1
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Cueny RR, Voter AF, McKenzie AM, Morgenstern M, Myers KS, Place MM, Peters JM, Coon JJ, Keck JL. Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607615. [PMID: 39185182 PMCID: PMC11343134 DOI: 10.1101/2024.08.12.607615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, reducing expression of certain translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our integrated systems approach allowed us to propose a model for how RNA G4s can present barriers to E. coli growth and that reducing the rate of translation can compensate for G4-related stress.
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Affiliation(s)
- Rachel R Cueny
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew F Voter
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aidan M McKenzie
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marcel Morgenstern
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, Madison Wisconsin, USA
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael M Place
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joshua J Coon
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, Madison Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - James L Keck
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Tang S, Conte V, Zhang DJ, Žedaveinytė R, Lampe GD, Wiegand T, Tang LC, Wang M, Walker MWG, George JT, Berchowitz LE, Jovanovic M, Sternberg SH. De novo gene synthesis by an antiviral reverse transcriptase. Science 2024:eadq0876. [PMID: 39116258 DOI: 10.1126/science.adq0876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024]
Abstract
Defense-associated reverse transcriptase (DRT) systems perform DNA synthesis to protect bacteria against viral infection, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems encode an unprecedented immune pathway that involves de novo gene synthesis via rolling circle reverse transcription of a non-coding RNA (ncRNA). Programmed template jumping on the ncRNA generates a concatemeric cDNA, which becomes double-stranded upon viral infection. Remarkably, this DNA product constitutes a protein-coding, nearly endless ORF (neo) gene whose expression leads to potent cell growth arrest, thereby restricting the viral infection. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.
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Affiliation(s)
- Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Valentin Conte
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Dennis J Zhang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Rimantė Žedaveinytė
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Lauren C Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Megan Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jerrin Thomas George
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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3
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Callan K, Prince CR, Feaga HA. RqcH supports survival in the absence of non-stop ribosome rescue factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603306. [PMID: 39026760 PMCID: PMC11257542 DOI: 10.1101/2024.07.12.603306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Ribosomes frequently translate truncated or damaged mRNAs due to the extremely short half-life of mRNAs in bacteria. When ribosomes translate mRNA that lacks a stop codon (non-stop mRNA), specialized pathways are required to rescue the ribosome from the 3' end of the mRNA. The most highly conserved non-stop rescue pathway is trans-translation, which is found in greater than 95% of bacterial genomes. In all Proteobacteria that have been studied, the alternative non-stop ribosome rescue factors, ArfA and ArfB, are essential in the absence of trans-translation. Here, we investigate the interaction between non-stop rescue pathways and RqcH, a ribosome quality control factor that is broadly conserved outside of Proteobacteria. RqcH does not act directly on non-stop ribosomes but adds a degron tag to stalled peptides that obstruct the large ribosomal subunit, which allows the stalled peptide to be cleared from the ribosome by peptidyl-tRNA hydrolase (PTH). We show that Bacillus subtilis can survive without trans-translation and BrfA (Bacillus ArfA homolog), due to the presence of RqcH. We also show that expression of RqcH and its helper protein RqcP rescues the synthetic lethality of ΔssrAΔarfA in Escherichia coli. These results suggest that non-stop ribosome complexes can be disassembled and then cleared because of the tagging activity of RqcH, and that this process is essential in the absence of non-stop ribosome rescue pathways. Moreover, we surveyed the conservation of ribosome rescue pathways in >14,000 bacterial genomes. Our analysis reveals a broad distribution of non-stop rescue pathways, especially trans-translation and RqcH, and a strong co-occurrence between the ribosome splitting factor MutS2 and RqcH. Altogether, our results support a role for RqcH in non-stop ribosome rescue and provide a broad survey of ribosome rescue pathways in diverse bacterial species.
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Affiliation(s)
- Katrina Callan
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | | | - Heather A. Feaga
- Department of Microbiology, Cornell University, Ithaca, NY 14853
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4
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Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nat Rev Mol Cell Biol 2024; 25:534-554. [PMID: 38509203 PMCID: PMC11199108 DOI: 10.1038/s41580-024-00706-2] [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] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3'-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3'-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Morgan Shine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jackson Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dagmar Zigackova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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5
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Awad S, Valleriani A, Chiarugi D. A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length. NAR Genom Bioinform 2024; 6:lqae036. [PMID: 38638702 PMCID: PMC11025885 DOI: 10.1093/nargab/lqae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Ribosomes are the molecular machinery that catalyse all the fundamental steps involved in the translation of mRNAs into proteins. Given the complexity of this process, the efficiency of protein synthesis depends on a large number of factors among which ribosome drop-off (i.e. the premature detachment of the ribosome from the mRNA template) plays an important role. However, an in vitro quantification of the extent to which ribosome drop-off occurs is not trivial due to difficulties in obtaining the needed experimental evidence. In this work we focus on the study of ribosome drop-off in Saccharomyces cerevisiae by using 'Ribofilio', a novel software tool that relies on a high sensitive strategy to estimate the ribosome drop-off rate from ribosome profiling data. Our results show that ribosome drop-off events occur at a significant rate also when S. cerevisiae is cultured in standard conditions. In this context, we also identified a correlation between the ribosome drop-off rate and the genes length: the longer the gene, the lower the drop-off rate.
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Affiliation(s)
- Sherine Awad
- Genomics and Bioinformatics Core Facility, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Davide Chiarugi
- Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraße 1a, 04103 Leipzig - Germany
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6
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Koomen J, Ma X, Bombelli A, Tempelaars MH, Boeren S, Zwietering MH, den Besten HMW, Abee T. Ribosomal mutations enable a switch between high fitness and high stress resistance in Listeria monocytogenes. Front Microbiol 2024; 15:1355268. [PMID: 38605704 PMCID: PMC11006974 DOI: 10.3389/fmicb.2024.1355268] [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: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
Multiple stress resistant variants of Listeria monocytogenes with mutations in rpsU encoding ribosomal protein RpsU have previously been isolated after a single exposure to acid stress. These variants, including L. monocytogenes LO28 variant V14 with a complete deletion of the rpsU gene, showed upregulation of the general stress sigma factor Sigma B-mediated stress resistance genes and had a lower maximum specific growth rate than the LO28 WT, signifying a trade-off between stress resistance and fitness. In the current work V14 has been subjected to an experimental evolution regime, selecting for higher fitness in two parallel evolving cultures. This resulted in two evolved variants with WT-like fitness: 14EV1 and 14EV2. Comparative analysis of growth performance, acid and heat stress resistance, in combination with proteomics and RNA-sequencing, indicated that in both lines reversion to WT-like fitness also resulted in WT-like stress sensitivity, due to lack of Sigma B-activated stress defense. Notably, genotyping of 14EV1 and 14EV2 provided evidence for unique point-mutations in the ribosomal rpsB gene causing amino acid substitutions at the same position in RpsB, resulting in RpsB22Arg-His and RpsB22Arg-Ser, respectively. Combined with data obtained with constructed RpsB22Arg-His and RpsB22Arg-Ser mutants in the V14 background, we provide evidence that loss of function of RpsU resulting in the multiple stress resistant and reduced fitness phenotype, can be reversed by single point mutations in rpsB leading to arginine substitutions in RpsB at position 22 into histidine or serine, resulting in a WT-like high fitness and low stress resistance phenotype. This demonstrates the impact of genetic changes in L. monocytogenes' ribosomes on fitness and stress resistance.
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Affiliation(s)
- Jeroen Koomen
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Xuchuan Ma
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alberto Bombelli
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | | | | | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
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7
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Fang W, Xu J, Wei Z, Wu J, Wu W, Wang Y, Chen S. Enhancing bactericidal activities of ciprofloxacin by targeting the trans-translation system that is involved in stress responses in Klebsiella pneumoniae. Arch Microbiol 2024; 206:154. [PMID: 38478112 DOI: 10.1007/s00203-024-03872-1] [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: 12/03/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 04/16/2024]
Abstract
Although the trans-translation system is a promising target for antcibiotic development, its antibacterial mechanism in Klebsiella pneumoniae (KP) is unclear. Considering that tmRNA was the core component of trans-translation, this study firstly investigated phenotypic changes caused by various environmental stresses in KP lacking trans-translation activities (tmRNA-deleted), and then aimed to evaluate antibacterial activities of the trans-translation-targeting antibiotic combination (tobramycin/ciprofloxacin) in clinical KP isolates based on inhibition activities of aminoglycosides against trans-translation. We found that the tmRNA-deleted strain P4325/ΔssrA was significantly more susceptible than the wild-type KP strain P4325 under environments with hypertonicity (0.5 and 1 M NaCl), hydrogen peroxide (40 mM), and UV irradiation. No significant differences in biofilm formation and survivals under human serum were observed between P4325/ΔssrA and P4325. tmRNA deletion caused twofold lower MIC values for aminoglycosides. As for the membrane permeability, tmRNA deletion increased ethidium bromide (EtBr) uptake of KP in the presence or absence of verapamil and carbonyl cyanide-m-chlorophenylhydrazone (CCCP), decreased EtBr uptake in presence of reserpine in P4325/ΔssrA, and reduced EtBr efflux in P4325/ΔssrA in the presence of CCCP. The time-kill curve and in vitro experiments revealed significant bactericidal activities of the tmRNA-targeting aminoglycoside-based antibiotic combination (tobramycin/ciprofloxacin). Thus, the corresponding tmRNA-targeting antibiotic combinations (aminoglycoside-based) might be effective and promising treatment options against multi-drug resistant KP.
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Affiliation(s)
- Wendong Fang
- Department of Laboratory Medicine, The PLA 307 Clinical College, Fifth Clinical Medical College of Anhui Medical University, Beijing, China
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Jie Xu
- Department of Laboratory Medicine, The PLA 307 Clinical College, Fifth Clinical Medical College of Anhui Medical University, Beijing, China
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Zilan Wei
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Jiahui Wu
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Weihui Wu
- Department of Microbiology, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China.
| | | | - Shuiping Chen
- Department of Laboratory Medicine, The PLA 307 Clinical College, Fifth Clinical Medical College of Anhui Medical University, Beijing, China.
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China.
- Medical School of Chinese PLA, Beijing, China.
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8
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Teran D, Zhang Y, Korostelev AA. Endogenous trans-translation structure visualizes the decoding of the first tmRNA alanine codon. Front Microbiol 2024; 15:1369760. [PMID: 38500588 PMCID: PMC10944890 DOI: 10.3389/fmicb.2024.1369760] [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: 01/12/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Ribosomes stall on truncated or otherwise damaged mRNAs. Bacteria rely on ribosome rescue mechanisms to replenish the pool of ribosomes available for translation. Trans-translation, the main ribosome-rescue pathway, uses a circular hybrid transfer-messenger RNA (tmRNA) to restart translation and label the resulting peptide for degradation. Previous studies have visualized how tmRNA and its helper protein SmpB interact with the stalled ribosome to establish a new open reading frame. As tmRNA presents the first alanine codon via a non-canonical mRNA path in the ribosome, the incoming alanyl-tRNA must rearrange the tmRNA molecule to read the codon. Here, we describe cryo-EM analyses of an endogenous Escherichia coli ribosome-tmRNA complex with tRNAAla accommodated in the A site. The flexible adenosine-rich tmRNA linker, which connects the mRNA-like domain with the codon, is stabilized by the minor groove of the canonically positioned anticodon stem of tRNAAla. This ribosome complex can also accommodate a tRNA near the E (exit) site, bringing insights into the translocation and dissociation of the tRNA that decoded the defective mRNA prior to tmRNA binding. Together, these structures uncover a key step of ribosome rescue, in which the ribosome starts translating the tmRNA reading frame.
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Affiliation(s)
| | | | - Andrei A. Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, United States
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9
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Aseev LV, Koledinskaya LS, Boni IV. Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. Int J Mol Sci 2024; 25:2957. [PMID: 38474204 DOI: 10.3390/ijms25052957] [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: 01/19/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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10
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light-inducible protein degradation in E. coli with the LOVdeg tag. eLife 2024; 12:RP87303. [PMID: 38270583 PMCID: PMC10945698 DOI: 10.7554/elife.87303] [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] [Indexed: 01/26/2024] Open
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.
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Affiliation(s)
- Nathan Tague
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Cristian Coriano-Ortiz
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Michael B Sheets
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
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11
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Vazulka S, Schiavinato M, Tauer C, Wagenknecht M, Cserjan-Puschmann M, Striedner G. RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling. Microb Cell Fact 2024; 23:14. [PMID: 38183013 PMCID: PMC10768439 DOI: 10.1186/s12934-023-02278-w] [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: 10/12/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Escherichia coli is a cost-effective expression system for production of antibody fragments like Fabs. Various yield improvement strategies have been applied, however, Fabs remain challenging to produce. This study aimed to characterize the gene expression response of commonly used E. coli strains BL21(DE3) and HMS174(DE3) to periplasmic Fab expression using RNA sequencing (RNA-seq). Two Fabs, Fabx and FTN2, fused to a post-translational translocation signal sequence, were produced in carbon-limited fed-batch cultivations. RESULTS Production of Fabx impeded cell growth substantially stronger than FTN2 and yields of both Fabs differed considerably. The most noticeable, common changes in Fab-producing cells suggested by our RNA-seq data concern the cell envelope. The Cpx and Psp stress responses, both connected to inner membrane integrity, were activated, presumably by recombinant protein aggregation and impairment of the Sec translocon. The data additionally suggest changes in lipopolysaccharide synthesis, adjustment of membrane permeability, and peptidoglycan maturation and remodeling. Moreover, all Fab-producing strains showed depletion of Mg2+, indicated by activation of the PhoQP two-component signal transduction system during the early stage and sulfur and phosphate starvation during the later stage of the process. Furthermore, our data revealed ribosome stalling, caused by the Fabx amino acid sequence, as a contributor to low Fabx yields. Increased Fabx yields were obtained by a site-specific amino acid exchange replacing the stalling sequence. Contrary to expectations, cell growth was not impacted by presence or removal of the stalling sequence. Considering ribosome rescue is a conserved mechanism, the substantial differences observed in gene expression between BL21(DE3) and HMS174(DE3) in response to ribosome stalling on the recombinant mRNA were surprising. CONCLUSIONS Through characterization of the gene expression response to Fab production under industrially relevant cultivation conditions, we identified potential cell engineering targets. Thereby, we hope to enable rational approaches to improve cell fitness and Fab yields. Furthermore, we highlight ribosome stalling caused by the amino acid sequence of the recombinant protein as a possible challenge during recombinant protein production.
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Affiliation(s)
- Sophie Vazulka
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV, GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1120, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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12
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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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13
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Douglas EA, Marshall B, Alghamadi A, Joseph EA, Duggan S, Vittorio S, De Luca L, Serpi M, Laabei M. Improved Antibacterial Activity of 1,3,4-Oxadiazole-Based Compounds That Restrict Staphylococcus aureus Growth Independent of LtaS Function. ACS Infect Dis 2023; 9:2141-2159. [PMID: 37828912 PMCID: PMC10644342 DOI: 10.1021/acsinfecdis.3c00250] [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: 05/31/2023] [Indexed: 10/14/2023]
Abstract
The lipoteichoic acid (LTA) biosynthesis pathway has emerged as a promising antimicrobial therapeutic target. Previous studies identified the 1,3,4 oxadiazole compound 1771 as an LTA inhibitor with activity against Gram-positive pathogens. We have succeeded in making six 1771 derivatives and, through subsequent hit validation, identified the incorporation of a pentafluorosulfanyl substituent as central in enhancing activity. Our newly described derivative, compound 13, showed a 16- to 32-fold increase in activity compared to 1771 when tested against a cohort of multidrug-resistant Staphylococcus aureus strains while simultaneously exhibiting an improved toxicity profile against mammalian cells. Molecular techniques were employed in which the assumed target, lipoteichoic acid synthase (LtaS), was both deleted and overexpressed. Neither deletion nor overexpression of LtaS altered 1771 or compound 13 susceptibility; however, overexpression of LtaS increased the MIC of Congo red, a previously identified LtaS inhibitor. These data were further supported by comparing the docking poses of 1771 and derivatives in the LtaS active site, which indicated the possibility of an additional target(s). Finally, we show that both 1771 and compound 13 have activity that is independent of LtaS, extending to cover Gram-negative species if the outer membrane is first permeabilized, challenging the classification that these compounds are strict LtaS inhibitors.
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Affiliation(s)
| | - Brandon Marshall
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Arwa Alghamadi
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Erin A. Joseph
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Seána Duggan
- Medical
Research Council Centre for Medical Mycology at the University of
Exeter, University of Exeter, Exeter EX4 4DQ, U.K.
| | - Serena Vittorio
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98125, Italy
| | - Laura De Luca
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98125, Italy
| | - Michaela Serpi
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Maisem Laabei
- Department
of Life Sciences, University of Bath, Bath BA2 7AY, U.K.
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14
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Marathe N, Nguyen HA, Alumasa JN, Kuzmishin Nagy AB, Vazquez M, Dunham CM, Keiler KC. Antibiotic that inhibits trans-translation blocks binding of EF-Tu to tmRNA but not to tRNA. mBio 2023; 14:e0146123. [PMID: 37681945 PMCID: PMC10653918 DOI: 10.1128/mbio.01461-23] [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: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 09/09/2023] Open
Abstract
IMPORTANCE Elongation factor thermo-unstable (EF-Tu) is a universally conserved translation factor that mediates productive interactions between tRNAs and the ribosome. In bacteria, EF-Tu also delivers transfer-messenger RNA (tmRNA)-SmpB to the ribosome during trans-translation. We report the first small molecule, KKL-55, that specifically inhibits EF-Tu activity in trans-translation without affecting its activity in normal translation. KKL-55 has broad-spectrum antibiotic activity, suggesting that compounds targeted to the tmRNA-binding interface of EF-Tu could be developed into new antibiotics to treat drug-resistant infections.
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Affiliation(s)
- Neeraja Marathe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ha An Nguyen
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, Georgia, USA
| | - John N. Alumasa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Alexandra B. Kuzmishin Nagy
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, Georgia, USA
| | - Michael Vazquez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christine M. Dunham
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, Georgia, USA
| | - Kenneth C. Keiler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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15
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light inducible protein degradation in E. coli with the LOVdeg tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530042. [PMID: 36865169 PMCID: PMC9980293 DOI: 10.1101/2023.02.25.530042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system, and introduce a powerful new tool for bacterial optogenetics.
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16
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Vázquez-Hernández M, Leedom SL, Keiler KC, Bandow JE. Physiology of trans-translation deficiency in Bacillus subtilis - a comparative proteomics study. Proteomics 2023; 23:e2200474. [PMID: 37496314 DOI: 10.1002/pmic.202200474] [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: 11/13/2022] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/28/2023]
Abstract
trans-Translation is the most effective ribosome rescue system known in bacteria. While it is essential in some bacteria, Bacillus subtilis possesses two additional alternative ribosome rescue mechanisms that require the proteins BrfA or RqcH. To investigate the physiology of trans-translation deficiency in the model organism B. subtilis, we compared the proteomes of B. subtilis 168 and a ΔssrA mutant in the mid-log phase using gel-free label-free quantitative proteomics. In chemically defined medium, the growth rate of the ssrA deletion mutant was 20% lower than that of B. subtilis 168. An 35 S-methionine incorporation assay demonstrated that protein synthesis rates were also lower in the ΔssrA strain. Alternative rescue factors were not detected. Among the 34 proteins overrepresented in the mutant strain were eight chemotaxis proteins. Indeed, both on LB agar and minimal medium the ΔssrA strain showed an altered motility and chemotaxis phenotype. Despite the lower growth rate, in the mutant proteome ribosomal proteins were more abundant while proteins related to amino acid biosynthesis were less abundant than in the parental strain. This overrepresentation of ribosomal proteins coupled with a lower protein synthesis rate and down-regulation of precursor supply reflects the slow ribosome recycling in the trans-translation-deficient mutant.
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Affiliation(s)
| | - Stephanie L Leedom
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kenneth C Keiler
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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17
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Nadler F, Richter-Dennerlein R. Translation termination in human mitochondria - substrate specificity of mitochondrial release factors. Biol Chem 2023; 404:769-779. [PMID: 37377370 DOI: 10.1515/hsz-2023-0127] [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: 02/08/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Mitochondria are the essential players in eukaryotic ATP production by oxidative phosphorylation, which relies on the maintenance and accurate expression of the mitochondrial genome. Even though the basic principles of translation are conserved due to the descendance from a bacterial ancestor, some deviations regarding translation factors as well as mRNA characteristics and the applied genetic code are present in human mitochondria. Together, these features are certain challenges during translation the mitochondrion has to handle. Here, we discuss the current knowledge regarding mitochondrial translation focusing on the termination process and the associated quality control mechanisms. We describe how mtRF1a resembles bacterial RF1 mechanistically and summarize in vitro and recent in vivo data leading to the conclusion of mtRF1a being the major mitochondrial release factor. On the other hand, we discuss the ongoing debate about the function of the second codon-dependent mitochondrial release factor mtRF1 regarding its role as a specialized termination factor. Finally, we link defects in mitochondrial translation termination to the activation of mitochondrial rescue mechanisms highlighting the importance of ribosome-associated quality control for sufficient respiratory function and therefore for human health.
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Affiliation(s)
- Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, D-37075 Göttingen, Germany
- Goettingen Center for Molecular Biosciences, University of Göttingen, D-37077 Göttingen, Germany
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18
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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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19
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Nagao A, Nakanishi Y, Yamaguchi Y, Mishina Y, Karoji M, Toya T, Fujita T, Iwasaki S, Miyauchi K, Sakaguchi Y, Suzuki T. Quality control of protein synthesis in the early elongation stage. Nat Commun 2023; 14:2704. [PMID: 37198183 PMCID: PMC10192219 DOI: 10.1038/s41467-023-38077-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
In the early stage of bacterial translation, peptidyl-tRNAs frequently dissociate from the ribosome (pep-tRNA drop-off) and are recycled by peptidyl-tRNA hydrolase. Here, we establish a highly sensitive method for profiling of pep-tRNAs using mass spectrometry, and successfully detect a large number of nascent peptides from pep-tRNAs accumulated in Escherichia coli pthts strain. Based on molecular mass analysis, we found about 20% of the peptides bear single amino-acid substitutions of the N-terminal sequences of E. coli ORFs. Detailed analysis of individual pep-tRNAs and reporter assay revealed that most of the substitutions take place at the C-terminal drop-off site and that the miscoded pep-tRNAs rarely participate in the next round of elongation but dissociate from the ribosome. These findings suggest that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yui Nakanishi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yutaro Yamaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshifumi Mishina
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Minami Karoji
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takafumi Toya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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20
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Peptidyl tRNA Hydrolase Is Required for Robust Prolyl-tRNA Turnover in Mycobacterium tuberculosis. mBio 2023; 14:e0346922. [PMID: 36695586 PMCID: PMC9973355 DOI: 10.1128/mbio.03469-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Enzymes involved in rescuing stalled ribosomes and recycling translation machinery are ubiquitous in bacteria and required for growth. Peptidyl tRNA drop-off is a type of abortive translation that results in the release of a truncated peptide that is still bound to tRNA (peptidyl tRNA) into the cytoplasm. Peptidyl tRNA hydrolase (Pth) recycles the released tRNA by cleaving off the unfinished peptide and is essential in most bacteria. We developed a sequencing-based strategy called copper sulfate-based tRNA sequencing (Cu-tRNAseq) to study the physiological role of Pth in Mycobacterium tuberculosis (Mtb). While most peptidyl tRNA species accumulated in a strain with impaired Pth expression, peptidyl prolyl-tRNA was particularly enriched, suggesting that Pth is required for robust peptidyl prolyl-tRNA turnover. Reducing Pth levels increased Mtb's susceptibility to tRNA synthetase inhibitors that are in development to treat tuberculosis (TB) and rendered this pathogen highly susceptible to macrolides, drugs that are ordinarily ineffective against Mtb. Collectively, our findings reveal the potency of Cu-tRNAseq for profiling peptidyl tRNAs and suggest that targeting Pth would open new therapeutic approaches for TB. IMPORTANCE Peptidyl tRNA hydrolase (Pth) is an enzyme that cuts unfinished peptides off tRNA that has been prematurely released from a stalled ribosome. Pth is essential in nearly all bacteria, including the pathogen Mycobacterium tuberculosis (Mtb), but it has not been clear why. We have used genetic and novel biochemical approaches to show that when Pth levels decline in Mtb, peptidyl tRNA accumulates to such an extent that usable tRNA pools drop. Thus, Pth is needed to maintain normal tRNA levels, most strikingly for prolyl-tRNAs. Many antibiotics act on protein synthesis and could be affected by altering the availability of tRNA. This is certainly true for tRNA synthetase inhibitors, several of which are drug candidates for tuberculosis. We find that their action is potentiated by Pth depletion. Furthermore, Pth depletion results in hypersensitivity to macrolides, drugs that are not active enough under ordinary circumstances to be useful for tuberculosis.
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21
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Lactobacillus for ribosome peptide editing cancer. Clin Transl Oncol 2023; 25:1522-1544. [PMID: 36694080 PMCID: PMC9873400 DOI: 10.1007/s12094-022-03066-5] [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: 09/28/2022] [Accepted: 12/24/2022] [Indexed: 01/25/2023]
Abstract
This study reviews newly discovered insect peptide point mutations as new possible cancer research targets. To interpret newly discovered peptide point mutations in insects as new possible cancer research targets, we focused on the numerous peptide changes found in the 'CSP' family on the sex pheromone gland of the female silkworm moth Bombyx mori. We predict that the Bombyx peptide modifications will have a significant effect on cancer CUP (cancers of unknown primary) therapy and that bacterial peptide editing techniques, specifically Lactobacillus combined to CRISPR, will be used to regulate ribosomes and treat cancer in humans.
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22
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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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23
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Aljghami ME, Barghash MM, Majaesic E, Bhandari V, Houry WA. Cellular functions of the ClpP protease impacting bacterial virulence. Front Mol Biosci 2022; 9:1054408. [PMID: 36533084 PMCID: PMC9753991 DOI: 10.3389/fmolb.2022.1054408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/15/2022] [Indexed: 09/28/2023] Open
Abstract
Proteostasis mechanisms significantly contribute to the sculpting of the proteomes of all living organisms. ClpXP is a central AAA+ chaperone-protease complex present in both prokaryotes and eukaryotes that facilitates the unfolding and subsequent degradation of target substrates. ClpX is a hexameric unfoldase ATPase, while ClpP is a tetradecameric serine protease. Substrates of ClpXP belong to many cellular pathways such as DNA damage response, metabolism, and transcriptional regulation. Crucially, disruption of this proteolytic complex in microbes has been shown to impact the virulence and infectivity of various human pathogenic bacteria. Loss of ClpXP impacts stress responses, biofilm formation, and virulence effector protein production, leading to decreased pathogenicity in cell and animal infection models. Here, we provide an overview of the multiple critical functions of ClpXP and its substrates that modulate bacterial virulence with examples from several important human pathogens.
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Affiliation(s)
- Mazen E. Aljghami
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Emily Majaesic
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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24
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Moreno S, Muriel-Millán LF, Rodríguez-Martínez K, Ortíz-Vasco C, Bedoya-Pérez LP, Espín G. The ribosome rescue pathways SsrA-SmpB, ArfA, and ArfB mediate tolerance to heat and antibiotic stresses in Azotobacter vinelandii. FEMS Microbiol Lett 2022; 369:6824435. [PMID: 36368695 DOI: 10.1093/femsle/fnac104] [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: 02/18/2022] [Revised: 08/29/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria have a mechanism to rescue stalled ribosomes known as trans-translation consisting of SsrA, a transfer-messenger RNA (tmRNA), and the small protein SmpB. Other alternative rescue mechanisms mediated by ArfA and ArfB proteins are present only in some species. Ribosome rescue mechanisms also play a role in tolerance to antibiotics and various stresses such as heat. This study shows that the genome of the soil bacterium A. vinelandii harbours genes encoding for tmRNA, SmpB, two paralogs of ArfA (arfA1 and arfA2), and ArfB. A number of mutant strains carrying mutations in the ssrA, arfA1, arfA2, and arfB genes were constructed and tested for their growth and susceptibility to heat and the antibiotic tetracycline. We found that the inactivation of both ssrA and one or the two arfA genes was detrimental to growth and caused a higher susceptibility to heat and to the antibiotic tetracycline. Interestingly, the arfB mutant strain was unable to grow after 2 h of incubation at 45°C. Inactivation of arfB in the ssrA-arfA1-arfA2 strain caused a lethal phenotype since the quadruple mutant could not be isolated. Taken together, our data suggest that both arfA1 and arfA2, as well as arfB, are functional as back up mechanisms, and that the ArfB pathway has an essential role that confers A. vinelandii resistance to high temperatures.
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Affiliation(s)
- Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Luis Felipe Muriel-Millán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad Universitaria, CDMX, México
| | - Karen Rodríguez-Martínez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Cristian Ortíz-Vasco
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Leidy Patricia Bedoya-Pérez
- Programa de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
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25
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Ng KY, Lutfullahoglu Bal G, Richter U, Safronov O, Paulin L, Dunn CD, Paavilainen VO, Richer J, Newman WG, Taylor RW, Battersby BJ. Nonstop mRNAs generate a ground state of mitochondrial gene expression noise. SCIENCE ADVANCES 2022; 8:eabq5234. [PMID: 36399564 PMCID: PMC9674279 DOI: 10.1126/sciadv.abq5234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/22/2022] [Indexed: 05/29/2023]
Abstract
A stop codon within the mRNA facilitates coordinated termination of protein synthesis, releasing the nascent polypeptide from the ribosome. This essential step in gene expression is impeded with transcripts lacking a stop codon, generating nonstop ribosome complexes. Here, we use deep sequencing to investigate sources of nonstop mRNAs generated from the human mitochondrial genome. We identify diverse types of nonstop mRNAs on mitochondrial ribosomes that are resistant to translation termination by canonical release factors. Failure to resolve these aberrations by the mitochondrial release factor in rescue (MTRFR) imparts a negative regulatory effect on protein synthesis that is associated with human disease. Our findings reveal a source of underlying noise in mitochondrial gene expression and the importance of responsive ribosome quality control mechanisms for cell fitness and human health.
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Affiliation(s)
- Kah Ying Ng
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Guleycan Lutfullahoglu Bal
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Uwe Richter
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Omid Safronov
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Cory D. Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ville O. Paavilainen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Julie Richer
- Department of Medical Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Brendan J. Battersby
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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26
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Safdari HA, Kasvandik S, Polte C, Ignatova Z, Tenson T, Wilson D. Structure of Escherichia coli heat shock protein Hsp15 in complex with the ribosomal 50S subunit bearing peptidyl-tRNA. Nucleic Acids Res 2022; 50:12515-12526. [PMID: 36370110 PMCID: PMC9757039 DOI: 10.1093/nar/gkac1035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 11/14/2022] Open
Abstract
In Escherichia coli, the heat shock protein 15 (Hsp15) is part of the cellular response to elevated temperature. Hsp15 interacts with peptidyl-tRNA-50S complexes that arise upon dissociation of translating 70S ribosomes, and is proposed to facilitate their rescue and recycling. A previous structure of E. coli Hsp15 in complex with peptidyl-tRNA-50S complex reported a binding site located at the central protuberance of the 50S subunit. By contrast, recent structures of RqcP, the Hsp15 homolog in Bacillus subtilis, in complex with peptidyl-tRNA-50S complexes have revealed a distinct site positioned between the anticodon-stem-loop (ASL) of the P-site tRNA and H69 of the 23S rRNA. Here we demonstrate that exposure of E. coli cells to heat shock leads to a decrease in 70S ribosomes and accumulation of 50S subunits, thus identifying a natural substrate for Hsp15 binding. Additionally, we have determined a cryo-EM reconstruction of the Hsp15-50S-peptidyl-tRNA complex isolated from heat shocked E. coli cells, revealing that Hsp15 binds to the 50S-peptidyl-tRNA complex analogously to its B. subtilis homolog RqcP. Collectively, our findings support a model where Hsp15 stabilizes the peptidyl-tRNA in the P-site and thereby promotes access to the A-site for putative rescue factors to release the aberrant nascent polypeptide chain.
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Affiliation(s)
- Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Sergo Kasvandik
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Christine Polte
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Tanel Tenson
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Daniel N Wilson
- To whom correspondence should be addressed. Tel: +49 40 42838 2841;
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27
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Abstract
Despite having a highly reduced genome, Chlamydia trachomatis undergoes a complex developmental cycle in which the bacteria differentiate between the following two functionally and morphologically distinct forms: the infectious, nonreplicative elementary body (EB) and the noninfectious, replicative reticulate body (RB). The transitions between EBs and RBs are not mediated by division events that redistribute intracellular proteins. Rather, both primary (EB to RB) and secondary (RB to EB) differentiation likely require bulk protein turnover. One system for targeted protein degradation is the trans-translation system for ribosomal rescue, where polypeptides stalled during translation are marked with an SsrA tag encoded by a hybrid tRNA-mRNA, tmRNA. ClpX recognizes the SsrA tag, leading to ClpXP-mediated degradation. We hypothesize that ClpX functions in chlamydial differentiation through targeted protein degradation. We found that mutation of a key residue (R230A) within the specific motif in ClpX associated with the recognition of SsrA-tagged substrates resulted in abrogated secondary differentiation while not reducing chlamydial replication or developmental cycle progression as measured by transcripts. Furthermore, inhibition of trans-translation through chemical and targeted genetic approaches also impeded chlamydial development. Knockdown of tmRNA and subsequent complementation with an allele mutated in the SsrA tag closely phenocopied the overexpression of ClpXR230A, thus suggesting that ClpX recognition of SsrA-tagged substrates plays a critical function in secondary differentiation. Taken together, these data provide mechanistic insight into the requirements for transitions between chlamydial developmental forms. IMPORTANCE Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections and preventable infectious blindness. This unique organism undergoes developmental transitions between infectious, nondividing forms and noninfectious, dividing forms. Therefore, the chlamydial developmental cycle is an attractive target for Chlamydia-specific antibiotics, which would minimize effects of broad-spectrum antibiotics on the spread of antibiotic resistance in other organisms. However, the lack of knowledge about chlamydial development on a molecular level impedes the identification of specific, druggable targets. This work describes a mechanism through which both the fundamental processes of trans-translation and proteomic turnover by ClpXP contribute to chlamydial differentiation, a critical facet of chlamydial growth and survival. Given the almost universal presence of trans-translation and ClpX in eubacteria, this mechanism may be conserved in developmental cycles of other bacterial species. Additionally, this study expands the fields of trans-translation and Clp proteases by emphasizing the functional diversity of these systems throughout bacterial evolution.
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28
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Wu Y, Tang M, Wang Z, Yang Y, Li Z, Liang S, Yin P, Qi H. Efficient In Vitro Full-Sense-Codons Protein Synthesis. Adv Biol (Weinh) 2022; 6:e2200023. [PMID: 35676219 DOI: 10.1002/adbi.202200023] [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: 01/30/2022] [Revised: 04/14/2022] [Indexed: 01/28/2023]
Abstract
Termination of translation is essential but hinders applications of genetic code engineering, e.g., unnatural amino acids incorporation and codon randomization mediated saturation mutagenesis. Here, for the first time, it is demonstrated that E. coli Pth and ArfB together play an efficient translation termination without codon preference in the absence of class-I release factors. By degradation of the targeted protein, both essential and alternative termination types of machinery are completely removed to disable codon-dependent termination in cell extract. Moreover, a total of 153 engineered tRNAs are screened for efficient all stop-codons decoding to construct a codon-dependent termination defect in vitro protein synthesis with all 64 sense-codons, iPSSC. Finally, this full sense genetic code achieves significant improvement in the incorporation of distinct unnatural amino acids at up to 12 positions and synthesis of protein encoding consecutive NNN codons. By decoding all information in nucleotides to amino acids, iPSSC may hold great potential in building artificial protein synthesis beyond the cell.
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Affiliation(s)
- Yang Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China.,College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
| | - Mengtong Tang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Youhui Yang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Zhong Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Shurui Liang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Peng Yin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin, China.,Zhejiang Institute of Tianjin University, Shaoxing, Zhejiang, China
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29
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Mahmoud SA, Aldikacti B, Chien P. ATP hydrolysis tunes specificity of a AAA+ protease. Cell Rep 2022; 40:111405. [PMID: 36130509 DOI: 10.1016/j.celrep.2022.111405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
In bacteria, AAA+ proteases such as Lon and ClpXP degrade substrates with exquisite specificity. These machines capture the energy of ATP hydrolysis to power unfolding and degradation of target substrates. Here, we show that a mutation in the ATP binding site of ClpX shifts protease specificity to promote degradation of normally Lon-restricted substrates. However, this ClpX mutant is worse at degrading ClpXP targets, suggesting an optimal balance in substrate preference for a given protease that is easy to alter. In vitro, wild-type ClpXP also degrades Lon-restricted substrates more readily when ATP levels are reduced, similar to the shifted specificity of mutant ClpXP, which has altered ATP hydrolysis kinetics. Based on these results, we suggest that the rates of ATP hydrolysis not only power substrate unfolding and degradation, but also tune protease specificity. We consider various models for this effect based on emerging structures of AAA+ machines showing conformationally distinct states.
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Affiliation(s)
- Samar A Mahmoud
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Berent Aldikacti
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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30
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Srinivas P, Keiler KC, Dunham CM. Druggable differences: Targeting mechanistic differences between trans-translation and translation for selective antibiotic action. Bioessays 2022; 44:e2200046. [PMID: 35719031 PMCID: PMC9308750 DOI: 10.1002/bies.202200046] [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: 02/21/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/03/2023]
Abstract
Bacteria use trans-translation to rescue stalled ribosomes and target incomplete proteins for proteolysis. Despite similarities between tRNAs and transfer-messenger RNA (tmRNA), the key molecule for trans-translation, new structural and biochemical data show important differences between translation and trans-translation at most steps of the pathways. tmRNA and its binding partner, SmpB, bind in the A site of the ribosome but do not trigger the same movements of nucleotides in the rRNA that are required for codon recognition by tRNA. tmRNA-SmpB moves from the A site to the P site of the ribosome without subunit rotation to generate hybrid states, and moves from the P site to a site outside the ribosome instead of to the E site. During catalysis, transpeptidation to tmRNA appears to require the ribosomal protein bL27, which is dispensable for translation, suggesting that this protein may be conserved in bacteria due to trans-translation. These differences provide insights into the fundamental nature of trans-translation, and provide targets for new antibiotics that may have decrease cross-reactivity with eukaryotic ribosomes.
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Affiliation(s)
- Pooja Srinivas
- Emory University School of Medicine, Department of Biochemistry, Atlanta, GA, USA
| | - Kenneth C. Keiler
- The Pennsylvania State University, Department of Biochemistry & Molecular Biology, University Park, PA, USA,Corresponding authors: Kenneth C. Keiler, , Christine M. Dunham,
| | - Christine M. Dunham
- Emory University School of Medicine, Department of Biochemistry, Atlanta, GA, USA,Corresponding authors: Kenneth C. Keiler, , Christine M. Dunham,
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31
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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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32
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Han D, Zhen H, Liu X, Zulewska J, Yang Z. Organelle 16S rRNA amplicon sequencing enables profiling of active gut microbiota in murine model. Appl Microbiol Biotechnol 2022; 106:5715-5728. [PMID: 35896837 DOI: 10.1007/s00253-022-12083-x] [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: 04/13/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
High-throughput sequencing of ribosomal RNA (rRNA) amplicons has served as a cornerstone in microbiome studies. Despite crucial implication of organelle 16S rRNA measurements to host gut microbial activities, genomic DNA (gDNA) was overwhelmingly targeted for amplicon sequencings. Although gDNA could be a reliable resource for gene existing validation, little information is revealed in regard to the activity of microorganisms owing to the limited changes gDNA undertaken in inactive, dormant, and dead bacteria. We applied both rRNA- and gDNA-derived sequencings on mouse cecal contents. Respective experimental designs were verified to be suitable for nucleic acid (NA) purification. Via benchmarking, mainstream 16S rRNA hypervariable region targets and reference databases were proven adequate for respective amplicon sequencing study. In phylogenetic studies, significant microbial composition differences were observed between two methods. Desulfovibrio spp. (an important group of anaerobic gut microorganisms that has caused analytical difficulties), Pediococcus spp., and Proteobacteria were drastically lower as represented by gDNA-derived compositions, while microbes like Firmicutes were higher as represented by gDNA-derived microbiome compositions. Also, using PICRUSt2 as an example, we illustrated that rRNA-derived sequencing might be more suitable for microbiome function predictions since pathways like sugar metabolism were lower as represented by rRNA-derived results. The findings of this study demonstrated that rRNA-derived amplicon sequencing could improve identification capability of specific gut microorganisms and might be more suitable for in silico microbiome function predictions. Therefore, rRNA-derived amplicon sequencings, preferably coupled with gDNA-derived ones, could be used as a capable tool to unveil active microbial components in host gut. KEY POINTS: • Conventional pipelines were adequate for the respective amplicon sequencing study • Groups, such as Desulfovibrio spp., were differently represented by two methods • Comparative amplicon sequencings could be useful in host active microbiota studies.
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Affiliation(s)
- Dong Han
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China.,Key Laboratory of Food Bioengineering, (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hongmin Zhen
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Xiaoyan Liu
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Justyna Zulewska
- Department of Dairy Science and Quality Management, Faculty of Food Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Zhennai Yang
- Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China.
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33
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Tian Y, Zeng F, Raybarman A, Fatma S, Carruthers A, Li Q, Huang RH. Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB. Proc Natl Acad Sci U S A 2022; 119:e2202464119. [PMID: 35858322 PMCID: PMC9304027 DOI: 10.1073/pnas.2202464119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/10/2022] [Indexed: 01/14/2023] Open
Abstract
RtcB is involved in transfer RNA (tRNA) splicing in archaeal and eukaryotic organisms. However, most RtcBs are found in bacteria, whose tRNAs have no introns. Because tRNAs are the substrates of archaeal and eukaryotic RtcB, it is assumed that bacterial RtcBs are for repair of damaged tRNAs. Here, we show that a subset of bacterial RtcB, denoted RtcB2 herein, specifically repair ribosomal damage in the decoding center. To access the damage site for repair, however, the damaged 70S ribosome needs to be dismantled first, and this is accomplished by bacterial PrfH. Peptide-release assays revealed that PrfH is only active with the damaged 70S ribosome but not with the intact one. A 2.55-Å cryo-electron microscopy structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into PrfH discriminating between the damaged and the intact ribosomes via specific recognition of the cleaved 3'-terminal nucleotide. RNA repair assays demonstrated that RtcB2 efficiently repairs the damaged 30S ribosomal subunit but not the damaged tRNAs. Cell-based assays showed that the RtcB2-PrfH pair reverse the damage inflicted by ribosome-specific ribotoxins in vivo. Thus, our combined biochemical, structural, and cell-based studies have uncovered a bacterial defense system specifically evolved to reverse the lethal ribosomal damage in the decoding center for cell survival.
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Affiliation(s)
- Yannan Tian
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fuxing Zeng
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, People’s Republic of China
| | - Adrika Raybarman
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Shirin Fatma
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Amy Carruthers
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Qingrong Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, People’s Republic of China
| | - Raven H. Huang
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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34
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Xu S, Cao Q, Liu Z, Chen J, Yan P, Li B, Xu Y. Transcriptomic Analysis Reveals the Role of tmRNA on Biofilm Formation in Bacillus subtilis. Microorganisms 2022; 10:microorganisms10071338. [PMID: 35889057 PMCID: PMC9319509 DOI: 10.3390/microorganisms10071338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus strains are widely distributed in terrestrial and marine environments, and some of them are used as biocontrol organisms for their biofilm-formation ability. In Bacillus subtilis, biofilm formation is fine-tuned by a complex network, a clear understanding of which still requires study. In bacteria, tmRNA, encoded by the ssrA gene, catalyzes trans-translation that can rescue ribosomes stalled on mRNA transcripts lacking a functional stop codon. tmRNA also affects physiological bioprocesses in some bacteria. In this study, we constructed a ssrA mutant in B. subtilis and found that the biofilm formation in the ssrA mutant was largely impaired. Moreover, we isolated a biofilm-formation suppressor of ssrA, in which the biofilm formation was restored to a level even stronger than that in the wild type. We further performed RNAseq assays with the wild type, ssrA mutant, and suppressor of ssrA for comparisons of their transcriptomes. By analyzing the transcriptomic data, we predicted the possible functions of some differentially expressed genes (DEGs) in the tmRNA regulation of biofilm formation in B. subtilis. Finally, we found that the overexpression of two DEGs, acoA and yhjR, could restore the biofilm formation in the ssrA mutant, indicating that AcoA and YhjR were immediate regulators involved in the tmRNA regulatory web controlling biofilm formation in B. subtilis. Our data can improve the knowledge about the molecular network involved in Bacillus biofilm formation and provide new targets for manipulation of Bacillus biofilms for future investigation.
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Affiliation(s)
- Shanshan Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Qianqian Cao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Zengzhi Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Junpeng Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Peiguang Yan
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Bingyu Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen 518055, China
- Correspondence: (B.L.); (Y.X.)
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- Correspondence: (B.L.); (Y.X.)
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35
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Tomasi FG, Hall AMJ, Schweber JTP, Dulberger CL, McGowen K, Liu Q, Fortune SM, Helaine S, Rubin EJ. A tRNA-Acetylating Toxin and Detoxifying Enzyme in Mycobacterium tuberculosis. Microbiol Spectr 2022; 10:e0058022. [PMID: 35638832 PMCID: PMC9241777 DOI: 10.1128/spectrum.00580-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Toxin-antitoxin (TA) systems allow bacteria to adapt to changing environments without altering gene expression. Despite being overrepresented in Mycobacterium tuberculosis, their physiological roles remain elusive. We describe a TA system in M. tuberculosis which we named TacAT due to its homology to previously discovered systems in Salmonella. The toxin, TacT, blocks growth by acetylating glycyl-tRNAs and inhibiting translation. Its effects are reversed by the enzyme peptidyl tRNA hydrolase (Pth), which also cleaves peptidyl tRNAs that are prematurely released from stalled ribosomes. Pth is essential in most bacteria and thereby has been proposed as a promising drug target for complex pathogens like M. tuberculosis. Transposon sequencing data suggest that the tacAT operon is nonessential for M. tuberculosis growth in vitro, and premature stop mutations in this TA system present in some clinical isolates suggest that it is also dispensable in vivo. We assessed whether TacT modulates pth essentiality in M. tuberculosis because drugs targeting Pth might prompt resistance if TacAT is disrupted. We show that pth essentiality is unaffected by the absence of tacAT. These results highlight a fundamental aspect of mycobacterial biology and indicate that Pth's essential role hinges on its peptidyl-tRNA hydrolase activity. Our work underscores Pth's potential as a viable target for new antibiotics. IMPORTANCE The global rise in antibiotic-resistant tuberculosis has prompted an urgent search for new drugs. Toxin-antitoxin (TA) systems allow bacteria to adapt rapidly to environmental changes, and Mycobacterium tuberculosis encodes more TA systems than any known pathogen. We have characterized a new TA system in M. tuberculosis: the toxin, TacT, acetylates charged tRNA to block protein synthesis. TacT's effects are reversed by the essential bacterial enzyme peptidyl tRNA hydrolase (Pth), which is currently being explored as an antibiotic target. Pth also cleaves peptidyl tRNAs that are prematurely released from stalled ribosomes. We assessed whether TacT modulates pth essentiality in M. tuberculosis because drugs targeting Pth might prompt resistance if TacT is disrupted. We show that pth essentiality is unaffected by the absence of this TA system, indicating that Pth's essential role hinges on its peptidyl-tRNA hydrolase activity. Our work underscores Pth's potential as a viable target for new antibiotics.
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Affiliation(s)
- Francesca G. Tomasi
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Jessica T. P. Schweber
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Charles L. Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kerry McGowen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sophie Helaine
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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36
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Maviza TP, Zarechenskaia AS, Burmistrova NR, Tchoub AS, Dontsova OA, Sergiev PV, Osterman IA. RtcB2-PrfH Operon Protects E. coli ATCC25922 Strain from Colicin E3 Toxin. Int J Mol Sci 2022; 23:6453. [PMID: 35742896 PMCID: PMC9223846 DOI: 10.3390/ijms23126453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
In the bid to survive and thrive in an environmental setting, bacterial species constantly interact and compete for resources and space in the microbial ecosystem. Thus, they have adapted to use various antibiotics and toxins to fight their rivals. Simultaneously, they have evolved an ability to withstand weapons that are directed against them. Several bacteria harbor colicinogenic plasmids which encode toxins that impair the translational apparatus. One of them, colicin E3 ribotoxin, mediates cleavage of the 16S rRNA in the decoding center of the ribosome. In order to thrive upon deployment of such ribotoxins, competing bacteria may have evolved counter-conflict mechanisms to prevent their demise. A recent study demonstrated the role of PrfH and the RtcB2 module in rescuing a damaged ribosome and the subsequent re-ligation of the cleaved 16S rRNA by colicin E3 in vitro. The rtcB2-prfH genes coexist as gene neighbors in an operon that is sporadically spread among different bacteria. In the current study, we report that the RtcB2-PrfH module confers resistance to colicin E3 toxicity in E. coli ATCC25922 cells in vivo. We demonstrated that the viability of E. coli ATCC25922 strain that is devoid of rtcB2 and prfH genes is impaired upon action of colicin E3, in contrast to the parental strain which has intact rtcB2 and prfH genes. Complementation of the rtcB2 and prfH gene knockout with a high copy number-plasmid (encoding either rtcB2 alone or both rtcB2-prfH operon) restored resistance to colicin E3. These results highlight a counter-conflict system that may have evolved to thwart colicin E3 activity.
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Affiliation(s)
- Tinashe P. Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
| | - Anastasiia S. Zarechenskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Nadezhda R. Burmistrova
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Andrey S. Tchoub
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 119992, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
- Genetics and Life Sciences Research Center, Sirius University of Science and Technology, 1 Olympic Ave., Sochi 354340, Russia
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Herzel L, Stanley JA, Yao CC, Li GW. Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome. Nucleic Acids Res 2022; 50:5029-5046. [PMID: 35524564 PMCID: PMC9122600 DOI: 10.1093/nar/gkac295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023] Open
Abstract
Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
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Affiliation(s)
- Lydia Herzel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Julian A Stanley
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Chun-Chen Yao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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38
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Ribosome collisions: New ways to initiate ribosome rescue. Curr Biol 2022; 32:R469-R472. [DOI: 10.1016/j.cub.2022.04.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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39
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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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40
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Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes. Noncoding RNA 2022; 8:ncrna8020022. [PMID: 35314615 PMCID: PMC8938821 DOI: 10.3390/ncrna8020022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, namely ribosome-associated non-coding RNAs (rancRNAs), has been discovered. These rancRNAs have proven to be efficient players in the regulation of translation as a first wave of stress adaptation by directly targeting the ribosome, the central enzyme of protein production. This underlying principle appears to be highly conserved, since rancRNAs are present in all three domains of life. Here, we review the major findings and mechanistic peculiarities of rancRNAs, a class of transcripts that is providing new and broader perspectives on the complexity of the ribosome and translation regulation.
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Mabanglo MF, Houry WA. Recent structural insights into the mechanism of ClpP protease regulation by AAA+ chaperones and small molecules. J Biol Chem 2022; 298:101781. [PMID: 35245501 PMCID: PMC9035409 DOI: 10.1016/j.jbc.2022.101781] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/19/2022] Open
Abstract
ClpP is a highly conserved serine protease that is a critical enzyme in maintaining protein homeostasis and is an important drug target in pathogenic bacteria and various cancers. In its functional form, ClpP is a self-compartmentalizing protease composed of two stacked heptameric rings that allow protein degradation to occur within the catalytic chamber. ATPase chaperones such as ClpX and ClpA are hexameric ATPases that form larger complexes with ClpP and are responsible for the selection and unfolding of protein substrates prior to their degradation by ClpP. Although individual structures of ClpP and ATPase chaperones have offered mechanistic insights into their function and regulation, their structures together as a complex have only been recently determined to high resolution. Here, we discuss the cryoelectron microscopy structures of ClpP-ATPase complexes and describe findings previously inaccessible from individual Clp structures, including how a hexameric ATPase and a tetradecameric ClpP protease work together in a functional complex. We then discuss the consensus mechanism for substrate unfolding and translocation derived from these structures, consider alternative mechanisms, and present their strengths and limitations. Finally, new insights into the allosteric control of ClpP gained from studies using small molecules and gain or loss-of-function mutations are explored. Overall, this review aims to underscore the multilayered regulation of ClpP that may present novel ideas for structure-based drug design.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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Harris NJ, Reading E, Booth PJ. Cell-Free Synthesis Strategies to Probe Co-translational Folding of Proteins Within Lipid Membranes. Methods Mol Biol 2022; 2433:273-292. [PMID: 34985751 DOI: 10.1007/978-1-0716-1998-8_17] [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] [Indexed: 06/14/2023]
Abstract
In order to comprehend the molecular basis of transmembrane protein biogenesis, methods are required that are capable of investigating the co-translational folding of these hydrophobic proteins. Equally, in artificial cell studies, controllable methods are desirable for in situ synthesis of membrane proteins that then direct reactions in the synthetic cell membrane. Here we describe a method that exploits cell-free expression systems and tunable membrane mimetics to facilitate co-translational studies. Alteration of the lipid bilayer composition improves the efficiency of the folding system. The approach also enables membrane transport proteins to be made and inserted into artificial cell platforms such as droplet interface bilayers. Importantly, this gives a new facet to the droplet networks by enabling specific transport of molecules across the synthetic bilayer against a concentration gradient. This method also includes a protocol to pause and restart translation of membrane proteins at specified positions during their co-translational folding. This stop-start strategy provides an avenue to investigate whether the proteins fold in sequence order, or if the correct fold of N-terminal regions is reliant on the synthesis of downstream residues.
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Affiliation(s)
| | - Eamonn Reading
- Department of Chemistry, King's College London, London, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, London, UK.
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Nadler F, Lavdovskaia E, Richter-Dennerlein R. Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors. RNA Biol 2021; 19:117-131. [PMID: 34923906 PMCID: PMC8786322 DOI: 10.1080/15476286.2021.2015561] [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: 10/27/2022] Open
Abstract
The universally conserved process of protein biosynthesis is crucial for maintaining cellular homoeostasis and in eukaryotes, mitochondrial translation is essential for aerobic energy production. Mitochondrial ribosomes (mitoribosomes) are highly specialized to synthesize 13 core subunits of the oxidative phosphorylation (OXPHOS) complexes. Although the mitochondrial translation machinery traces its origin from a bacterial ancestor, it has acquired substantial differences within this endosymbiotic environment. The cycle of mitoribosome function proceeds through the conserved canonical steps of initiation, elongation, termination and mitoribosome recycling. However, when mitoribosomes operate in the context of limited translation factors or on aberrant mRNAs, they can become stalled and activation of rescue mechanisms is required. This review summarizes recent advances in the understanding of protein biosynthesis in mitochondria, focusing especially on the mechanistic and physiological details of translation termination, and mitoribosome recycling and rescue.
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Affiliation(s)
- Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Elena Lavdovskaia
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
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44
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Li H, Ming X, Xu D, Mo H, Liu Z, Hu L, Zhou X. Transcriptome Analysis and Weighted Gene Co-expression Network Reveal Multitarget-Directed Antibacterial Mechanisms of Benzyl Isothiocyanate against Staphylococcus aureus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11733-11741. [PMID: 34558287 DOI: 10.1021/acs.jafc.1c03979] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Staphylococcus aureus can cause many diseases and has a strong tendency to develop resistance to multiple antibiotics. In this study, benzyl isothiocyanate (BITC) was shown to have an excellent inhibitory effect on S. aureus ATCC25923 and methicillin-resistant S. aureus strains, with a minimum inhibitory concentration of 10 μg/mL. Under a scanning electron microscope, shrinkage and lysis of the cellular envelope were observed when exposed to BITC, and a bactericidal mode of BITC against S. aureus was further confirmed through flow cytometry. Additionally, the RNA profiles of S. aureus cells exposed to BITC indicated a violent transcriptional response to BITC. Through Kyoto Encyclopedia of Genes and Genomes analysis, it was found that many pathways involving bacterial survival were significantly affected, such as RNA degradation, oxidative phosphorylation, arginine biosynthesis, and so forth. A gene co-expression network was constructed using weighted gene co-expression network analysis, and six biologically meaningful co-expression modules and 125 hub genes were identified from the network. Among them, EfeB, GroES, SmpB, and Lsp were possibly targeted by BITC, leading to the death of S. aureus. Our results indicated a great potential of BITC to be applied in food safety and pharmaceuticals, highlighting its multitarget-directed bactericidal effects on S. aureus.
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Affiliation(s)
- Hongbo Li
- Department of Food and Bioengineering, Shaanxi University of Science and Technology, Shaanxi 710021, China
| | - Xujia Ming
- Department of Food and Bioengineering, Shaanxi University of Science and Technology, Shaanxi 710021, China
| | - Dan Xu
- Department of Food and Bioengineering, Shaanxi University of Science and Technology, Shaanxi 710021, China
| | - Haizhen Mo
- Department of Food and Bioengineering, Shaanxi University of Science and Technology, Shaanxi 710021, China
| | - Zhenbin Liu
- Department of Food and Bioengineering, Shaanxi University of Science and Technology, Shaanxi 710021, China
| | - Liangbin Hu
- Department of Food and Bioengineering, Shaanxi University of Science and Technology, Shaanxi 710021, China
| | - Xiaohui Zhou
- Department of Pathobiology & Veterinary Science, University of Connecticut, 61 North Eagleville Road, Storrs, Connecticut 06269, United States
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Korostelev AA. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. BIOCHEMISTRY (MOSCOW) 2021; 86:1107-1121. [PMID: 34565314 DOI: 10.1134/s0006297921090066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
When a ribosome encounters the stop codon of an mRNA, it terminates translation, releases the newly made protein, and is recycled to initiate translation on a new mRNA. Termination is a highly dynamic process in which release factors (RF1 and RF2 in bacteria; eRF1•eRF3•GTP in eukaryotes) coordinate peptide release with large-scale molecular rearrangements of the ribosome. Ribosomes stalled on aberrant mRNAs are rescued and recycled by diverse bacterial, mitochondrial, or cytoplasmic quality control mechanisms. These are catalyzed by rescue factors with peptidyl-tRNA hydrolase activity (bacterial ArfA•RF2 and ArfB, mitochondrial ICT1 and mtRF-R, and cytoplasmic Vms1), that are distinct from each other and from release factors. Nevertheless, recent structural studies demonstrate a remarkable similarity between translation termination and ribosome rescue mechanisms. This review describes how these pathways rely on inherent ribosome dynamics, emphasizing the active role of the ribosome in all translation steps.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
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46
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Burgos R, Weber M, Gallo C, Lluch-Senar M, Serrano L. Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control. iScience 2021; 24:102985. [PMID: 34485867 PMCID: PMC8403727 DOI: 10.1016/j.isci.2021.102985] [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: 05/27/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
Trans-translation is a ubiquitous bacterial mechanism of ribosome rescue mediated by a transfer-messenger RNA (tmRNA) that adds a degradation tag to the truncated nascent polypeptide. Here, we characterize this quality control system in a genome-reduced bacterium, Mycoplasma pneumoniae (MPN), and perform a comparative analysis of protein quality control components in slow and fast-growing prokaryotes. We show in vivo that in MPN the sole quality control cytoplasmic protease (Lon) degrades efficiently tmRNA-tagged proteins. Analysis of tmRNA-mutants encoding a tag resistant to proteolysis reveals extensive tagging activity under normal growth. Unlike knockout strains, these mutants are viable demonstrating the requirement of tmRNA-mediated ribosome recycling. Chaperone and Lon steady-state levels maintain proteostasis in these mutants suggesting a model in which co-evolution of Lon and their substrates offer simple mechanisms of regulation without specialized degradation machineries. Finally, comparative analysis shows relative increase in Lon/Chaperone levels in slow-growing bacteria suggesting physiological adaptation to growth demand. Lon degrades efficiently tmRNA-tagged proteins in a genome-reduced bacterium tmRNA-tag mutants are viable and reveal extensive tagging activity in M. pneumoniae Co-evolution of Lon and their substrates offer simple mechanisms of regulation Chaperone and Lon relative levels correlate with bacterial growth rates
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Affiliation(s)
- Raul Burgos
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Corresponding author
| | - Marc Weber
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author
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Abstract
Translation of the genetic information into proteins, performed by the ribosome, is a key cellular process in all organisms. Translation usually proceeds smoothly, but, unfortunately, undesirable events can lead to stalling of translating ribosomes. To rescue these faulty arrested ribosomes, bacterial cells possess three well-characterized quality control systems, tmRNA, ArfA, and ArfB. Recently, an additional ribosome rescue mechanism has been discovered in Bacillus subtilis. In contrast to the "canonical" systems targeting the 70S bacterial ribosome, this latter mechanism operates by first splitting the ribosome into the small (30S) and large (50S) subunits to then clearing the resultant jammed large subunit from the incomplete nascent polypeptide. Here, I will discuss the recent microbiological, biochemical, and structural data regarding functioning of this novel rescue system.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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48
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Ren H, Zhang J, Zhou J, Xu C, Fan Z, Pan X, Li S, Liang Y, Chen S, Xu J, Wang P, Zhang Y, Zhu G, Liu H, Jin Y, Bai F, Cheng Z, Pletzer D, Wu W. Synergistic bactericidal activities of tobramycin with ciprofloxacin and azithromycin against Klebsiella pneumoniae. J Antibiot (Tokyo) 2021; 74:528-537. [PMID: 34050325 DOI: 10.1038/s41429-021-00427-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/09/2022]
Abstract
Trans-translation is a unique bacterial ribosome rescue system that plays important roles in the tolerance to environmental stresses. It is composed of an ssrA-encoded tmRNA and a protein SmpB. In this study, we examined the role of trans-translation in antibiotic tolerance in Klebsiella pneumoniae and explored whether the inhibition of this mechanism could enhance the bactericidal activities of antibiotics. We found that deletion of the ssrA gene reduced the survival of K. pneumoniae after treatment with kanamycin, tobramycin, azithromycin, and ciprofloxacin, indicating an important role of the trans-translation in bacterial antibiotic tolerance. By using a modified ssrA gene with a 6×His tag we demonstrated that tobramycin suppressed the azithromycin and ciprofloxacin-elicited activation of trans-translation. The results were further confirmed with a trans-translation reporter system that is composed of a normal mCherry gene and a gfp gene without the stop codon. Compared to each individual antibiotic, combination of tobramycin with azithromycin or ciprofloxacin synergistically enhanced the killing activities against planktonic K. pneumoniae cells and improved bacterial clearance in a murine cutaneous abscess infection model. In addition, the combination of tobramycin and ciprofloxacin increased the bactericidal activities against biofilm-associated cells. Overall, our results suggest that the combination of tobramycin with azithromycin or ciprofloxacin is a promising strategy in combating K. pneumoniae infections.
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Affiliation(s)
- Huan Ren
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jingyi Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jingyi Zhou
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Congjuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zheng Fan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shouyi Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yuying Liang
- Department of laboratory medicine, 5th medical center of PLA general hospital, Beijing, 100071, China
| | - Shuiping Chen
- Department of laboratory medicine, 5th medical center of PLA general hospital, Beijing, 100071, China
| | - Jun Xu
- NHC Key Laboratory of Hormones and Development (Tianjin Medical University), Tianjin Key Laboratory of Metabolic Diseases, Diabetic foot Department, Tianjin Medical University Metabolic Disease Hospital & Chu Hsien-I Memorial Hospital, Tianjin, 300070, China
| | - Penghua Wang
- NHC Key Laboratory of Hormones and Development (Tianjin Medical University), Tianjin Key Laboratory of Metabolic Diseases, Diabetic foot Department, Tianjin Medical University Metabolic Disease Hospital & Chu Hsien-I Memorial Hospital, Tianjin, 300070, China
| | - Yanhong Zhang
- Nankai University Affiliated Hospital (Tianjin Forth Hospital), Tianjin, 300222, China
| | - Guangbo Zhu
- Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin, 300121, China
| | - Huimin Liu
- Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin, 300121, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Daniel Pletzer
- Department of Microbiology & Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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Zhao L, Castanié-Cornet MP, Kumar S, Genevaux P, Hayer-Hartl M, Hartl FU. Bacterial RF3 senses chaperone function in co-translational folding. Mol Cell 2021; 81:2914-2928.e7. [PMID: 34107307 DOI: 10.1016/j.molcel.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/05/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
Molecular chaperones assist with protein folding by interacting with nascent polypeptide chains (NCs) during translation. Whether the ribosome can sense chaperone defects and, in response, abort translation of misfolding NCs has not yet been explored. Here we used quantitative proteomics to investigate the ribosome-associated chaperone network in E. coli and the consequences of its dysfunction. Trigger factor and the DnaK (Hsp70) system are the major NC-binding chaperones. HtpG (Hsp90), GroEL, and ClpB contribute increasingly when DnaK is deficient. Surprisingly, misfolding because of defects in co-translational chaperone function or amino acid analog incorporation results in recruitment of the non-canonical release factor RF3. RF3 recognizes aberrant NCs and then moves to the peptidyltransferase site to cooperate with RF2 in mediating chain termination, facilitating clearance by degradation. This function of RF3 reduces the accumulation of misfolded proteins and is critical for proteostasis maintenance and cell survival under conditions of limited chaperone availability.
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Affiliation(s)
- Liang Zhao
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marie-Pierre Castanié-Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Sneha Kumar
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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Kummer E, Schubert KN, Schoenhut T, Scaiola A, Ban N. Structural basis of translation termination, rescue, and recycling in mammalian mitochondria. Mol Cell 2021; 81:2566-2582.e6. [PMID: 33878294 DOI: 10.1016/j.molcel.2021.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
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Affiliation(s)
- Eva Kummer
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Katharina Noel Schubert
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schoenhut
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Alain Scaiola
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Nenad Ban
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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