an approved vaccine, and the use of broad-spectrum antibiotics for treatment of infections, an understanding of chlamydial growth and development is critical for the advancement of novel targeted antibiotics. The Clp proteins comprise an important and conserved protease system in bacteria. Our work highlights the importance of the chlamydial Clp proteins to this clinically important bacterium. Additionally, our study implicates the Clp system playing an integral role in chlamydial developmental cycle progression, which may help establish models of how Chlamydia spp. and other bacteria progress through their respective developmental cycles. Our work also contributes to a growing body of Clp-specific research that underscores the importance and versatility of this system throughout bacterial evolution and further validates Clp proteins as drug targets. Chlamydia trachomatis is an obligate intracellular bacterium that undergoes a complex developmental cycle in which the bacterium differentiates between two functionally and morphologically distinct forms, the elementary body (EB) and reticulate body (RB), each of which expresses its own specialized repertoire of proteins. Both primary (EB to RB) and secondary (RB to EB) differentiations require protein turnover, and we hypothesize that proteases are critical for mediating differentiation. The Clp protease system is well conserved in bacteria and important for protein turnover. Minimally, the system relies on a serine protease subunit, ClpP, and an AAA+ ATPase, such as ClpX, that recognizes and unfolds substrates for ClpP degradation. In Chlamydia, ClpX is encoded within an operon 3′ to clpP2. We present evidence that the chlamydial ClpX and ClpP2 orthologs are essential to organism viability and development. We demonstrate here that chlamydial ClpX is a functional ATPase and forms the expected homohexamer in vitro. Overexpression of a ClpX mutant lacking ATPase activity had a limited impact on DNA replication or secondary differentiation but, nonetheless, reduced EB viability with observable defects in EB morphology noted. Conversely, overexpression of a catalytically inactive ClpP2 mutant significantly impacted developmental cycle progression by reducing the overall number of organisms. Blocking clpP2X transcription using CRISPR interference led to a decrease in bacterial growth, and this effect was complemented in trans by a plasmid copy of clpP2. Taken together, our data indicate that ClpX and the associated ClpP2 serve distinct functions in chlamydial developmental cycle progression and differentiation.
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Abstract
Stalled protein synthesis produces defective nascent chains that can harm cells. In response, cells degrade these nascent chains via a process called ribosome-associated quality control (RQC). Here, we review the irregularities in the translation process that cause ribosomes to stall as well as how cells use RQC to detect stalled ribosomes, ubiquitylate their tethered nascent chains, and deliver the ubiquitylated nascent chains to the proteasome. We additionally summarize how cells respond to RQC failure.
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Affiliation(s)
- Cole S Sitron
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA;
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35
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Tollerson R, Ibba M. Translational regulation of environmental adaptation in bacteria. J Biol Chem 2020; 295:10434-10445. [PMID: 32518156 DOI: 10.1074/jbc.rev120.012742] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/08/2020] [Indexed: 01/26/2023] Open
Abstract
Bacteria must rapidly respond to both intracellular and environmental changes to survive. One critical mechanism to rapidly detect and adapt to changes in environmental conditions is control of gene expression at the level of protein synthesis. At each of the three major steps of translation-initiation, elongation, and termination-cells use stimuli to tune translation rate and cellular protein concentrations. For example, changes in nutrient concentrations in the cell can lead to translational responses involving mechanisms such as dynamic folding of riboswitches during translation initiation or the synthesis of alarmones, which drastically alter cell physiology. Moreover, the cell can fine-tune the levels of specific protein products using programmed ribosome pausing or inducing frameshifting. Recent studies have improved understanding and revealed greater complexity regarding long-standing paradigms describing key regulatory steps of translation such as start-site selection and the coupling of transcription and translation. In this review, we describe how bacteria regulate their gene expression at the three translational steps and discuss how translation is used to detect and respond to changes in the cellular environment. Finally, we appraise the costs and benefits of regulation at the translational level in bacteria.
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Affiliation(s)
- Rodney Tollerson
- 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
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36
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Ziemski M, Leodolter J, Taylor G, Kerschenmeyer A, Weber-Ban E. Genome-wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin-antitoxin systems as a major substrate class. FEBS J 2020; 288:111-126. [PMID: 32301575 DOI: 10.1111/febs.15335] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/12/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022]
Abstract
In Mycobacterium tuberculosis (Mtb), the Clp protease degradation pathway, mediated by the modular ClpCP and ClpXP protease complexes, is essential for growth and presents an attractive drug target. Employing a bacterial adenylate cyclase two-hybrid (BACTH) screening approach that we adapted to screen the proteome of an Mtb ORF library, we identify protein interaction partners of the ClpC1 chaperone on a genome-wide level. Our results demonstrate that bipartite type II toxin-antitoxin (TA) systems represent a major substrate class. Out of the 67 type II TA systems known in Mtb, 25 appear as ClpC1 interaction partners in the BACTH screen, including members of the VapBC, MazEF, and ParDE families, as well as a RelBE member that was identified biochemically. We show that antitoxins of the Vap and Rel families are degraded by ClpCP in vitro. We also demonstrate that ClpCP is responsible for mediating the N-end rule pathway, since the adaptor protein ClpS supports ClpC-dependent degradation of an N-end rule model substrate in vitro.
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Affiliation(s)
- Michal Ziemski
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | - Julia Leodolter
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | - Gabrielle Taylor
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | | | - Eilika Weber-Ban
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
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37
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Joazeiro CAP. Mechanisms and functions of ribosome-associated protein quality control. Nat Rev Mol Cell Biol 2020; 20:368-383. [PMID: 30940912 DOI: 10.1038/s41580-019-0118-2] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The stalling of ribosomes during protein synthesis results in the production of truncated polypeptides that can have deleterious effects on cells and therefore must be eliminated. In eukaryotes, this function is carried out by a dedicated surveillance mechanism known as ribosome-associated protein quality control (RQC). The E3 ubiquitin ligase Ltn1 (listerin in mammals) plays a key part in RQC by targeting the aberrant nascent polypeptides for proteasomal degradation. Consistent with having an important protein quality control function, mutations in listerin cause neurodegeneration in mice. Ltn1/listerin is part of the multisubunit RQC complex, and recent findings have revealed that the Rqc2 subunit of this complex catalyses the formation of carboxy-terminal alanine and threonine tails (CAT tails), which are extensions of nascent chains known to either facilitate substrate ubiquitylation and targeting for degradation or induce protein aggregation. RQC, originally described for quality control on ribosomes translating cytosolic proteins, is now known to also have a role on the surfaces of the endoplasmic reticulum and mitochondria. This Review describes our current knowledge on RQC mechanisms, highlighting key features of Ltn1/listerin action that provide a paradigm for understanding how E3 ligases operate in protein quality control in general, and discusses how defects in this pathway may compromise cellular function and lead to disease.
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Affiliation(s)
- Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany. .,Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA.
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Inada T. Quality controls induced by aberrant translation. Nucleic Acids Res 2020; 48:1084-1096. [PMID: 31950154 PMCID: PMC7026593 DOI: 10.1093/nar/gkz1201] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/01/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
During protein synthesis, translating ribosomes encounter many challenges imposed by various types of defective mRNAs that can lead to reduced cellular fitness and, in some cases, even threaten cell viability. Aberrant translation leads to activation of one of several quality control pathways depending on the nature of the problem. These pathways promote the degradation of the problematic mRNA as well as the incomplete translation product, the nascent polypeptide chain. Many of these quality control systems feature critical roles for specialized regulatory factors that work in concert with conventional factors. This review focuses on the mechanisms used by these quality control pathways to recognize aberrant ribosome stalling and discusses the conservation of these systems.
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Affiliation(s)
- Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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Kumaran NAM, Karthik M, Kumar V, Jebasingh T, Munavar MH. Two new mutations in dnaJ suppress DNA damage hypersensitivity and capsule overproduction phenotypes of Δlon mutant of Escherichia coli by modulating the expression of clpYQ (hslUV) and rcsA genes. Gene 2020; 726:144135. [DOI: 10.1016/j.gene.2019.144135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022]
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Yamasaki R, Song S, Benedik MJ, Wood TK. Persister Cells Resuscitate Using Membrane Sensors that Activate Chemotaxis, Lower cAMP Levels, and Revive Ribosomes. iScience 2020; 23:100792. [PMID: 31926430 PMCID: PMC6957856 DOI: 10.1016/j.isci.2019.100792] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/03/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022] Open
Abstract
Persistence, the stress-tolerant state, is arguably the most vital phenotype since nearly all cells experience nutrient stress, which causes a sub-population to become dormant. However, how persister cells wake to reconstitute infections is not understood well. Here, using single-cell observations, we determined that Escherichia coli persister cells resuscitate primarily when presented with specific carbon sources, rather than spontaneously. In addition, we found that the mechanism of persister cell waking is through sensing nutrients by chemotaxis and phosphotransferase membrane proteins. Furthermore, nutrient transport reduces the level of secondary messenger cAMP through enzyme IIA; this reduction in cAMP levels leads to ribosome resuscitation and rescue. Resuscitating cells also immediately commence chemotaxis toward nutrients, although flagellar motion is not required for waking. Hence, persister cells wake by perceiving nutrients via membrane receptors that relay the signal to ribosomes via the secondary messenger cAMP, and persisters wake and utilize chemotaxis to acquire nutrients.
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Affiliation(s)
- Ryota Yamasaki
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA
| | - Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA
| | - Michael J Benedik
- Department of Biology, Texas A & M University, College Station, TX 77843-3122, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA; The Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802-4400, USA.
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41
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Sitron CS, Park JH, Giafaglione JM, Brandman O. Aggregation of CAT tails blocks their degradation and causes proteotoxicity in S. cerevisiae. PLoS One 2020; 15:e0227841. [PMID: 31945107 PMCID: PMC6964901 DOI: 10.1371/journal.pone.0227841] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
The Ribosome-associated Quality Control (RQC) pathway co-translationally marks incomplete polypeptides from stalled translation with two signals that trigger their proteasome-mediated degradation. The E3 ligase Ltn1 adds ubiquitin and Rqc2 directs the large ribosomal subunit to append carboxy-terminal alanine and threonine residues (CAT tails). When excessive amounts of incomplete polypeptides evade Ltn1, CAT-tailed proteins accumulate and can self-associate into aggregates. CAT tail aggregation has been hypothesized to either protect cells by sequestering potentially toxic incomplete polypeptides or harm cells by disrupting protein homeostasis. To distinguish between these possibilities, we modulated CAT tail aggregation in Saccharomyces cerevisiae with genetic and chemical tools to analyze CAT tails in aggregated and un-aggregated states. We found that enhancing CAT tail aggregation induces proteotoxic stress and antagonizes degradation of CAT-tailed proteins, while inhibiting aggregation reverses these effects. Our findings suggest that CAT tail aggregation harms RQC-compromised cells and that preventing aggregation can mitigate this toxicity.
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Affiliation(s)
- Cole S. Sitron
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
| | - Joseph H. Park
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, United States of America
| | - Jenna M. Giafaglione
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
- * E-mail:
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Hu L, Yang Y, Yan X, Zhang T, Xiang J, Gao Z, Chen Y, Yang S, Fei Q. Molecular Mechanism Associated With the Impact of Methane/Oxygen Gas Supply Ratios on Cell Growth of Methylomicrobium buryatense 5GB1 Through RNA-Seq. Front Bioeng Biotechnol 2020; 8:263. [PMID: 32318556 PMCID: PMC7154130 DOI: 10.3389/fbioe.2020.00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/13/2020] [Indexed: 11/13/2022] Open
Abstract
The methane (CH4)/oxygen (O2) gas supply ratios significantly affect the cell growth and metabolic pathways of aerobic obligate methanotrophs. However, few studies have explored the CH4/O2 ratios of the inlet gas, especially for the CH4 concentrations within the explosion range (5∼15% of CH4 in air). This study thoroughly investigated the molecular mechanisms associated with the impact of different CH4/O2 ratios on cell growth of a model type I methanotroph Methylomicrobium buryatense 5GB1 cultured at five different CH4/O2 supply molar ratios from 0.28 to 5.24, corresponding to CH4 content in gas mixture from 5% to 50%, using RNA-Seq transcriptomics approach. In the batch cultivation, the highest growth rate of 0.287 h-1 was achieved when the CH4/O2 supply molar ratio was 0.93 (15% CH4 in air), and it is crucial to keep the availability of carbon and oxygen levels balanced for optimal growth. At this ratio, genes related to methane metabolism, phosphate uptake system, and nitrogen fixation were significantly upregulated. The results indicated that the optimal CH4/O2 ratio prompted cell growth by increasing genes involved in metabolic pathways of carbon, nitrogen and phosphate utilization in M. buryatense 5GB1. Our findings provided an effective gas supply strategy for methanotrophs, which could enhance the production of key intermediates and enzymes to improve the performance of bioconversion processes using CH4 as the only carbon and energy source. This research also helps identify genes associated with the optimal CH4/O2 ratio for balancing energy metabolism and carbon flux, which could be candidate targets for future metabolic engineering practice.
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Affiliation(s)
- Lizhen Hu
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tianqing Zhang
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Jing Xiang
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Zixi Gao
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
- *Correspondence: Shihui Yang,
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Key Laboratory of Energy Chemical Process Intensification, Xi’an Jiaotong University, Xi’an, China
- Qiang Fei,
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43
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Thomas EN, Kim KQ, McHugh EP, Marcinkiewicz T, Zaher HS. Alkylative damage of mRNA leads to ribosome stalling and rescue by trans translation in bacteria. eLife 2020; 9:61984. [PMID: 32940602 PMCID: PMC7521929 DOI: 10.7554/elife.61984] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
Similar to DNA replication, translation of the genetic code by the ribosome is hypothesized to be exceptionally sensitive to small chemical changes to its template mRNA. Here we show that the addition of common alkylating agents to growing cultures of Escherichia coli leads to the accumulation of several adducts within RNA, including N(1)-methyladenosine (m1A). As expected, the introduction of m1A to model mRNAs was found to reduce the rate of peptide bond formation by three orders of magnitude in a well-defined in vitro system. These observations suggest that alkylative stress is likely to stall translation in vivo and necessitates the activation of ribosome-rescue pathways. Indeed, the addition of alkylation agents was found to robustly activate the transfer-messenger RNA system, even when transcription was inhibited. Our findings suggest that bacteria carefully monitor the chemical integrity of their mRNA and they evolved rescue pathways to cope with its effect on translation.
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Affiliation(s)
- Erica N Thomas
- Department of Biology, Washington University in St. LouisSt. LouisUnited States
| | - Kyusik Q Kim
- Department of Biology, Washington University in St. LouisSt. LouisUnited States
| | - Emily P McHugh
- Department of Biology, Washington University in St. LouisSt. LouisUnited States
| | | | - Hani S Zaher
- Department of Biology, Washington University in St. LouisSt. LouisUnited States
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Gaucher F, Kponouglo K, Rabah H, Bonnassie S, Ossemond J, Pottier S, Jardin J, Briard-Bion V, Marchand P, Blanc P, Jeantet R, Jan G. Propionibacterium freudenreichii CIRM-BIA 129 Osmoadaptation Coupled to Acid-Adaptation Increases Its Viability During Freeze-Drying. Front Microbiol 2019; 10:2324. [PMID: 31681198 PMCID: PMC6797830 DOI: 10.3389/fmicb.2019.02324] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022] Open
Abstract
Propionibacterium freudenreichii is a beneficial bacterium with documented effects on the gut microbiota and on inflammation. Its presence within the animal and human intestinal microbiota was correlated with immunomodulatory effects, mediated by both propionibacterial surface components and by secreted metabolites. It is widely implemented, both in the manufacture of fermented dairy products such as Swiss-type cheeses, and in the production of probiotic food complements, under the form of freeze-dried powders. The bottleneck of this drying process consists in the limited survival of bacteria during drying and storage. Protective pre-treatments have been applied to other bacteria and may, in a strain-dependent manner, confer enhanced resistance. However, very little information was yet published on P. freudenreichii adaptation to freeze-drying. In this report, an immunomodulatory strain of this probiotic bacterium was cultured under hyperosmotic constraint in order to trigger osmoadaptation. This adaptation was then combined with acid or thermal pre-treatment. Such combination led to accumulation of key stress proteins, of intracellular compatible solute glycine betaine, to modulation of the propionibacterial membrane composition, and to enhanced survival upon freeze-drying. This work opens new perspectives for efficient production of live and active probiotic propionibacteria.
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Affiliation(s)
- Floriane Gaucher
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
- Bioprox, Levallois-Perret, France
| | | | - Houem Rabah
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
- Bba, Pôle Agronomique Ouest, Régions Bretagne et Pays de la Loire, Rennes, France
| | - Sylvie Bonnassie
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
- Université de Rennes I, Rennes, France
| | | | - Sandrine Pottier
- CNRS, ISCR – UMR 6226, PRISM, BIOSIT – UMS 3480 Université de Rennes I, Rennes, France
| | | | | | | | | | | | - Gwénaël Jan
- UMR STLO, Agrocampus Ouest, INRA, Rennes, France
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45
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Abstract
AAA+ proteolytic machines use energy from ATP hydrolysis to degrade damaged, misfolded, or unneeded proteins. Protein degradation occurs within a barrel-shaped self-compartmentalized peptidase. Before protein substrates can enter this peptidase, they must be unfolded and then translocated through the axial pore of an AAA+ ring hexamer. An unstructured region of the protein substrate is initially engaged in the axial pore, and conformational changes in the ring, powered by ATP hydrolysis, generate a mechanical force that pulls on and denatures the substrate. The same conformational changes in the hexameric ring then mediate mechanical translocation of the unfolded polypeptide into the peptidase chamber. For the bacterial ClpXP and ClpAP AAA+ proteases, the mechanical activities of protein unfolding and translocation have been directly visualized by single-molecule optical trapping. These studies in combination with structural and biochemical experiments illuminate many principles that underlie this universal mechanism of ATP-fueled protein unfolding and subsequent destruction.
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Affiliation(s)
- Adrian O Olivares
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Tania A Baker
- Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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46
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Lytvynenko I, Paternoga H, Thrun A, Balke A, Müller TA, Chiang CH, Nagler K, Tsaprailis G, Anders S, Bischofs I, Maupin-Furlow JA, Spahn CMT, Joazeiro CAP. Alanine Tails Signal Proteolysis in Bacterial Ribosome-Associated Quality Control. Cell 2019; 178:76-90.e22. [PMID: 31155236 DOI: 10.1016/j.cell.2019.05.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/11/2019] [Accepted: 04/30/2019] [Indexed: 11/19/2022]
Abstract
In ribosome-associated quality control (RQC), Rqc2/NEMF closely supports the E3 ligase Ltn1/listerin in promoting ubiquitylation and degradation of aberrant nascent-chains obstructing large (60S) ribosomal subunits-products of ribosome stalling during translation. However, while Ltn1 is eukaryote-specific, Rqc2 homologs are also found in bacteria and archaea; whether prokaryotic Rqc2 has an RQC-related function has remained unknown. Here, we show that, as in eukaryotes, a bacterial Rqc2 homolog (RqcH) recognizes obstructed 50S subunits and promotes nascent-chain proteolysis. Unexpectedly, RqcH marks nascent-chains for degradation in a direct manner, by appending C-terminal poly-alanine tails that act as degrons recognized by the ClpXP protease. Furthermore, RqcH acts redundantly with tmRNA/ssrA and protects cells against translational and environmental stresses. Our results uncover a proteolytic-tagging mechanism with implications toward the function of related modifications in eukaryotes and suggest that RQC was already active in the last universal common ancestor (LUCA) to help cope with incomplete translation.
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Affiliation(s)
- Iryna Lytvynenko
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Helge Paternoga
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Anna Thrun
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Annika Balke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Tina A Müller
- Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA
| | - Christina H Chiang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Katja Nagler
- BioQuant Center, University of Heidelberg, 69120 Heidelberg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | | | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Ilka Bischofs
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; BioQuant Center, University of Heidelberg, 69120 Heidelberg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
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Improvement in the Orthogonal Protein Degradation in Escherichia coli by Truncated mf-ssrA Tag. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s12209-019-00193-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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48
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Amor AJ, Schmitz KR, Baker TA, Sauer RT. Roles of the ClpX IGF loops in ClpP association, dissociation, and protein degradation. Protein Sci 2019; 28:756-765. [PMID: 30767302 DOI: 10.1002/pro.3590] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/08/2019] [Indexed: 11/11/2022]
Abstract
IGF-motif loops project from the hexameric ring of ClpX and are required for docking with the self-compartmentalized ClpP peptidase, which consists of heptameric rings stacked back-to-back. Here, we show that ATP or ATPγS support assembly by changing the conformation of the ClpX ring, bringing the IGF loops closer to each other and allowing efficient multivalent contacts with docking clefts on ClpP. In single-chain ClpX pseudohexamers, deletion of one or two IGF loops modestly slows association with ClpP but strongly accelerates dissociation of ClpXP complexes. We probe how changes in the sequence and length of the IGF loops affect ClpX-ClpP interactions and show that deletion of one or two IGF loops slows ATP-dependent proteolysis by ClpXP. We also find that ClpXP degradation is less processive when two IGF loops are deleted.
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Affiliation(s)
- Alvaro J Amor
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Karl R Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
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SmpB down-regulates proton-motive force for the persister tolerance to aminoglycosides in Aeromonas veronii. Biochem Biophys Res Commun 2018; 507:407-413. [PMID: 30449596 DOI: 10.1016/j.bbrc.2018.11.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/09/2018] [Indexed: 11/21/2022]
Abstract
Bacterial persisters comprise a small fraction of phenotypically heterogeneous variants with transient capability for survival when exposed to high concentrations of antibiotic. In aquatic pathogenic bacteria Aeromonas veronii, Small Protein B (SmpB), the core factor of trans-translation system, was identified as a new persistence-related gene. The SmpB deletion exhibited a higher susceptibility and lower persister cell formation under aminoglycosides antibiotics pressure compared with wild type. The transcriptional and translational activities of smpB gene were significantly enhanced by the gentamicin challenge in exponential phase, but not changed in stationary phase. The transcriptomic analysis revealed that the smpB deletion stimulated the production of proton-motive force (PMF). The cell survival induced by carbonyl cyanide m-chlorophenyl hydrazone (CCCP) further verified that SmpB variation affected the quantities of PMF. Taken together, these results uncovered a novel mechanism of persister formation mediated by SmpB under aminoglycosides treatments.
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50
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Expression, purification and characterization of the full-length SmpB protein from Mycobacterium tuberculosis. Protein Expr Purif 2018; 151:9-17. [DOI: 10.1016/j.pep.2018.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/26/2018] [Accepted: 05/28/2018] [Indexed: 11/20/2022]
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