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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: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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2
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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:ijms23126453. [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] [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
- Correspondence:
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3
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Cuthbert BJ, Hayes CS, Goulding CW. Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. Front Mol Biosci 2022; 9:866854. [PMID: 35558562 PMCID: PMC9086364 DOI: 10.3389/fmolb.2022.866854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/25/2022] Open
Abstract
Bacteria live in complex communities and environments, competing for space and nutrients. Within their niche habitats, bacteria have developed various inter-bacterial mechanisms to compete and communicate. One such mechanism is contact-dependent growth inhibition (CDI). CDI is found in many Gram-negative bacteria, including several pathogens. These CDI+ bacteria encode a CdiB/CdiA two-partner secretion system that delivers inhibitory toxins into neighboring cells upon contact. Toxin translocation results in the growth inhibition of closely related strains and provides a competitive advantage to the CDI+ bacteria. CdiB, an outer-membrane protein, secretes CdiA onto the surface of the CDI+ bacteria. When CdiA interacts with specific target-cell receptors, CdiA delivers its C-terminal toxin region (CdiA-CT) into the target-cell. CdiA-CT toxin proteins display a diverse range of toxic functions, such as DNase, RNase, or pore-forming toxin activity. CDI+ bacteria also encode an immunity protein, CdiI, that specifically binds and neutralizes its cognate CdiA-CT, protecting the CDI+ bacteria from auto-inhibition. In Gram-negative bacteria, toxin/immunity (CdiA-CT/CdiI) pairs have highly variable sequences and functions, with over 130 predicted divergent toxin/immunity complex families. In this review, we will discuss biochemical and structural advances made in the characterization of CDI. This review will focus on the diverse array of CDI toxin/immunity complex structures together with their distinct toxin functions. Additionally, we will discuss the most recent studies on target-cell recognition and toxin entry, along with the discovery of a new member of the CDI loci. Finally, we will offer insights into how these diverse toxin/immunity complexes could be harnessed to fight human diseases.
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Affiliation(s)
- Bonnie J. Cuthbert
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Christopher S. Hayes
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Celia W. Goulding
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
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4
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How Gut Microbes Nurture Intestinal Stem Cells: A Drosophila Perspective. Metabolites 2022; 12:metabo12020169. [PMID: 35208243 PMCID: PMC8878600 DOI: 10.3390/metabo12020169] [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: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
Host-microbiota interactions are key modulators of host physiology and behavior. Accumulating evidence suggests that the complex interplay between microbiota, diet and the intestine controls host health. Great emphasis has been given on how gut microbes have evolved to harvest energy from the diet to control energy balance, host metabolism and fitness. In addition, many metabolites essential for intestinal homeostasis are mainly derived from gut microbiota and can alleviate nutritional imbalances. However, due to the high complexity of the system, the molecular mechanisms that control host-microbiota mutualism, as well as whether and how microbiota affects host intestinal stem cells (ISCs) remain elusive. Drosophila encompasses a low complexity intestinal microbiome and has recently emerged as a system that might uncover evolutionarily conserved mechanisms of microbiota-derived nutrient ISC regulation. Here, we review recent studies using the Drosophila model that directly link microbiota-derived metabolites and ISC function. This research field provides exciting perspectives for putative future treatments of ISC-related diseases based on monitoring and manipulating intestinal microbiota.
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Francis MLR, Webby MN, Housden NG, Kaminska R, Elliston E, Chinthammit B, Lukoyanova N, Kleanthous C. Porin threading drives receptor disengagement and establishes active colicin transport through Escherichia coli OmpF. EMBO J 2021; 40:e108610. [PMID: 34515361 PMCID: PMC8561637 DOI: 10.15252/embj.2021108610] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022] Open
Abstract
Bacteria deploy weapons to kill their neighbours during competition for resources and to aid survival within microbiomes. Colicins were the first such antibacterial system identified, yet how these bacteriocins cross the outer membrane (OM) of Escherichia coli is unknown. Here, by solving the structures of translocation intermediates via cryo‐EM and by imaging toxin import, we uncover the mechanism by which the Tol‐dependent nuclease colicin E9 (ColE9) crosses the bacterial OM. We show that threading of ColE9’s disordered N‐terminal domain through two pores of the trimeric porin OmpF causes the colicin to disengage from its primary receptor, BtuB, and reorganises the translocon either side of the membrane. Subsequent import of ColE9 through the lumen of a single OmpF subunit is driven by the proton‐motive force, which is delivered by the TolQ‐TolR‐TolA‐TolB assembly. Our study answers longstanding questions, such as why OmpF is a better translocator than OmpC, and reconciles the mechanisms by which both Tol‐ and Ton‐dependent bacteriocins cross the bacterial outer membrane.
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Affiliation(s)
| | - Melissa N Webby
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emma Elliston
- Department of Biochemistry, University of Oxford, Oxford, UK
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6
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Abstract
Bacteria often secrete diffusible protein toxins (bacteriocins) to kill bystander cells during interbacterial competition. Here, we use biochemical, biophysical and structural analyses to show how a bacteriocin exploits TolC, a major outer-membrane antibiotic efflux channel in Gram-negative bacteria, to transport itself across the outer membrane of target cells. Klebicin C (KlebC), a rRNase toxin produced by Klebsiella pneumoniae, binds TolC of a related species (K. quasipneumoniae) with high affinity through an N-terminal, elongated helical hairpin domain common amongst bacteriocins. The KlebC helical hairpin opens like a switchblade to bind TolC. A cryo-EM structure of this partially translocated state, at 3.1 Å resolution, reveals that KlebC associates along the length of the TolC channel. Thereafter, the unstructured N-terminus of KlebC protrudes beyond the TolC iris, presenting a TonB-box sequence to the periplasm. Association with proton-motive force-linked TonB in the inner membrane drives toxin import through the channel. Finally, we demonstrate that KlebC binding to TolC blocks drug efflux from bacteria. Our results indicate that TolC, in addition to its known role in antibiotic export, can function as a protein import channel for bacteriocins. Bacteria can secrete diffusible protein toxins that kill competing bacteria. Here, the authors use biochemical, biophysical and structural analyses to show how one of these toxins exploits TolC (a major antibiotic efflux channel) to transport itself across the outer membrane of target cells.
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7
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Liu Y, Gong W, Yang Z, Li C. SNB-PSSM: A spatial neighbor-based PSSM used for protein-RNA binding site prediction. J Mol Recognit 2021; 34:e2887. [PMID: 33442949 DOI: 10.1002/jmr.2887] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 01/09/2023]
Abstract
Protein-RNA interactions play essential roles in a wide variety of biological processes. Recognition of RNA-binding residues on proteins has been a challenging problem. Most of methods utilize the position-specific scoring matrix (PSSM). It has been found that considering the evolutionary information of sequence neighboring residues can improve the prediction. In this work, we introduce a novel method SNB-PSSM (spatial neighbor-based PSSM) combined with the structure window scheme where the evolutionary information of spatially neighboring residues is considered. The results show our method consistently outperforms the standard and smoothed PSSM methods. Tested on multiple datasets, this approach shows an encouraging performance compared with RNABindRPlus, BindN+, PPRInt, xypan, Predict_RBP, SpaPF, PRNA, and KYG, although is inferior to RNAProSite, RBscore, and aaRNA. In addition, since our method is not sensitive to protein structure changes, it can be applied well on binding site predictions of modeled structures. Thus, the result also suggests the evolution of binding sites is spatially cooperative. The proposed method as an effective tool of considering evolutionary information can be widely used for the nucleic acid-/protein-binding site prediction and functional motif finding.
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Affiliation(s)
- Yang Liu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Zhen Yang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
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8
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Sulthana R, Archer AC. Bacteriocin nanoconjugates: boon to medical and food industry. J Appl Microbiol 2021; 131:1056-1071. [PMID: 33368869 DOI: 10.1111/jam.14982] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022]
Abstract
Resistance to antibiotics is an ongoing problem in the biomedical industry. Developing active, alternative drug therapies would reduce our reliance on antibiotics that induce resistance in micro-organisms. To date, bacteriocins and antimicrobial peptides have shown a positive outcome as antibiotic substitutes and synergists apart from phage therapy, antibodies and probiotics. Bacteriocins are proteinaceous antimicrobial peptides synthesized by lactic acid bacteria extensively used as bio-preservatives and alternative to traditional antibiotics to overcome the problem of drug-resistant pathogens. Nonetheless, the use of bacteriocins has several limitations such as limited antimicrobial spectrum, requiring high dose, sensitivity to proteolytic enzymes, etc. Nanoparticles are one of the promising area of research explored to improve antimicrobial spectrum of bacteriocins. This review therefore highlights the recent developments and research pertaining to use of nanoparticles and bacteriocin conjugates to tackle the resistance crisis as well as its applications in food industry.
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Affiliation(s)
- R Sulthana
- Division of Microbiology and Tissue Culture, School of Life Sciences, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, Karnataka, India
| | - A C Archer
- Division of Microbiology and Tissue Culture, School of Life Sciences, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, Karnataka, India
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9
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Non-Lytic Antibacterial Peptides That Translocate Through Bacterial Membranes to Act on Intracellular Targets. Int J Mol Sci 2019; 20:ijms20194877. [PMID: 31581426 PMCID: PMC6801614 DOI: 10.3390/ijms20194877] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 11/28/2022] Open
Abstract
The advent of multidrug resistance among pathogenic bacteria has attracted great attention worldwide. As a response to this growing challenge, diverse studies have focused on the development of novel anti-infective therapies, including antimicrobial peptides (AMPs). The biological properties of this class of antimicrobials have been thoroughly investigated, and membranolytic activities are the most reported mechanisms by which AMPs kill bacteria. Nevertheless, an increasing number of works have pointed to a different direction, in which AMPs are seen to be capable of displaying non-lytic modes of action by internalizing bacterial cells. In this context, this review focused on the description of the in vitro and in vivo antibacterial and antibiofilm activities of non-lytic AMPs, including indolicidin, buforin II PR-39, bactenecins, apidaecin, and drosocin, also shedding light on how AMPs interact with and further translocate through bacterial membranes to act on intracellular targets, including DNA, RNA, cell wall and protein synthesis.
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10
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Jin X, Kightlinger W, Hong SH. Optimizing Cell-Free Protein Synthesis for Increased Yield and Activity of Colicins. Methods Protoc 2019; 2:28. [PMID: 36358105 PMCID: PMC6632115 DOI: 10.3390/mps2020028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/19/2022] Open
Abstract
Colicins are antimicrobial proteins produced by Escherichia coli that hold great promise as viable complements or alternatives to antibiotics. Cell-free protein synthesis (CFPS) is a useful production platform for toxic proteins because it eliminates the need to maintain cell viability, a common problem in cell-based production. Previously, we demonstrated that colicins produced by CFPS based on crude Escherichia coli lysates are effective in eradicating antibiotic-tolerant bacteria known as persisters. However, we also found that some colicins have poor solubility or low cell-killing activity. In this study, we improved the solubility of colicin M from 16% to nearly 100% by producing it in chaperone-enriched E. coli extracts, resulting in enhanced cell-killing activity. We also improved the cytotoxicity of colicin E3 by adding or co-expressing the E3 immunity protein during the CFPS reaction, suggesting that the E3 immunity protein enhances colicin E3 activity in addition to protecting the host strain. Finally, we confirmed our previous finding that active colicins can be rapidly synthesized by observing colicin E1 production over time in CFPS. Within three hours of CFPS incubation, colicin E1 reached its maximum production yield and maintained high cytotoxicity during longer incubations up to 20 h. Taken together, our findings indicate that colicin production can be easily optimized for improved solubility and activity using the CFPS platform.
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Affiliation(s)
- Xing Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA;
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA;
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA;
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Smolkin B, Khononov A, Pieńko T, Shavit M, Belakhov V, Trylska J, Baasov T. Towards Catalytic Antibiotics: Redesign of Aminoglycosides To Catalytically Disable Bacterial Ribosomes. Chembiochem 2018; 20:247-259. [DOI: 10.1002/cbic.201800549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/20/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Boris Smolkin
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Alina Khononov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Tomasz Pieńko
- Centre of New Technologies; University of Warsaw; Banacha 2c 02-097 Warsaw Poland
- Department of Drug Chemistry; Faculty of Pharmacy with the Laboratory Medicine Division; Medical University of Warsaw; Banacha 1a 02-097 Warsaw Poland
| | - Michal Shavit
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Valery Belakhov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Joanna Trylska
- Centre of New Technologies; University of Warsaw; Banacha 2c 02-097 Warsaw Poland
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory; Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200003 Israel
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12
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Li Z, Quan G, Jiang X, Yang Y, Ding X, Zhang D, Wang X, Hardwidge PR, Ren W, Zhu G. Effects of Metabolites Derived From Gut Microbiota and Hosts on Pathogens. Front Cell Infect Microbiol 2018; 8:314. [PMID: 30276161 PMCID: PMC6152485 DOI: 10.3389/fcimb.2018.00314] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022] Open
Abstract
Intestinal metabolites participate in various physiological processes, including energy metabolism, cell-to-cell communication, and host immunity. These metabolites mainly originate from gut microbiota and hosts. Although many host metabolites are dominant in intestines, such as free fatty acids, amino acids and vitamins, the metabolites derived from gut microbiota are also essential for intestinal homeostasis. In addition, some metabolites are only generated and released by gut microbiota, such as bacteriocins, short-chain fatty acids, and quorum-sensing autoinducers. In this review, we summarize recent studies regarding the crosstalk between pathogens and metabolites from different sources, including the influence on bacterial development and the activation/inhibition of immune responses of hosts. All of these functions would affect the colonization of and infection by pathogens. This review provides clear ideas and directions for further exploring the regulatory mechanisms and effects of metabolites on pathogens.
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Affiliation(s)
- Zhendong Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
| | - Guomei Quan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
| | - Xinyi Jiang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
| | - Yang Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
| | - Xueyan Ding
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
| | - Dong Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
| | - Xiuqing Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University Manhattan, KS, United States
| | - Wenkai Ren
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University Guangzhou, Guangdong, China
| | - Guoqiang Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Jiangsu Co-innovation Center for Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University, Yangzhou, China
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13
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Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 2018; 86 Suppl 1:27-50. [PMID: 28960539 PMCID: PMC5820184 DOI: 10.1002/prot.25392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 12/27/2022]
Abstract
The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Pedro Bule
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Alessandro T Caputo
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Ana Luisa Carvalho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Cien⁁cias e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Kinlin L Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Krzysztof Fidelis
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Folmer Fredslund
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry/Pharmaceutical Sciences, University of California Irvine, Irvine, California, 92697
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology/Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, 93106
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
| | - Johan C Hill
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Andrzej Joachimiak
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Building A1.5, Saarbrücken, Saarland, D-66123, Germany
| | - Roman I Koning
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, 2333, CC Leiden, The Netherlands
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Karolina Michalska
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
| | - John Moult
- Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850
| | - Shabir Najmudin
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Valentina Nardone
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Didier Ndeh
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Thanh-Hong Nguyen
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Villeurbanne, 69100, France
| | - Sandra Postel
- University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Mark J van Raaij
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Pietro Roversi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK
| | - Amir Shimon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Abhimanyu K Singh
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom
| | - Eric J Sundberg
- Department of Medicine and Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Kaspars Tars
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
- Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Torsten Schwede
- Biozentrum/SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, Basel, 4056, Switzerland
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14
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Invasion speeds in microbial systems with toxin production and quorum sensing. J Theor Biol 2017; 420:290-303. [PMID: 28126526 DOI: 10.1016/j.jtbi.2017.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 11/20/2022]
Abstract
The theory of invasions and invasion speeds has traditionally been studied in macroscopic systems. Surprisingly, microbial invasions have received less attention. Although microbes share many of the features associated with competition between larger-bodied organisms, they also exhibit distinctive behaviors that require new mathematical treatments to fully understand invasions in microbial systems. Most notable is the possibility for long-distance interactions, including competition between populations mediated by diffusible toxins and cooperation among individuals of a single population using quorum sensing. In this paper, we model bacterial invasion using a system of coupled partial differential equations based on Fisher's equation. Our model considers a competitive system with diffusible toxins that, in some cases, are expressed in response to quorum sensing. First, we derive analytical approximations for invasion speeds in the limits of fast and slow toxin diffusion. We then test the validity of our analytical approximations and explore intermediate rates of toxin diffusion using numerical simulations. Interestingly, we find that toxins should diffuse quickly when used offensively, but that there are two optimal strategies when toxins are used as a defense mechanism. Specifically, toxins should diffuse quickly when their killing efficacy is high, but should diffuse slowly when their killing efficacy is low. Our approach permits an explicit investigation of the properties and characteristics of diffusible compounds used in non-local competition, and is relevant for microbial systems and select macroscopic taxa, such as plants and corals, that can interact through biochemicals.
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15
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Crowther CV, Jones LE, Morelli JN, Mastrogiacomo EM, Porterfield C, Kent JL, Serra MJ. Influence of two bulge loops on the stability of RNA duplexes. RNA (NEW YORK, N.Y.) 2017; 23:217-228. [PMID: 27872162 PMCID: PMC5238796 DOI: 10.1261/rna.056168.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 11/13/2016] [Indexed: 05/24/2023]
Abstract
Fifty-three RNA duplexes containing two single nucleotide bulge loops were optically melted in 1 M NaCl in order to determine the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each duplex. Because of the large number of possible combinations and lack of sequence effects observed previously, we limited our initial investigation to adenosine bulges, the most common naturally occurring bulge. For example, the following duplexes were investigated: 5'GGCAXYAGGC/3'CCG YX CCG, 5'GGCAXY GCC/3'CCG YXACGG, and 5'GGC XYAGCC/3'CCGAYX CGG. The identity of XY (where XY are Watson-Crick base pairs) and the total number of base pairs in the terminal and central stems were varied. As observed for duplexes with a single bulge loop, the effect of the two bulge loops on duplex stability is primarily influenced by non-nearest neighbor interactions. In particular, the stability of the stems influences the destabilization of the duplex by the inserted bulge loops. The model proposed to predict the influence of multiple bulge loops on duplex stability suggests that the destabilization of each bulge is related to the stability of the adjacent stems. A database of RNA secondary structures was examined to determine the naturally occurring abundance of duplexes containing multiple bulge loops. Of the 2000 examples found in the database, over 65% of the two bulge loops occur within 3 base pairs of each other. A database of RNA three-dimensional structures was examined to determine the structure of duplexes containing two single nucleotide bulge loops. The structures of the bulge loops are described.
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Affiliation(s)
- Claire V Crowther
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Laura E Jones
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Jessica N Morelli
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | | | - Claire Porterfield
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Jessica L Kent
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Martin J Serra
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
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16
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Pham VH, Maaroufi H, Balg C, Blais SP, Messier N, Roy PH, Otis F, Voyer N, Lapointe J, Chênevert R. Inhibition ofHelicobacter pyloriGlu-tRNAGlnamidotransferase by novel analogues of the putative transamidation intermediate. FEBS Lett 2016; 590:3335-3345. [DOI: 10.1002/1873-3468.12380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Van Hau Pham
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie; Université Laval; Québec Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
| | - Christian Balg
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
| | - Sébastien P. Blais
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie; Université Laval; Québec Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
| | - Nancy Messier
- CHU de Québec; Centre de Recherche en Infectiologie; Université Laval; Québec Canada
| | - Paul H. Roy
- CHU de Québec; Centre de Recherche en Infectiologie; Université Laval; Québec Canada
| | - François Otis
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
| | - Normand Voyer
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
| | - Jacques Lapointe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie; Université Laval; Québec Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
| | - Robert Chênevert
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
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17
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Németh E, Balogh RK, Borsos K, Czene A, Thulstrup PW, Gyurcsik B. Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study. Protein Sci 2016; 25:1977-1988. [PMID: 27508941 DOI: 10.1002/pro.3010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/08/2016] [Indexed: 12/21/2022]
Abstract
X-ray diffractometry dominates protein studies, as it can provide 3D structures of these diverse macromolecules or their molecular complexes with interacting partners: substrates, inhibitors, and/or cofactors. Here, we show that under cocrystallization conditions the results could reflect induced protein folds instead of the (partially) disordered original structures. The analysis of synchrotron radiation circular dichroism spectra revealed that the Im7 immunity protein stabilizes the native-like solution structure of unfolded NColE7 nuclease mutants via complex formation. This is consistent with the fact that among the several available crystal structures with its inhibitor or substrate, all NColE7 structures are virtually the same. Our results draw attention to the possible structural consequence of protein modifications, which is often hidden by compensational effects of intermolecular interactions. The growing evidence on the importance of protein intrinsic disorder thus, demands more extensive complementary experiments in solution phase with the unligated form of the protein of interest.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary.,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Katalin Borsos
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Anikó Czene
- MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary. .,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary.
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18
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Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res 2016; 44:8525-8555. [PMID: 27536007 PMCID: PMC5062991 DOI: 10.1093/nar/gkw722] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 12/16/2022] Open
Abstract
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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19
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Hwang IY, Koh E, Kim HR, Yew WS, Chang MW. Reprogrammable microbial cell-based therapeutics against antibiotic-resistant bacteria. Drug Resist Updat 2016; 27:59-71. [DOI: 10.1016/j.drup.2016.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 01/01/2023]
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20
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Ogawa T. tRNA-targeting ribonucleases: molecular mechanisms and insights into their physiological roles. Biosci Biotechnol Biochem 2016; 80:1037-45. [PMID: 26967967 DOI: 10.1080/09168451.2016.1148579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Most bacteria produce antibacterial proteins known as bacteriocins, which aid bacterial defence systems to provide a physiological advantage. To date, many kinds of bacteriocins have been characterized. Colicin has long been known as a plasmidborne bacteriocin that kills other Escherichia coli cells lacking the same plasmid. To defeat other cells, colicins exert specific activities such as ion-channel, DNase, and RNase activity. Colicin E5 and colicin D impair protein synthesis in sensitive E. coli cells; however, their physiological targets have not long been identified. This review describes our finding that colicins E5 and D are novel RNases targeting specific E. coli tRNAs and elucidates their enzymatic properties based on biochemical analyses and X-ray crystal structures. Moreover, tRNA cleavage mediates bacteriostasis, which depends on trans-translation. Based on these results and others, cell growth regulation depending on tRNA cleavage is also discussed.
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Affiliation(s)
- Tetsuhiro Ogawa
- a Department of Biotechnology , The University of Tokyo , Tokyo , Japan
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21
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Panja SK, Dwivedi N, Saha S. Highly stable naphthalene core based novel cleft-shaped strain molecule: influence of intermolecular H-bonding architectures. RSC Adv 2016. [DOI: 10.1039/c6ra06855c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
High thermal stability of a 8 membered naphthalene core based fused nitrogen bridged 1,5-dioxocin is found to be due to the coexistence of several weak interactions. Catalytic property of this molecule for a condensation reaction is also explored.
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Affiliation(s)
- Sumit Kumar Panja
- Department of Chemistry
- Institute of Science
- Banaras Hindu University
- Varanasi-221005
- India
| | - Nidhi Dwivedi
- Department of Chemistry
- Institute of Science
- Banaras Hindu University
- Varanasi-221005
- India
| | - Satyen Saha
- Department of Chemistry
- Institute of Science
- Banaras Hindu University
- Varanasi-221005
- India
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22
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Cavera VL, Arthur TD, Kashtanov D, Chikindas ML. Bacteriocins and their position in the next wave of conventional antibiotics. Int J Antimicrob Agents 2015; 46:494-501. [PMID: 26341839 DOI: 10.1016/j.ijantimicag.2015.07.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 12/13/2022]
Abstract
Micro-organisms are capable of producing a range of defence mechanisms, including antibiotics, bacteriocins, lytic agents, protein exotoxins, etc. Such mechanisms have been identified in nearly 99% of studied bacteria. The multiplicity and diversity of bacteriocins and the resultant effects of their interactions with targeted bacteria on microbial ecology has been thoroughly studied and remains an area of investigation attracting many researchers. However, the incorporation of bacteriocins into drug delivery systems used in conjunction with, or as potential alternatives to, conventional antibiotics is only a recent, although rapidly expanding, field. The extensive array of bacteriocins positions them as one of the most promising options in the next wave of antibiotics. The goal of this review was to explore bacteriocins as novel antimicrobials, alone and in combination with established antibiotics, and thus position them as a potential tool for addressing the current antibiotic crisis.
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Affiliation(s)
- Veronica L Cavera
- Department of Biochemistry and Microbiology, Rutgers State University, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Timothy D Arthur
- Department of Biochemistry and Microbiology, Rutgers State University, 76 Lipman Drive, New Brunswick, NJ 08901, USA
| | - Dimitri Kashtanov
- School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, New Brunswick, NJ 08901, USA
| | - Michael L Chikindas
- School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, New Brunswick, NJ 08901, USA.
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23
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Abstract
In this issue of Structure, Beck and colleagues describe the structure of the Enterobacter cloacae contact-dependent growth inhibition (CDI) toxin in complex with its immunity protein. Further functional studies reveal that CDI targets translation by cleaving 16S ribosomal RNA.
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24
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Papadakos G, Sharma A, Lancaster LE, Bowen R, Kaminska R, Leech AP, Walker D, Redfield C, Kleanthous C. Consequences of Inducing Intrinsic Disorder in a High-Affinity Protein–Protein Interaction. J Am Chem Soc 2015; 137:5252-5. [DOI: 10.1021/ja512607r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Grigorios Papadakos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Amit Sharma
- Astbury
Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lorna E. Lancaster
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| | - Rebecca Bowen
- Department of Biology, University of York, Heslington Road, York YO10 5DD, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Andrew P. Leech
- Department of Biology, University of York, Heslington Road, York YO10 5DD, United Kingdom
| | - Daniel Walker
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, Glasgow G12 8AT, United Kingdom
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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25
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Zhang D, Iyer LM, Burroughs AM, Aravind L. Resilience of biochemical activity in protein domains in the face of structural divergence. Curr Opin Struct Biol 2014; 26:92-103. [PMID: 24952217 DOI: 10.1016/j.sbi.2014.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/20/2014] [Indexed: 01/07/2023]
Abstract
Recent studies point to the prevalence of the evolutionary phenomenon of drastic structural transformation of protein domains while continuing to preserve their basic biochemical function. These transformations span a wide spectrum, including simple domains incorporated into larger structural scaffolds, changes in the structural core, major active site shifts, topological rewiring and extensive structural transmogrifications. Proteins from biological conflict systems, such as toxin-antitoxin, restriction-modification, CRISPR/Cas, polymorphic toxin and secondary metabolism systems commonly display such transformations. These include endoDNases, metal-independent RNases, deaminases, ADP ribosyltransferases, immunity proteins, kinases and E1-like enzymes. In eukaryotes such transformations are seen in domains involved in chromatin-related peptide recognition and protein/DNA-modification. Intense selective pressures from 'arms-race'-like situations in conflict and macromolecular modification systems could favor drastic structural divergence while preserving function.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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26
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Beck CM, Morse RP, Cunningham DA, Iniguez A, Low DA, Goulding CW, Hayes CS. CdiA from Enterobacter cloacae delivers a toxic ribosomal RNase into target bacteria. Structure 2014; 22:707-18. [PMID: 24657090 DOI: 10.1016/j.str.2014.02.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/11/2014] [Accepted: 02/16/2014] [Indexed: 12/31/2022]
Abstract
Contact-dependent growth inhibition (CDI) is one mechanism of inter-bacterial competition. CDI(+) cells export large CdiA effector proteins, which carry a variety of C-terminal toxin domains (CdiA-CT). CdiA-CT toxins are specifically neutralized by cognate CdiI immunity proteins to protect toxin-producing cells from autoinhibition. Here, we use structure determination to elucidate the activity of a CDI toxin from Enterobacter cloacae (ECL). The structure of CdiA-CT(ECL) resembles the C-terminal nuclease domain of colicin E3, which cleaves 16S ribosomal RNA to disrupt protein synthesis. In accord with this structural homology, we show that CdiA-CT(ECL) uses the same nuclease activity to inhibit bacterial growth. Surprisingly, although colicin E3 and CdiA(ECL) carry equivalent toxin domains, the corresponding immunity proteins are unrelated in sequence, structure, and toxin-binding site. Together, these findings reveal unexpected diversity among 16S rRNases and suggest that these nucleases are robust and versatile payloads for a variety of toxin-delivery platforms.
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Affiliation(s)
- Christina M Beck
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Robert P Morse
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - David A Cunningham
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Angelina Iniguez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - David A Low
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA; Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA; Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA.
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McCaughey LC, Grinter R, Josts I, Roszak AW, Waløen KI, Cogdell RJ, Milner J, Evans T, Kelly S, Tucker NP, Byron O, Smith B, Walker D. Lectin-like bacteriocins from Pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor. PLoS Pathog 2014; 10:e1003898. [PMID: 24516380 PMCID: PMC3916391 DOI: 10.1371/journal.ppat.1003898] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/10/2013] [Indexed: 11/24/2022] Open
Abstract
Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins. Due to rapidly increasing rates of antibiotic resistance observed among Gram-negative pathogens, such as Pseudomonas aeruginosa, there is an urgent requirement for novel approaches to the treatment of bacterial infections. Lectin-like bacteriocins are highly potent protein antibiotics that display an unusual ability to kill a select group of bacteria within a specific genus. In this work, we show how the lectin-like protein antibiotic, pyocin L1, can kill Pseudomonas aeruginosa with extraordinary potency through specific binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide. The CPA is predominantly a homopolymer of the sugar d-rhamnose that although generally rare in nature is found frequently as a component of the lipopolysaccharide of members of the genus Pseudomonas. The targeting of d-rhamnose containing polysaccharides by pyocin L1 and a related lectin-like protein antibiotic, putidacin L1, explains the unusual genus- specific killing activity of the lectin-like bacteriocins. As we learn more about the link between changes to the microbiome and a range of chronic diseases there is a growing realisation that the ability to target specific bacterial pathogens while maintaining the normal gut flora is a desirable property for next generation antibiotics.
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Affiliation(s)
- Laura C. McCaughey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rhys Grinter
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Inokentijs Josts
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Aleksander W. Roszak
- WestCHEM, School of Chemistry, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kai I. Waløen
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joel Milner
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tom Evans
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sharon Kelly
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicholas P. Tucker
- Strathclyde Institute for Pharmaceutical and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Brian Smith
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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Kumar S, Das A. Observation of exclusively π-stacked heterodimer of indole and hexafluorobenzene in the gas phase. J Chem Phys 2013; 139:104311. [DOI: 10.1063/1.4820532] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G. A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun 2013; 4:1355. [PMID: 23322043 PMCID: PMC3552334 DOI: 10.1038/ncomms2346] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/30/2012] [Indexed: 11/09/2022] Open
Abstract
During protein synthesis, the ribosome selects aminoacyl-tRNAs with anticodons matching the mRNA codon present in the A-site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogs (ASLs) and mRNA. Our crystal structures display a significant local distortion of 16S rRNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate ASL complex, while destabilizing the cognate ASL complex. These data reveal how streptomycin disrupts the recognition of cognate ASLs and yet improves recognition of a near-cognate ASL.
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Affiliation(s)
- Hasan Demirci
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct 2013; 8:15. [PMID: 23768067 PMCID: PMC3710099 DOI: 10.1186/1745-6150-8-15] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/09/2013] [Indexed: 12/20/2022] Open
Abstract
Background The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity. Results The HEPN superfamily is comprised of all α-helical domains that were first identified as being associated with DNA polymerase β-type nucleotidyltransferases in prokaryotes and animal Sacsin proteins. Using sensitive sequence and structure comparison methods, we vastly extend the HEPN superfamily by identifying numerous novel families and by detecting diverged HEPN domains in several known protein families. The new HEPN families include the RNase LS and LsoA catalytic domains, KEN domains (e.g. RNaseL and Ire1) and the RNase domains of RloC and PrrC. The majority of HEPN domains contain conserved motifs that constitute a metal-independent endoRNase active site. Some HEPN domains lacking this motif probably function as non-catalytic RNA-binding domains, such as in the case of the mannitol repressor MtlR. Our analysis shows that HEPN domains function as toxins that are shared by numerous systems implicated in intra-genomic, inter-genomic and intra-organismal conflicts across the three domains of cellular life. In prokaryotes HEPN domains are essential components of numerous toxin-antitoxin (TA) and abortive infection (Abi) systems and in addition are tightly associated with many restriction-modification (R-M) and CRISPR-Cas systems, and occasionally with other defense systems such as Pgl and Ter. We present evidence of multiple modes of action of HEPN domains in these systems, which include direct attack on viral RNAs (e.g. LsoA and RNase LS) in conjunction with other RNase domains (e.g. a novel RNase H fold domain, NamA), suicidal or dormancy-inducing attack on self RNAs (RM systems and possibly CRISPR-Cas systems), and suicidal attack coupled with direct interaction with phage components (Abi systems). These findings are compatible with the hypothesis on coupling of pathogen-targeting (immunity) and self-directed (programmed cell death and dormancy induction) responses in the evolution of robust antiviral strategies. We propose that altruistic cell suicide mediated by HEPN domains and other functionally similar RNases was essential for the evolution of kin and group selection and cell cooperation. HEPN domains were repeatedly acquired by eukaryotes and incorporated into several core functions such as endonucleolytic processing of the 5.8S-25S/28S rRNA precursor (Las1), a novel ER membrane-associated RNA degradation system (C6orf70), sensing of unprocessed transcripts at the nuclear periphery (Swt1). Multiple lines of evidence suggest that, similar to prokaryotes, HEPN proteins were recruited to antiviral, antitransposon, apoptotic systems or RNA-level response to unfolded proteins (Sacsin and KEN domains) in several groups of eukaryotes. Conclusions Extensive sequence and structure comparisons reveal unexpectedly broad presence of the HEPN domain in an enormous variety of defense and stress response systems across the tree of life. In addition, HEPN domains have been recruited to perform essential functions, in particular in eukaryotic rRNA processing. These findings are expected to stimulate experiments that could shed light on diverse cellular processes across the three domains of life. Reviewers This article was reviewed by Martijn Huynen, Igor Zhulin and Nick Grishin
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Affiliation(s)
- Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Vankemmelbeke M, O′Shea P, James R, Penfold CN. Interaction of nuclease colicins with membranes: insertion depth correlates with bilayer perturbation. PLoS One 2012; 7:e46656. [PMID: 23029560 PMCID: PMC3460906 DOI: 10.1371/journal.pone.0046656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/05/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Protein transport across cellular membranes is an important aspect of toxin biology. Escherichia coli cell killing by nuclease colicins occurs through DNA (DNases) or RNA (RNases) hydrolysis and to this end their cytotoxic domains require transportation across two sets of membranes. In order to begin to unravel the molecular mechanisms underlying the membrane translocation of colicin nuclease domains, we have analysed the membrane association of four DNase domains (E9, a charge reduction E9 mutant, E8, and E7) and one ribosomal RNase domain (E3) using a biomembrane model system. PRINCIPAL RESULTS We demonstrate, through the use of large unilamellar vesicles composed of synthetic and E. coli lipids and a membrane surface potential sensor, that the colicin nuclease domains bind anionic membranes only, with micromolar affinity and via a cooperative binding mechanism. The evaluation of the nuclease bilayer insertion depth, through a fluorescence quenching analysis using brominated lipids, indicates that the nucleases locate to differential regions in the bilayer. Colicin DNases target the interfacial region of the lipid bilayer, with the DNase E7 showing the deepest insertion, whereas the ribosomal RNase E3 penetrates into the hydrophobic core region of the bilayer. Furthermore, the membrane association of the DNase E7 and the ribosomal RNase E3 induces vesicle aggregation, lipid mixing and content leakage to a much larger extent than that of the other DNases analysed. CONCLUSIONS/SIGNIFICANCE Our results show, for the first time, that after the initial electrostatically driven membrane association, the pleiotropic membrane effects induced by colicin nuclease domains relate to their bilayer insertion depth and may be linked to their in vivo membrane translocation.
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Affiliation(s)
- Mireille Vankemmelbeke
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
- * E-mail:
| | - Paul O′Shea
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Richard James
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Christopher N. Penfold
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
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Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L. Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct 2012; 7:18. [PMID: 22731697 PMCID: PMC3482391 DOI: 10.1186/1745-6150-7-18] [Citation(s) in RCA: 358] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific conflicts. They are characterized by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. Prior analysis revealed a striking diversity of nuclease and deaminase domains among the toxin modules. We systematically investigated polymorphic toxin systems using comparative genomics, sequence and structure analysis. RESULTS Polymorphic toxin systems are distributed across all major bacterial lineages and are delivered by at least eight distinct secretory systems. In addition to type-II, these include type-V, VI, VII (ESX), and the poorly characterized "Photorhabdus virulence cassettes (PVC)", PrsW-dependent and MuF phage-capsid-like systems. We present evidence that trafficking of these toxins is often accompanied by autoproteolytic processing catalyzed by HINT, ZU5, PrsW, caspase-like, papain-like, and a novel metallopeptidase associated with the PVC system. We identified over 150 distinct toxin domains in these systems. These span an extraordinary catalytic spectrum to include 23 distinct clades of peptidases, numerous previously unrecognized versions of nucleases and deaminases, ADP-ribosyltransferases, ADP ribosyl cyclases, RelA/SpoT-like nucleotidyltransferases, glycosyltranferases and other enzymes predicted to modify lipids and carbohydrates, and a pore-forming toxin domain. Several of these toxin domains are shared with host-directed effectors of pathogenic bacteria. Over 90 families of immunity proteins might neutralize anywhere between a single to at least 27 distinct types of toxin domains. In some organisms multiple tandem immunity genes or immunity protein domains are organized into polyimmunity loci or polyimmunity proteins. Gene-neighborhood-analysis of polymorphic toxin systems predicts the presence of novel trafficking-related components, and also the organizational logic that allows toxin diversification through recombination. Domain architecture and protein-length analysis revealed that these toxins might be deployed as secreted factors, through directed injection, or via inter-cellular contact facilitated by filamentous structures formed by RHS/YD, filamentous hemagglutinin and other repeats. Phyletic pattern and life-style analysis indicate that polymorphic toxins and polyimmunity loci participate in cooperative behavior and facultative 'cheating' in several ecosystems such as the human oral cavity and soil. Multiple domains from these systems have also been repeatedly transferred to eukaryotes and their viruses, such as the nucleo-cytoplasmic large DNA viruses. CONCLUSIONS Along with a comprehensive inventory of toxins and immunity proteins, we present several testable predictions regarding active sites and catalytic mechanisms of toxins, their processing and trafficking and their role in intra-specific and inter-specific interactions between bacteria. These systems provide insights regarding the emergence of key systems at different points in eukaryotic evolution, such as ADP ribosylation, interaction of myosin VI with cargo proteins, mediation of apoptosis, hyphal heteroincompatibility, hedgehog signaling, arthropod toxins, cell-cell interaction molecules like teneurins and different signaling messengers.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Abstract
It is more than 80 years since Gratia first described 'a remarkable antagonism between two strains of Escherichia coli'. Shown subsequently to be due to the action of proteins (or peptides) produced by one bacterium to kill closely related species with which it might be cohabiting, such bacteriocins have since been shown to be commonplace in the internecine warfare between bacteria. Bacteriocins have been studied primarily from the twin perspectives of how they shape microbial communities and how they penetrate bacteria to kill them. Here, we review the modes of action of a family of bacteriocins that cleave nucleic acid substrates in E. coli, known collectively as nuclease colicins, and the specific immunity (inhibitor) proteins that colicin-producing organisms make in order to avoid committing suicide. In a process akin to targeting in mitochondria, nuclease colicins engage in a variety of cellular associations in order to translocate their cytotoxic domains through the cell envelope to the cytoplasm. As well as informing on the process itself, the study of nuclease colicin import has also illuminated functional aspects of the host proteins they parasitize. We also review recent studies where nuclease colicins and their immunity proteins have been used as model systems for addressing fundamental problems in protein folding and protein-protein interactions, areas of biophysics that are intimately linked to the role of colicins in bacterial competition and to the import process itself.
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1167] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF. Proc Natl Acad Sci U S A 2010; 107:21412-7. [PMID: 21098297 DOI: 10.1073/pnas.1010780107] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The porins OmpF and OmpC are trimeric β-barrel proteins with narrow channels running through each monomer that exclude molecules > 600 Da while mediating the passive diffusion of small nutrients and metabolites across the Gram-negative outer membrane (OM). Here, we elucidate the mechanism by which an entire soluble protein domain (> 6 kDa) is delivered through the lumen of such porins. Following high-affinity binding to the vitamin B(12) receptor in Escherichia coli, the bacteriocin ColE9 recruits OmpF or OmpC using an 83-residue intrinsically unstructured translocation domain (IUTD) to deliver a 16-residue TolB-binding epitope (TBE) in the center of the IUTD to the periplasm where it triggers toxin entry. We demonstrate that the IUTD houses two OmpF-binding sites, OBS1 (residues 2-18) and OBS2 (residues 54-63), which flank the TBE and bind with K(d)s of 2 and 24 μM, respectively, at pH 6.5 and 25 ºC. We show the two OBSs share the same binding site on OmpF and that the colicin must house at least one of them for antibiotic activity. Finally, we report the structure of the OmpF-OBS1 complex that shows the colicin bound within the porin lumen spanning the membrane bilayer. Our study explains how colicins exploit porins to deliver epitope signals to the bacterial periplasm and, more broadly, how the inherent flexibility and narrow cross-sectional area of an IUP domain can endow it with the ability to traverse a biological membrane via the constricted lumen of a β-barrel membrane protein.
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