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Liu J, He C, Tan W, Zheng JH. Path to bacteriotherapy: From bacterial engineering to therapeutic perspectives. Life Sci 2024; 352:122897. [PMID: 38971366 DOI: 10.1016/j.lfs.2024.122897] [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: 01/11/2024] [Revised: 06/30/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
The major reason for the failure of conventional therapies is the heterogeneity and complexity of tumor microenvironments (TMEs). Many malignant tumors reprogram their surface antigens to evade the immune surveillance, leading to reduced antigen-presenting cells and hindered T-cell activation. Bacteria-mediated cancer immunotherapy has been extensively investigated in recent years. Scientists have ingeniously modified bacteria using synthetic biology and nanotechnology to enhance their biosafety with high tumor specificity, resulting in robust anticancer immune responses. To enhance the antitumor efficacy, therapeutic proteins, cytokines, nanoparticles, and chemotherapeutic drugs have been efficiently delivered using engineered bacteria. This review provides a comprehensive understanding of oncolytic bacterial therapies, covering bacterial design and the intricate interactions within TMEs. Additionally, it offers an in-depth comparison of the current techniques used for bacterial modification, both internally and externally, to maximize their therapeutic effectiveness. Finally, we outlined the challenges and opportunities ahead in the clinical application of oncolytic bacterial therapies.
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Affiliation(s)
- Jinling Liu
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China; College of Biology, Hunan University, Changsha 410082, China
| | - Chongsheng He
- College of Biology, Hunan University, Changsha 410082, China
| | - Wenzhi Tan
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, Hunan 410114, China.
| | - Jin Hai Zheng
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China.
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2
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A fluorescence-based genetic screen reveals diverse mechanisms silencing small RNA signaling in E. coli. Proc Natl Acad Sci U S A 2021; 118:2106964118. [PMID: 34210798 DOI: 10.1073/pnas.2106964118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As key players of gene regulation in many bacteria, small regulatory RNAs (sRNAs) associated with the RNA chaperone Hfq shape numerous phenotypic traits, including metabolism, stress response and adaptation, as well as virulence. sRNAs can alter target messenger RNA (mRNA) translation and stability via base pairing. sRNA synthesis is generally under tight transcriptional regulation, but other levels of regulation of sRNA signaling are less well understood. Here we used a fluorescence-based functional screen to identify regulators that can quench sRNA signaling of the iron-responsive sRNA RyhB in Escherichia coli The identified regulators fell into two classes, general regulators (affecting signaling by many sRNAs) and RyhB-specific regulators; we focused on the specific ones here. General regulators include three Hfq-interacting sRNAs, CyaR, ChiX, and McaS, previously found to act through Hfq competition, RNase T, a 3' to 5' exonuclease not previously implicated in sRNA degradation, and YhbS, a putative GCN5-related N-acetyltransferase (GNAT). Two specific regulators were identified. AspX, a 3'end-derived small RNA, specifically represses RyhB signaling via an RNA sponging mechanism. YicC, a previously uncharacterized but widely conserved protein, triggers rapid RyhB degradation via collaboration with the exoribonuclease PNPase. These findings greatly expand our knowledge of regulation of bacterial sRNA signaling and suggest complex regulatory networks for controlling iron homeostasis in bacteria. The fluorescence-based genetic screen system described here is a powerful tool expected to accelerate the discovery of novel regulators of sRNA signaling in many bacteria.
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Crozier L, Marshall J, Holmes A, Wright KM, Rossez Y, Merget B, Humphris S, Toth I, Jackson RW, Holden NJ. The role of l-arabinose metabolism for Escherichia coli O157:H7 in edible plants. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001070. [PMID: 34319868 PMCID: PMC8489885 DOI: 10.1099/mic.0.001070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022]
Abstract
Arabinose is a major plant aldopentose in the form of arabinans complexed in cell wall polysaccharides or glycoproteins (AGP), but comparatively rare as a monosaccharide. l-arabinose is an important bacterial metabolite, accessed by pectolytic micro-organisms such as Pectobacterium atrosepticum via pectin and hemicellulose degrading enzymes. However, not all plant-associated microbes encode cell-wall-degrading enzymes, yet can metabolize l-arabinose, raising questions about their use of and access to the glycan in plants. Therefore, we examined l-arabinose metabolism in the food-borne pathogen Escherichia coli O157:H7 (isolate Sakai) during its colonization of plants. l-arabinose metabolism (araBA) and transport (araF) genes were activated at 18 °C in vitro by l-arabinose and expressed over prolonged periods in planta. Although deletion of araBAD did not impact the colonization ability of E. coli O157:H7 (Sakai) on spinach and lettuce plants (both associated with STEC outbreaks), araA was induced on exposure to spinach cell-wall polysaccharides. Furthermore, debranched and arabinan oligosaccharides induced ara metabolism gene expression in vitro, and stimulated modest proliferation, while immobilized pectin did not. Thus, E. coli O157:H7 (Sakai) can utilize pectin/AGP-derived l-arabinose as a metabolite. Furthermore, it differs fundamentally in ara gene organization, transport and regulation from the related pectinolytic species P. atrosepticum, reflective of distinct plant-associated lifestyles.
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Affiliation(s)
- Louise Crozier
- The James Hutton Institute, Cell & Molecular Sciences, Dundee, DD2 5DA, UK
| | | | - Ashleigh Holmes
- The James Hutton Institute, Cell & Molecular Sciences, Dundee, DD2 5DA, UK
| | | | - Yannick Rossez
- The James Hutton Institute, Cell & Molecular Sciences, Dundee, DD2 5DA, UK
- Université de Technologie de Compiègne, CNRS-FRE 3580, Centre de Recherche de Royallieu, 60203 COMPIEGNE CEDEX, France
| | - Bernhard Merget
- The James Hutton Institute, Cell & Molecular Sciences, Dundee, DD2 5DA, UK
| | - Sonia Humphris
- The James Hutton Institute, Cell & Molecular Sciences, Dundee, DD2 5DA, UK
| | - Ian Toth
- The James Hutton Institute, Cell & Molecular Sciences, Dundee, DD2 5DA, UK
| | - Robert Wilson Jackson
- School of Biological Sciences, The University of Reading, Reading, UK
- Birmingham Institute of Forest Research and School of Biosciences University of Birmingham, Birmingham B15 2TT, UK
| | - Nicola Jean Holden
- The James Hutton Institute, Cell & Molecular Sciences, Dundee, DD2 5DA, UK
- SRUC, Department of Rural Land Use, Aberdeen, AB21 9YA, UK
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Raden M, Gutmann F, Uhl M, Backofen R. CopomuS-Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments. Int J Mol Sci 2020; 21:ijms21113852. [PMID: 32481751 PMCID: PMC7311995 DOI: 10.3390/ijms21113852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/18/2020] [Accepted: 05/25/2020] [Indexed: 11/16/2022] Open
Abstract
In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application.
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Affiliation(s)
- Martin Raden
- Bioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany; (F.G.); (M.U.); (R.B.)
- Correspondence:
| | - Fabio Gutmann
- Bioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany; (F.G.); (M.U.); (R.B.)
| | - Michael Uhl
- Bioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany; (F.G.); (M.U.); (R.B.)
| | - Rolf Backofen
- Bioinformatics, Department of Computer Science, University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany; (F.G.); (M.U.); (R.B.)
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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Mann M, Wright PR, Backofen R. IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. Nucleic Acids Res 2019; 45:W435-W439. [PMID: 28472523 PMCID: PMC5570192 DOI: 10.1093/nar/gkx279] [Citation(s) in RCA: 370] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/02/2017] [Indexed: 01/01/2023] Open
Abstract
The IntaRNA algorithm enables fast and accurate prediction of RNA-RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA-RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage.
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Affiliation(s)
- Martin Mann
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Patrick R Wright
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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Durica-Mitic S, Göpel Y, Görke B. Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs. Microbiol Spectr 2018; 6. [PMID: 29573258 DOI: 10.1128/microbiolspec.rwr-0013-2017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 12/11/2022] Open
Abstract
Survival of bacteria in ever-changing habitats with fluctuating nutrient supplies requires rapid adaptation of their metabolic capabilities. To this end, carbohydrate metabolism is governed by complex regulatory networks including posttranscriptional mechanisms that involve small regulatory RNAs (sRNAs) and RNA-binding proteins. sRNAs limit the response to substrate availability and set the threshold or time required for induction and repression of carbohydrate utilization systems. Carbon catabolite repression (CCR) also involves sRNAs. In Enterobacteriaceae, sRNA Spot 42 cooperates with the transcriptional regulator cyclic AMP (cAMP)-receptor protein (CRP) to repress secondary carbohydrate utilization genes when a preferred sugar is consumed. In pseudomonads, CCR operates entirely at the posttranscriptional level, involving RNA-binding protein Hfq and decoy sRNA CrcZ. Moreover, sRNAs coordinate fluxes through central carbohydrate metabolic pathways with carbohydrate availability. In Gram-negative bacteria, the interplay between RNA-binding protein CsrA and its cognate sRNAs regulates glycolysis and gluconeogenesis in response to signals derived from metabolism. Spot 42 and cAMP-CRP jointly downregulate tricarboxylic acid cycle activity when glycolytic carbon sources are ample. In addition, bacteria use sRNAs to reprogram carbohydrate metabolism in response to anaerobiosis and iron limitation. Finally, sRNAs also provide homeostasis of essential anabolic pathways, as exemplified by the hexosamine pathway providing cell envelope precursors. In this review, we discuss the manifold roles of bacterial sRNAs in regulation of carbon source uptake and utilization, substrate prioritization, and metabolism.
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Affiliation(s)
- Svetlana Durica-Mitic
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
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Chen J, Gottesman S. Hfq links translation repression to stress-induced mutagenesis in E. coli. Genes Dev 2017; 31:1382-1395. [PMID: 28794186 PMCID: PMC5580658 DOI: 10.1101/gad.302547.117] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Here, Chen et al. show an example of Hfq repressing translation in the absence of sRNAs via major remodeling of the mRNA. They demonstrate that, by interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis. Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA–RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis. Here we report that Hfq deploys dual mechanisms to control mutS expression. First, Hfq binds directly to an (AAN)3 motif within the mutS 5′ untranslated region (UTR), repressing translation in the absence of sRNA partners both in vivo and in vitro. Second, Hfq acts in a canonical pathway, promoting base-pairing of ArcZ sRNA with the mutS leader to inhibit translation. Most importantly, using pathway-specific mutS chromosomal alleles that specifically abrogate either regulatory pathway or both, we demonstrate that tight control of MutS levels in stationary phase contributes to stress-induced mutagenesis. By interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis.
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Affiliation(s)
- Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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