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Ormsby MJ, Woodford L, White HL, Fellows R, Quilliam RS. The plastisphere can protect Salmonella Typhimurium from UV stress under simulated environmental conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124464. [PMID: 38964649 DOI: 10.1016/j.envpol.2024.124464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
Plastic waste is found with increasing frequency in the environment, in low- and middle-income countries. Plastic pollution has increased concurrently with both economic development and rapid urbanisation, amplifying the effects of inadequate waste management. Distinct microbial communities can quickly colonise plastic surfaces in what is collectively known as the 'plastisphere'. The plastisphere can act as a reservoir for human pathogenic bacteria, including Salmonella enterica sp. (such as S. Typhimurium), which can persist for long periods, retain pathogenicity, and pose an increased public health risk. Through employing a novel mesocosm setup, we have shown here that the plastisphere provides enhanced protection against environmental pressures such as ultraviolet (UV) radiation and allows S. Typhimurium to persist at concentrations (>1 × 103 CFU/ml) capable of causing human infection, for up to 28 days. Additionally, using a Galleria Mellonella model of infection, S. Typhimurium exhibits greater pathogenicity following recovery from the UV-exposed plastisphere, suggesting that the plastisphere may select for more virulent variants. This study demonstrates the protection afforded by the plastisphere and provides further evidence of environmental plastic waste acting as a reservoir for dangerous clinical pathogens. Quantifying the role of plastic pollution in facilitating the survival, persistence, and dissemination of human pathogens is critical for a more holistic understanding of the potential public health risks associated with plastic waste.
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Affiliation(s)
- Michael J Ormsby
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - Luke Woodford
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Hannah L White
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Rosie Fellows
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
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2
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Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems 2024; 9:e0030524. [PMID: 38829048 PMCID: PMC11264592 DOI: 10.1128/msystems.00305-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Fast growth phenotypes are achieved through optimal transcriptomic allocation, in which cells must balance tradeoffs in resource allocation between diverse functions. One such balance between stress readiness and unbridled growth in E. coli has been termed the fear versus greed (f/g) tradeoff. Two specific RNA polymerase (RNAP) mutations observed in adaptation to fast growth have been previously shown to affect the f/g tradeoff, suggesting that genetic adaptations may be primed to control f/g resource allocation. Here, we conduct a greatly expanded study of the genetic control of the f/g tradeoff across diverse conditions. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and obtained expression profiles of each. We found that these single RNAP mutation strains resulted in large shifts in the f/g tradeoff primarily in the RpoS regulon and ribosomal genes, likely through modifying RNAP-DNA interactions. Two of these mutations additionally caused condition-specific transcriptional adaptations. While this tradeoff was previously characterized by the RpoS regulon and ribosomal expression, we find that the GAD regulon plays an important role in stress readiness and ppGpp in translation activity, expanding the scope of the tradeoff. A phylogenetic analysis found the greed-related genes of the tradeoff present in numerous bacterial species. The results suggest that the f/g tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.IMPORTANCETo increase growth, E. coli must raise ribosomal content at the expense of non-growth functions. Previous studies have linked RNAP mutations to this transcriptional shift and increased growth but were focused on only two mutations found in the protein's central region. RNAP mutations, however, commonly occur over a large structural range. To explore RNAP mutations' impact, we have introduced 12 RNAP mutations found in laboratory evolution experiments and obtained expression profiles of each. The mutations nearly universally increased growth rates by adjusting said tradeoff away from non-growth functions. In addition to this shift, a few caused condition-specific adaptations. We explored the prevalence of this tradeoff across phylogeny and found it to be a widespread and conserved trend among bacteria.
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Affiliation(s)
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Ying Hefner
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Arjun Patel
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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3
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Jiang H, Milanov M, Jüngert G, Angebauer L, Flender C, Smudde E, Gather F, Vogel T, Jessen HJ, Koch HG. Control of a chemical chaperone by a universally conserved ATPase. iScience 2024; 27:110215. [PMID: 38993675 PMCID: PMC11237923 DOI: 10.1016/j.isci.2024.110215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The universally conserved YchF/Ola1 ATPases regulate stress response pathways in prokaryotes and eukaryotes. Deletion of YchF/Ola1 leads to increased resistance against environmental stressors, such as reactive oxygen species, while their upregulation is associated with tumorigenesis in humans. The current study shows that in E. coli, the absence of YchF stimulates the synthesis of the alternative sigma factor RpoS by a transcription-independent mechanism. Elevated levels of RpoS then enhance the transcription of major stress-responsive genes. In addition, the deletion of ychF increases the levels of polyphosphate kinase, which in turn boosts the production of the evolutionary conserved and ancient chemical chaperone polyphosphate. This potentially provides a unifying concept for the increased stress resistance in bacteria and eukaryotes upon YchF/Ola1 deletion. Intriguingly, the simultaneous deletion of ychF and the polyphosphate-degrading enzyme exopolyphosphatase causes synthetic lethality in E. coli, demonstrating that polyphosphate production needs to be fine-tuned to prevent toxicity.
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Affiliation(s)
- Hong Jiang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriela Jüngert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Clara Flender
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Eva Smudde
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Fabian Gather
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute for Organic Chemistry, Faculty of Chemistry and Pharmacy, University Freiburg 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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4
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Braga RE, Najar FZ, Murphy CL, Patrauchan MA. Carbonic anhydrases in bacterial pathogens. Enzymes 2024; 55:313-342. [PMID: 39222996 DOI: 10.1016/bs.enz.2024.05.007] [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] [Indexed: 09/04/2024]
Abstract
Carbonic anhydrases (CAs) catalyze the reversable hydration of carbon dioxide to bicarbonate placing them into the core of the biochemical carbon cycle. Due to the fundamental importance of their function, they evolved independently into eight classes, three of which have been recently discovered. Most research on CAs has focused on their representatives in eukaryotic organisms, while prokaryotic CAs received significantly less attention. Nevertheless, prokaryotic CAs play a key role in the fundamental ability of the biosphere to acquire CO2 for photosynthesis and to decompose the organic matter back to CO2. They also contribute to a broad spectrum of processes in pathogenic bacteria, enhancing their ability to survive in a host and, therefore, present a promising target for developing antimicrobials. This review focuses on the distribution of CAs among bacterial pathogens and their importance in bacterial virulence and host-pathogen interactions.
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Affiliation(s)
- Reygan E Braga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Fares Z Najar
- Bioinformatics Core, Oklahoma State University, Stillwater, OK, United States
| | - Chelsea L Murphy
- Bioinformatics Core, Oklahoma State University, Stillwater, OK, United States
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States.
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Cao J, Xue B, Yang S, Yang X, Zhang X, Qiu Z, Shen Z, Wang J. Chlorite and bromate alter the conjugative transfer of antibiotic resistance genes: Co-regulation of oxidative stress and energy supply. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134257. [PMID: 38636236 DOI: 10.1016/j.jhazmat.2024.134257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
The widespread use of disinfectants during the global response to the 2019 coronavirus pandemic has increased the co-occurrence of disinfection byproducts (DBPs) and antibiotic resistance genes (ARGs). Although DBPs pose major threats to public health globally, there is limited knowledge regarding their biological effects on ARGs. This study aimed to investigate the effects of two inorganic DBPs (chlorite and bromate) on the conjugative transfer of RP4 plasmid among Escherichia coli strains at environmentally relevant concentrations. Interestingly, the frequency of conjugative transfer was initially inhibited when the exposure time to chlorite or bromate was less than 24 h. However, this inhibition transformed into promotion when the exposure time was extended to 36 h. Short exposures to chlorite or bromate were shown to impede the electron transport chain, resulting in an ATP shortage and subsequently inhibiting conjugative transfer. Consequently, this stimulates the overproduction of reactive oxygen species (ROS) and activation of the SOS response. Upon prolonged exposure, the resurgent energy supply promoted conjugative transfer. These findings offer novel and valuable insights into the effects of environmentally relevant concentrations of inorganic DBPs on the conjugative transfer of ARGs, thereby providing a theoretical basis for the management of DBPs.
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Affiliation(s)
- Jinrui Cao
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Bin Xue
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin 300050, China
| | - Shuran Yang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Xiaobo Yang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin 300050, China
| | - Xi Zhang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin 300050, China
| | - Zhigang Qiu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin 300050, China
| | - Zhiqiang Shen
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin 300050, China.
| | - Jingfeng Wang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin 300050, China.
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6
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Han X, Fu L, Yu J, Li K, Deng Z, Shu R, Wang D, You J, Zeng EY. Effects of erythromycin on biofilm formation and resistance mutation of Escherichia coli on pristine and UV-aged polystyrene microplastics. WATER RESEARCH 2024; 256:121628. [PMID: 38677035 DOI: 10.1016/j.watres.2024.121628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/23/2024] [Accepted: 04/16/2024] [Indexed: 04/29/2024]
Abstract
Microplastics (MPs) and antibiotics co-occur widely in the environment and pose combined risk to microbial communities. The present study investigated the effects of erythromycin on biofilm formation and resistance mutation of a model bacterium, E. coli, on the surface of pristine and UV-aged polystyrene (PS) MPs sized 1-2 mm. The properties of UV-aged PS were significantly altered compared to pristine PS, with notable increases in specific surface area, carbonyl index, hydrophilicity, and hydroxyl radical content. Importantly, the adsorption capacity of UV-aged PS towards erythromycin was approximately 8-fold higher than that of pristine PS. Biofilms colonizing on UV-aged PS had a greater cell count (5.6 × 108 CFU mg-1) and a higher frequency of resistance mutation (1.0 × 10-7) than those on pristine PS (1.4 × 108 CFU mg-1 and 1.4 × 10-8, respectively). Moreover, erythromycin at 0.1 and 1.0 mg L-1 significantly (p < 0.05) promoted the formation and resistance mutation of biofilm on both pristine and UV-aged PS. DNA sequencing results confirmed that the biofilm resistance was attributed to point mutations in rpoB segment of the bacterial genome. qPCR results demonstrated that both UV aging and erythromycin repressed the expression levels of a global regulator rpoS in biofilm bacteria, as well as two DNA mismatch repair genes mutS and uvrD, which was likely to contribute to increased resistance mutation frequency.
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Affiliation(s)
- Xiaofeng Han
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Center for Environmental Microplastics Studies, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 511443, China
| | - Long Fu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Center for Environmental Microplastics Studies, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 511443, China
| | - Jing Yu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Center for Environmental Microplastics Studies, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 511443, China
| | - Kunting Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Center for Environmental Microplastics Studies, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 511443, China
| | | | | | - Dali Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Center for Environmental Microplastics Studies, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 511443, China.
| | - Jing You
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Center for Environmental Microplastics Studies, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 511443, China
| | - Eddy Y Zeng
- Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
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7
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Banerjee J, Batabyal S, Biswas S, Bhattacharyya D, Habib M, Das AK, Nanda PK, Samanta I, Dandapat P, Bandyopadhyay S. Stray Dogs (Mongrels) Are Potent Reservoir of Drug-Resistant Pathogens: A Study in Peri-Urban Areas of Kolkata, India. Microb Drug Resist 2024; 30:215-230. [PMID: 38656133 DOI: 10.1089/mdr.2023.0249] [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] [Indexed: 04/26/2024] Open
Abstract
This study depicts the drug-resistance and phylogenomic characteristics of 365 Escherichia coli (EC) and 76 Klebsiella pneumoniae (KP) isolated from stray dogs (293) in and around Kolkata, India. Initial screening found 59 isolates, including 48 E. coli and 11 KP multidrug resistant, which included 33 extended-spectrum β-lactamase, 41 AmpC β-lactamase and 18 metallo-β-lactamase producers carrying blaNDM-1 (11) and blaNDM-5 (7) genes. Majority of them had the resistant genes such as blaCTX-M (33), blaTEM (18), blaSHV (4), blaOXA (17), blaFOX (2), blaDHA (2), blaCITM (15), blaCMY-2 (13), blaGES (2) and blaVEB (2), qnrS (15), qnrB (3), aac-6'-Ib-cr (14), tetA (26), tetB (14), sul-1 (25), armA (2) and rmtB (6), in addition to adherence genes such as csgA (33), fimA (27), fliC (13), sdiA (33), rcsA (38), and rpoS (39). They also carried plasmid of diverse replicon types of which IncFIA and FIB were the most frequent. Phylogrouping categorized most of the MDR E. coli in phylogroup A (20), B1 (14), and B2 (6). Enterobacteriaceae repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) showed genetic diversity of multidrug resistant isolates irrespective of their origin, resistance, and virulence types, differentiating the EC in five clades (A-E) and KP in four clades (A-D). As these stray dogs, which had no history or scope of previous antimicrobial therapy, were found to have contracted potential antimicrobial resistance pathogens, the role of environment in spread of such pathogens and further possibility of human infections cannot be ruled out.
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Affiliation(s)
- Jaydeep Banerjee
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Subhasis Batabyal
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Suman Biswas
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | | | - Md Habib
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Arun K Das
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Pramod K Nanda
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Indranil Samanta
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Premanshu Dandapat
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
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8
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Zhu M, Dai X. Shaping of microbial phenotypes by trade-offs. Nat Commun 2024; 15:4238. [PMID: 38762599 PMCID: PMC11102524 DOI: 10.1038/s41467-024-48591-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024] Open
Abstract
Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.
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Affiliation(s)
- Manlu Zhu
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Xiongfeng Dai
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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9
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Wölflingseder M, Fengler VH, Standhartinger V, Wagner GE, Reidl J. The regulatory network comprising ArcAB-RpoS-RssB influences motility in Vibrio cholerae. Mol Microbiol 2024; 121:850-864. [PMID: 38323722 DOI: 10.1111/mmi.15235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 02/08/2024]
Abstract
The diarrheal disease cholera is caused by the versatile and responsive bacterium Vibrio cholerae, which is capable of adapting to environmental changes. Among others, the alternative sigma factor RpoS activates response pathways, including regulation of motility- and chemotaxis-related genes under nutrient-poor conditions in V. cholerae. Although RpoS has been well characterised, links between RpoS and other regulatory networks remain unclear. In this study, we identified the ArcAB two-component system to control rpoS transcription and RpoS protein stability in V. cholerae. In a manner similar to that seen in Escherichia coli, the ArcB kinase not only activates the response regulator ArcA but also RssB, the anti-sigma factor of RpoS. Our results demonstrated that, in V. cholerae, RssB is phosphorylated by ArcB, which subsequently activates RpoS proteolysis. Furthermore, ArcA acts as a repressor of rpoS transcription. Additionally, we determined that the cysteine residue at position 180 of ArcB is crucial for signal recognition and activity. Thus, our findings provide evidence linking RpoS response to the anoxic redox control system ArcAB in V. cholerae.
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Affiliation(s)
- Martina Wölflingseder
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Vera H Fengler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Verena Standhartinger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Gabriel E Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Joachim Reidl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
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10
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Jiang Z, Qin L, Chen A, Tang X, Gao W, Gao X, Jiang Q, Zhang X. rpoS involved in immune response of Macrobrachium nipponens to Vibrio mimicus infection. FISH & SHELLFISH IMMUNOLOGY 2024; 147:109440. [PMID: 38342414 DOI: 10.1016/j.fsi.2024.109440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Vibrio mimicus is a pathogenic bacterium that cause red body disease in Macrobrachium nipponense, leading to high mortality and financial loss. Based on previous studies, rpoS gene contribute to bacterial pathogenicity during infection, but the role of RpoS involved in the immune response of M. nipponense under V. mimicus infection remains unclear. In this study, the pathogen load and the RNA-seq of M. nipponense under wild-type and ΔrpoS strain V. mimicus infection were investigated. Over the entire infection period, the ΔrpoS strain pathogen load was always lower than that of the wild-type strain in the M. nipponense hemolymph, hepatopancreas, gill and muscle. Furthermore, the expression level of rpoS gene in the hepatopancreas was the highest at 24 hours post infection (hpi), then the samples of hepatopancreas tissue infected with the wild type and ΔrpoS strain at 24 hpi were selected for RNA-seq sequencing. The results revealed a significant change in the transcriptomes of the hepatopancreases infected with ΔrpoS strain. In contrast to the wild-type infected group, the ΔrpoS strain infected group exhibited differentially expressed genes (DEGs) enriched in 181 KEGG pathways at 24 hpi. Among these pathways, 8 immune system-related pathways were enriched, including ECM-receptor interaction, PI3K-Akt signaling pathway, Rap1 signaling pathway, Gap junction, and Focal adhesion, etc. Among these pathways, up-regulated genes related to Kazal-type serine protease inhibitors, S-antigen protein, copper zinc superoxide dismutase, tight junction protein, etc. were enriched. This study elucidates that rpoS can affect tissue bacterial load and immune-related pathways, thereby impacting the survival rate of M. nipponense under V. mimicus infection. These findings validate the potential of rpoS as a promising target for the development of a live attenuated vaccine against V. mimicus.
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Affiliation(s)
- Ziyan Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Lijie Qin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Anting Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xinzhe Tang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Weifeng Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaojian Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qun Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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11
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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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12
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Lefèvre-Morand RYL, Nikel PI, Acevedo-Rocha CG. How many Mutations are needed to Evolve the Chemical Makeup of a Synthetic Cell? Chembiochem 2024; 25:e202300829. [PMID: 38226957 DOI: 10.1002/cbic.202300829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
The chemical evolution of a synthetic cell endowed with a synthetic amino acid as building block, analog to tryptophan, required the emergence of key mutations in genes involved in, inter alia, the general stress response, amino acid metabolism, stringent response, and chemotaxis. Understanding adaptation mechanisms to non-canonical biomass components will inform strategies for engineering synthetic metabolic pathways and cells.
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Affiliation(s)
- Rodrigue Yves Louis Lefèvre-Morand
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kongens Lyngby, Denmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kongens Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kongens Lyngby, Denmark
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13
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Valencia EY, de Moraes Gomes F, Ospino K, Spira B. RpoS role in antibiotic resistance, tolerance and persistence in E. coli natural isolates. BMC Microbiol 2024; 24:72. [PMID: 38443813 PMCID: PMC11323705 DOI: 10.1186/s12866-024-03222-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND The intrinsic concentration of RpoS, the second most abundant sigma factor, varies widely across the E. coli species. Bacterial isolates that express high levels of RpoS display high resistance to environmental stresses, such as temperature, pH and osmolarity shifts, but are less nutritional competent, making them less capable of utilising alternative nutrient sources. The role of RpoS in antibiotic resistance and persistence in standard laboratory domesticated strains has been examined in several studies, most demonstrating a positive role for RpoS. RESULTS Using disk diffusion assays we examined bacterial resistance to 15 different antibiotics, including β -lactams (penicillins, monobactams, carbapenems and cephalosporins), aminoglycosides, quinolones and anti-folates, in a representative collection of 328 E. coli natural isolates displaying a continuum of different levels of RpoS. There was an overall trend that isolates with higher levels of RpoS were slightly more resistant to these antibiotics. In addition, the effect of RpoS on bacterial tolerance and persistence to 3 different antibiotics - ampicillin, ciprofloxacin and kanamycin was evaluated through time-kill curves. Again, there was a small beneficial effect of RpoS on tolerance and persistence to these antibiotics, but this difference was not statistically significant. Finally, a K-12 strain expressing high levels of RpoS was compared with its isogenic RpoS-null counterpart, and no significant effect of RpoS was found. CONCLUSION Based on a representative collection of the species E. coli, RpoS was found to have a very small impact on antibiotic resistance, tolerance, or persistence.
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Affiliation(s)
- Estela Ynés Valencia
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Felipe de Moraes Gomes
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Katia Ospino
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Beny Spira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brazil.
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14
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Schiavolin L, Deneubourg G, Steinmetz J, Smeesters PR, Botteaux A. Group A Streptococcus adaptation to diverse niches: lessons from transcriptomic studies. Crit Rev Microbiol 2024; 50:241-265. [PMID: 38140809 DOI: 10.1080/1040841x.2023.2294905] [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: 07/12/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Group A Streptococcus (GAS) is a major human pathogen, causing diseases ranging from mild superficial infections of the skin and pharyngeal epithelium to severe systemic and invasive diseases. Moreover, post infection auto-immune sequelae arise by a yet not fully understood mechanism. The ability of GAS to cause a wide variety of infections is linked to the expression of a large set of virulence factors and their transcriptional regulation in response to various physiological environments. The use of transcriptomics, among others -omics technologies, in addition to traditional molecular methods, has led to a better understanding of GAS pathogenesis and host adaptation mechanisms. This review focusing on bacterial transcriptomic provides new insight into gene-expression patterns in vitro, ex vivo and in vivo with an emphasis on metabolic shifts, virulence genes expression and transcriptional regulators role.
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Affiliation(s)
- Lionel Schiavolin
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Geoffrey Deneubourg
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Jenny Steinmetz
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
| | - Pierre R Smeesters
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Brussels, Belgium
| | - Anne Botteaux
- Microbiology Laboratory, European Plotkin Institute of Vaccinology, Université libre de Bruxelles, Brussels, Belgium
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15
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Bouillet S, Hamdallah I, Majdalani N, Tripathi A, Gottesman S. A negative feedback loop is critical for recovery of RpoS after stress in Escherichia coli. PLoS Genet 2024; 20:e1011059. [PMID: 38466775 PMCID: PMC10957080 DOI: 10.1371/journal.pgen.1011059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/21/2024] [Accepted: 01/17/2024] [Indexed: 03/13/2024] Open
Abstract
RpoS is an alternative sigma factor needed for the induction of the general stress response in many gammaproteobacteria. Tight regulation of RpoS levels and activity is required for bacterial growth and survival under stress. In Escherichia coli, various stresses lead to higher levels of RpoS due to increased translation and decreased degradation. During non-stress conditions, RpoS is unstable, because the adaptor protein RssB delivers RpoS to the ClpXP protease. RpoS degradation is prevented during stress by the sequestration of RssB by anti-adaptors, each of which is induced in response to specific stresses. Here, we examined how the stabilization of RpoS is reversed during recovery of the cell from stress. We found that RpoS degradation quickly resumes after recovery from phosphate starvation, carbon starvation, and when transitioning from stationary phase back to exponential phase. This process is in part mediated by the anti-adaptor IraP, known to promote RpoS stabilization during phosphate starvation via the sequestration of adaptor RssB. The rapid recovery from phosphate starvation is dependent upon a feedback loop in which RpoS transcription of rssB, encoding the adaptor protein, plays a critical role. Crl, an activator of RpoS that specifically binds to and stabilizes the complex between the RNA polymerase and RpoS, is also required for the feedback loop to function efficiently, highlighting a critical role for Crl in restoring RpoS basal levels.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Issam Hamdallah
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Arti Tripathi
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
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Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V. Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. mSystems 2024; 9:e0060623. [PMID: 38189271 PMCID: PMC10878099 DOI: 10.1128/msystems.00606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Acinetobacter baumannii causes severe infections in humans, resists multiple antibiotics, and survives in stressful environmental conditions due to modulations of its complex transcriptional regulatory network (TRN). Unfortunately, our global understanding of the TRN in this emerging opportunistic pathogen is limited. Here, we apply independent component analysis, an unsupervised machine learning method, to a compendium of 139 RNA-seq data sets of three multidrug-resistant A. baumannii international clonal complex I strains (AB5075, AYE, and AB0057). This analysis allows us to define 49 independently modulated gene sets, which we call iModulons. Analysis of the identified A. baumannii iModulons reveals validating parallels to previously defined biological operons/regulons and provides a framework for defining unknown regulons. By utilizing the iModulons, we uncover potential mechanisms for a RpoS-independent general stress response, define global stress-virulence trade-offs, and identify conditions that may induce plasmid-borne multidrug resistance. The iModulons provide a model of the TRN that emphasizes the importance of transcriptional regulation of virulence phenotypes in A. baumannii. Furthermore, they suggest the possibility of future interventions to guide gene expression toward diminished pathogenic potential.IMPORTANCEThe rise in hospital outbreaks of multidrug-resistant Acinetobacter baumannii infections underscores the urgent need for alternatives to traditional broad-spectrum antibiotic therapies. The success of A. baumannii as a significant nosocomial pathogen is largely attributed to its ability to resist antibiotics and survive environmental stressors. However, there is limited literature available on the global, complex regulatory circuitry that shapes these phenotypes. Computational tools that can assist in the elucidation of A. baumannii's transcriptional regulatory network architecture can provide much-needed context for a comprehensive understanding of pathogenesis and virulence, as well as for the development of targeted therapies that modulate these pathways.
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Affiliation(s)
- Nitasha D. Menon
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Anand V. Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Nicholas Dillon
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Biological Sciences, University of Texas at Dallas, Dallas, Texas, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yujiro Hirose
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Microbiology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
| | - Bipin G. Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Geetha B. Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Victor Nizet
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
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Mugnai G, Borruso L, Wu YL, Gallinaro M, Cappitelli F, Zerboni A, Villa F. Ecological strategies of bacterial communities in prehistoric stone wall paintings across weathering gradients: A case study from the Borana zone in southern Ethiopia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168026. [PMID: 37907101 DOI: 10.1016/j.scitotenv.2023.168026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/18/2023] [Accepted: 10/20/2023] [Indexed: 11/02/2023]
Abstract
Rock art paintings represent fragile ecosystems supporting complex microbial communities tuned to the lithic substrate and climatic conditions. The composition and activity of these microbial communities associated with different weathering patterns affecting rock art sites remain unexplored. This study aimed to explore how bacterial communities adapt their ecological strategies based on substrate weathering, while also examining the role of their metabolic pathways in either biodeterioration or bioprotection of the underlying stone. SEM-EDS investigations coupled with 16S rRNA gene sequencing and PICRUSt2 analysis were applied on different weathered surfaces that affect southern Ethiopian rock paintings to investigate the relationships between the current stone microbiome and weathering patterns. The findings revealed that samples experiencing low and high weathering reached a climax stage characterized by stable microenvironments and limited resources. This condition favored K-strategist microorganisms, leading to reduced α-biodiversity and a community with a positive or neutral impact on the substrate. In contrast, moderately-weathered samples displayed diverse microhabitats, resulting in the prevalence of r-strategist bacteria, increased α-biodiversity, and the presence of specialist microorganisms. Moreover, the bacterial communities in moderately-weathered samples demonstrated the highest potential for carbon fixation, stress responses, and complete nitrogen and sulfur cycles. This bacterial community also showed the potential to negatively impact the underlying substrate. This research provided valuable insights into the little-understood ecology of bacterial communities inhabiting deteriorated surfaces, shedding light on the potential role of these microorganisms in the sustainable conservation of rock art.
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Affiliation(s)
- Gianmarco Mugnai
- Department of Agriculture, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, I-06121 Perugia (PG), IT, Italy.
| | - Luigimaria Borruso
- Free University of Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Universitá 5, 39100 Bolzano, Italy.
| | - Ying-Li Wu
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, 20133 Milan, Italy.
| | - Marina Gallinaro
- Dipartimento di Scienze dell'Antichità, Università di Roma La Sapienza, 00185 Rome, Italy.
| | - Francesca Cappitelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, 20133 Milan, Italy.
| | - Federica Villa
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
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18
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Wang HT, Gan QY, Li G, Zhu D. Effects of Zinc Thiazole and Oxytetracycline on the Microbial Metabolism, Antibiotic Resistance, and Virulence Factor Genes of Soil, Earthworm Gut, and Phyllosphere. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:160-170. [PMID: 38148496 DOI: 10.1021/acs.est.3c06513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Pesticides and antibiotics are believed to increase the incidence of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), constituting a serious threat to global health. However, the impact of this combined pollution on the microbiome and that of the related ARGs and VFGs on soil-plant-animal systems remain unknown. In this study, a 60-day microcosm experiment was conducted to reveal the effects of zinc thiazole (ZT) and oxytetracycline (OTC) on microbial communities, antibiotic resistomes, and virulence factors in soil, earthworm gut, and phyllosphere samples using metagenomics. ZT exposure perturbed microbial communities and nutrient metabolism and increased the abundance of ARGs and VFGs in the gut. Combined exposure changed the profiles of ARGs and VFGs by decreasing microbial diversity in the phyllosphere. Host-tracking analysis identified some genera, such as Citrobacter and Aeromonas, as frequent hosts of ARGs and VFGs in the gut. Notably, some co-occurrence patterns of ARGs and MGEs were observed on the metagenome-assembled contigs. More importantly, ZT markedly increased the abundance of potentially drug-resistant pathogens Acinetobacter soli and Acinetobacter junii in the phyllosphere. Overall, this study expands our current understanding of the spread of ARGs and VFGs in soil-plant-animal systems under pollutant-induced stress and the associated health risks.
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Affiliation(s)
- Hong-Tao Wang
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions (Henan University), Ministry of Education, Kaifeng 475004, China
| | - Qiu-Yu Gan
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
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Charron R, Lemée P, Huguet A, Minlong O, Boulanger M, Houée P, Soumet C, Briandet R, Bridier A. Polyhexamethylene biguanide promotes adaptive cross-resistance to gentamicin in Escherichia coli biofilms. Front Cell Infect Microbiol 2023; 13:1324991. [PMID: 38149014 PMCID: PMC10750414 DOI: 10.3389/fcimb.2023.1324991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Antimicrobial resistance is a critical public health issue that requires a thorough understanding of the factors that influence the selection and spread of antibiotic-resistant bacteria. Biocides, which are widely used in cleaning and disinfection procedures in a variety of settings, may contribute to this resistance by inducing similar defense mechanisms in bacteria against both biocides and antibiotics. However, the strategies used by bacteria to adapt and develop cross-resistance remain poorly understood, particularly within biofilms -a widespread bacterial habitat that significantly influences bacterial tolerance and adaptive strategies. Using a combination of adaptive laboratory evolution experiments, genomic and RT-qPCR analyses, and biofilm structural characterization using confocal microscopy, we investigated in this study how Escherichia coli biofilms adapted after 28 days of exposure to three biocidal active substances and the effects on cross-resistance to antibiotics. Interestingly, polyhexamethylene biguanide (PHMB) exposure led to an increase of gentamicin resistance (GenR) phenotypes in biofilms formed by most of the seven E. coli strains tested. Nevertheless, most variants that emerged under biocidal conditions did not retain the GenR phenotype after removal of antimicrobial stress, suggesting a transient adaptation (adaptive resistance). The whole genome sequencing of variants with stable GenR phenotypes revealed recurrent mutations in genes associated with cellular respiration, including cytochrome oxidase (cydA, cyoC) and ATP synthase (atpG). RT-qPCR analysis revealed an induction of gene expression associated with biofilm matrix production (especially curli synthesis), stress responses, active and passive transport and cell respiration during PHMB exposure, providing insight into potential physiological responses associated with adaptive crossresistance. In addition, confocal laser scanning microscopy (CLSM) observations demonstrated a global effect of PHMB on biofilm architectures and compositions formed by most E. coli strains, with the appearance of dense cellular clusters after a 24h-exposure. In conclusion, our results showed that the PHMB exposure stimulated the emergence of an adaptive cross-resistance to gentamicin in biofilms, likely induced through the activation of physiological responses and biofilm structural modulations altering gradients and microenvironmental conditions in the biological edifice.
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Affiliation(s)
- Raphaël Charron
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
- Université Paris-Saclay, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Lemée
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Antoine Huguet
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Ornella Minlong
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Marine Boulanger
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Paméla Houée
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Christophe Soumet
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Romain Briandet
- Université Paris-Saclay, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
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20
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Bouillet S, Hamdallah I, Majdalani N, Tripathi A, Gottesman S. A negative feedback loop is critical for recovery of RpoS after stress in Escherichia coli.. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566509. [PMID: 38077006 PMCID: PMC10705548 DOI: 10.1101/2023.11.09.566509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
RpoS is an alternative sigma factor needed for the induction of the general stress response in many gammaproteobacteria. Tight regulation of RpoS levels and activity is required for bacterial growth and survival under stress. In Escherichia coli, various stresses lead to higher levels of RpoS due to increased translation and decreased degradation. During non-stress conditions, RpoS is unstable, because the adaptor protein RssB delivers RpoS to the ClpXP protease. RpoS degradation is prevented during stress by the sequestration of RssB by anti-adaptors, each of which is induced in response to specific stresses. Here, we examined how the stabilization of RpoS is reversed during recovery of the cell from stress. We found that RpoS degradation quickly resumes after recovery from phosphate starvation, carbon starvation, and when transitioning from stationary phase back to exponential phase. This process is in part mediated by the anti-adaptor IraP, known to promote RpoS stabilization during phosphate starvation via the sequestration of adaptor RssB. The rapid recovery from phosphate starvation is dependent upon a feedback loop in which RpoS transcription of rssB, encoding the adaptor protein, plays a critical role. Crl, an activator of RpoS that specifically binds to and stabilizes the complex between the RNA polymerase and RpoS, is also required for the feedback loop to function efficiently, highlighting a critical role for Crl in restoring RpoS basal levels.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Issam Hamdallah
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Arti Tripathi
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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21
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Durrani B, Mohammad A, Ljubetic BM, Dobberfuhl AD. The Potential Role of Persister Cells in Urinary Tract Infections. Curr Urol Rep 2023; 24:541-551. [PMID: 37907771 DOI: 10.1007/s11934-023-01182-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 11/02/2023]
Abstract
PURPOSE OF REVIEW This review explores the role of persister cells in urinary tract infections (UTIs). UTIs are one of the most common bacterial infections, affecting millions of people worldwide. Persister cells are a subpopulation of bacteria with dormant metabolic activity which allows survival in the presence of antibiotics. RECENT FINDINGS This review summarizes recent research on the pathogenesis of persister cell formation in UTIs, the impact of persister cells on the effectiveness of antibiotics, the challenges they pose for treatment, and the need for new strategies to target these cells. Furthermore, this review examines the current state of research on the identification and characterization of persister cells in UTIs, as well as the future directions for investigations in this field. This review highlights the importance of understanding the role of persister cells in UTIs and the potential impact of targeting these cells in the development of new treatments.
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Affiliation(s)
- Butool Durrani
- Department of Internal Medicine, Aga Khan University Hospital, National Stadium Rd, Karachi, Karachi City, Pakistan
| | - Ashu Mohammad
- Department of Urology, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Urology-5656, Palo Alto, CA, 94304, USA
| | - Bernardita M Ljubetic
- Department of Urology, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Urology-5656, Palo Alto, CA, 94304, USA
| | - Amy D Dobberfuhl
- Department of Urology, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Urology-5656, Palo Alto, CA, 94304, USA.
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22
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Cordell WT, Avolio G, Takors R, Pfleger BF. Milligrams to kilograms: making microbes work at scale. Trends Biotechnol 2023; 41:1442-1457. [PMID: 37271589 DOI: 10.1016/j.tibtech.2023.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023]
Abstract
If biomanufacturing can become a sustainable route for producing chemicals, it will provide a critical step in reducing greenhouse gas emissions to fight climate change. However, efforts to industrialize microbial synthesis of chemicals have met with varied success, due, in part, to challenges in translating laboratory successes to industrial scale. With a particular focus on Escherichia coli, this review examines the lessons learned when studying microbial physiology and metabolism under conditions that simulate large-scale bioreactors and methods to minimize cellular waste through reduction of maintenance energy, optimizing the stress response and minimizing culture heterogeneity. With general strategies to overcome these challenges, biomanufacturing process scale-up could be de-risked and the time and cost of bringing promising syntheses to market could be reduced.
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Affiliation(s)
- William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gennaro Avolio
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Center Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
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23
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Evans CR, Smiley MK, Asahara Thio S, Wei M, Florek LC, Dayton H, Price-Whelan A, Min W, Dietrich LEP. Spatial heterogeneity in biofilm metabolism elicited by local control of phenazine methylation. Proc Natl Acad Sci U S A 2023; 120:e2313208120. [PMID: 37847735 PMCID: PMC10614215 DOI: 10.1073/pnas.2313208120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Within biofilms, gradients of electron acceptors such as oxygen stimulate the formation of physiological subpopulations. This heterogeneity can enable cross-feeding and promote drug resilience, features of the multicellular lifestyle that make biofilm-based infections difficult to treat. The pathogenic bacterium Pseudomonas aeruginosa produces pigments called phenazines that can support metabolic activity in hypoxic/anoxic biofilm subzones, but these compounds also include methylated derivatives that are toxic to their producer under some conditions. In this study, we uncover roles for the global regulators RpoS and Hfq/Crc in controlling the beneficial and detrimental effects of methylated phenazines in biofilms. Our results indicate that RpoS controls phenazine methylation by modulating activity of the carbon catabolite repression pathway, in which the Hfq/Crc complex inhibits translation of the phenazine methyltransferase PhzM. We find that RpoS indirectly inhibits expression of CrcZ, a small RNA that binds to and sequesters Hfq/Crc, specifically in the oxic subzone of P. aeruginosa biofilms. Deletion of rpoS or crc therefore leads to overproduction of methylated phenazines, which we show leads to increased metabolic activity-an apparent beneficial effect-in hypoxic/anoxic subpopulations within biofilms. However, we also find that under specific conditions, biofilms lacking RpoS and/or Crc show increased sensitivity to phenazines indicating that the increased metabolic activity in these mutants comes at a cost. Together, these results suggest that complex regulation of PhzM allows P. aeruginosa to simultaneously exploit the benefits and limit the toxic effects of methylated phenazines.
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Affiliation(s)
| | - Marina K. Smiley
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Sean Asahara Thio
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY10027
| | - Lindsey C. Florek
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY10027
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24
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Cutugno L, O'Byrne C, Pané‐Farré J, Boyd A. Rifampicin-resistant RpoB S522L Vibrio vulnificus exhibits disturbed stress response and hypervirulence traits. Microbiologyopen 2023; 12:e1379. [PMID: 37877661 PMCID: PMC10493491 DOI: 10.1002/mbo3.1379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 10/26/2023] Open
Abstract
Rifampicin resistance, which is genetically linked to mutations in the RNA polymerase β-subunit gene rpoB, has a global impact on bacterial transcription and cell physiology. Previously, we identified a substitution of serine 522 in RpoB (i.e., RpoBS522L ) conferring rifampicin resistance to Vibrio vulnificus, a human food-borne and wound-infecting pathogen associated with a high mortality rate. Transcriptional and physiological analysis of V. vulnificus expressing RpoBS522L showed increased basal transcription of stress-related genes and global virulence regulators. Phenotypically these transcriptional changes manifest as disturbed osmo-stress responses and toxin-associated hypervirulence as shown by reduced hypoosmotic-stress resistance and enhanced cytotoxicity of the RpoBS522L strain. These results suggest that RpoB-linked rifampicin resistance has a significant impact on V. vulnificus survival in the environment and during infection.
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Affiliation(s)
- Laura Cutugno
- School of Natural SciencesUniversity of GalwayGalwayIreland
| | - Conor O'Byrne
- School of Biological and Chemical SciencesUniversity of GalwayGalwayIreland
| | - Jan Pané‐Farré
- Centre for Synthetic Microbiology (SYNMIKRO) & Department of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Aoife Boyd
- School of Natural SciencesUniversity of GalwayGalwayIreland
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25
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Zhang H, Zhai Y, Chen K, Shi H. Adhesion of Escherichia coli O157:H7 during sublethal injury and resuscitation: Importance of pili and surface properties. Food Microbiol 2023; 115:104329. [PMID: 37567635 DOI: 10.1016/j.fm.2023.104329] [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: 04/08/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 08/13/2023]
Abstract
Escherichia coli O157:H7 can recover from sublethally injured (SI) state, which causes threat of foodborne illness. Adhesion plays a key role in the carriage of pathogens in food. In this study, we investigated the adhesion ability of SI and recovered E. coli O157:H7 wildtype and its three pili-deficient mutants (curli, type 1 fimbriae, and type IV pili) on six food-related surfaces. Plate counting was used to determine adhesion population after washing and oscillating the surfaces. Spinach exhibited the stronger adhesion population of E. coli O157:H7 than the other fresh produces (p < 0.05). In addition, at least one key pili dominated adhesion on these surfaces, and curli was always included. The adhesion population and contribution of different types of pili were jointly affected by surface and physiological state. This can be attributed to high hydrophobicity and positive charge density on surface and different expression levels of csgB, fimA, fimC and ppdD in SI and recovered cells. Among glucose, mannose, maltose, fructose, lactose, and sucrose, addition of 0.5% mannose could reduce adhesion of cells at all physiological states on stainless steel. Overall, this research will provide support for controlling adhesion of SI and recovered E. coli O157:H7.
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Affiliation(s)
- Hongchen Zhang
- College of Food Science, Southwest University, Chongqing, China
| | - Yujun Zhai
- College of Food Science, Southwest University, Chongqing, China
| | - Kewei Chen
- College of Food Science, Southwest University, Chongqing, China
| | - Hui Shi
- College of Food Science, Southwest University, Chongqing, China.
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26
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Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Rep 2023; 42:113105. [PMID: 37713311 PMCID: PMC10591938 DOI: 10.1016/j.celrep.2023.113105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/09/2023] [Accepted: 08/23/2023] [Indexed: 09/17/2023] Open
Abstract
Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently developed data analytic method for characterizing the transcriptome can simplify interpretation by grouping genes into independently modulated sets (iModulons). Here, we demonstrate how iModulons reveal deep understanding of the effects of causal mutations and metabolic rewiring. We use adaptive laboratory evolution to generate E. coli strains that tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulons, and metabolic models to elucidate six interacting stress-tolerance mechanisms: (1) modification of transport, (2) activation of ROS stress responses, (3) use of ROS-sensitive iron regulation, (4) motility, (5) broad transcriptional reallocation toward growth, and (6) metabolic rewiring to decrease NADH production. This work thus demonstrates the power of iModulon knowledge mapping for evolution analysis.
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Affiliation(s)
- Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Tan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cameron Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Elsayed Tharwat Tolba Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Patrick V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Amitesh Anand
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, Maharashtra, India
| | - Connor A Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joon Ho Park
- Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Building 76, Cambridge, MA 02139, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Laurence Yang
- Department of Chemical Engineering, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark.
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27
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Metaane S, Monteil V, Douché T, Giai Gianetto Q, Matondo M, Maufrais C, Norel F. Loss of CorA, the primary magnesium transporter of Salmonella, is alleviated by MgtA and PhoP-dependent compensatory mechanisms. PLoS One 2023; 18:e0291736. [PMID: 37713445 PMCID: PMC10503707 DOI: 10.1371/journal.pone.0291736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of stationary phase cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have recently shown that a ΔrpoS mutation decreases the magnesium content and expression level of the housekeeping Mg2+-transporter CorA in stationary phase Salmonella. The other two Mg2+-transporters of Salmonella are encoded by the PhoP-activated mgtA and mgtB genes and are expressed under magnesium starvation. The σS control of corA prompted us to evaluate the impact of CorA in stationary phase Salmonella cells, by using global and analytical proteomic analyses and physiological assays. The ΔcorA mutation conferred a competitive disadvantage to exit from stationary phase, and slightly impaired motility, but had no effect on total and free cellular magnesium contents. In contrast to the wild-type strain, the ΔcorA mutant produced MgtA, but not MgtB, in the presence of high extracellular magnesium concentration. Under these conditions, MgtA production in the ΔcorA mutant did not require PhoP. Consistently, a ΔmgtA, but not a ΔphoP, mutation slightly reduced the magnesium content of the ΔcorA mutant. Synthetic phenotypes were observed when the ΔphoP and ΔcorA mutations were combined, including a strong reduction in growth and motility, independently of the extracellular magnesium concentration. The abundance of several proteins involved in flagella formation, chemotaxis and secretion was lowered by the ΔcorA and ΔphoP mutations in combination, but not alone. These findings unravel the importance of PhoP-dependent functions in the absence of CorA when magnesium is sufficient. Altogether, our data pinpoint a regulatory network, where the absence of CorA is sensed by the cell and compensated by MgtA and PhoP- dependent mechanisms.
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Affiliation(s)
- Selma Metaane
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Véronique Monteil
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Thibaut Douché
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Quentin Giai Gianetto
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Mariette Matondo
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Corinne Maufrais
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Françoise Norel
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
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28
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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29
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Ashrafudoulla M, Mevo SIU, Song M, Chowdhury MAH, Shaila S, Kim DH, Nahar S, Toushik SH, Park SH, Ha SD. Antibiofilm mechanism of peppermint essential oil to avert biofilm developed by foodborne and food spoilage pathogens on food contact surfaces. J Food Sci 2023; 88:3935-3955. [PMID: 37477280 DOI: 10.1111/1750-3841.16712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/10/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
Establishing efficient methods to combat bacterial biofilms is a major concern. Natural compounds, such as essential oils derived from plants, are among the favored and recommended strategies for combatting bacteria and their biofilm. Therefore, we evaluated the antibiofilm properties of peppermint oil as well as the activities by which it kills bacteria generally and particularly their biofilms. Peppermint oil antagonistic activities were investigated against Vibrio parahaemolyticus, Listeria monocytogenes, Pseudomonas aeruginosa, Escherichia coli O157:H7, and Salmonella Typhimurium on four food contact surfaces (stainless steel, rubber, high-density polyethylene, and polyethylene terephthalate). Biofilm formation on each studied surface, hydrophobicity, autoaggregation, metabolic activity, and adenosine triphosphate quantification were evaluated for each bacterium in the presence and absence (control) of peppermint oil. Real-time polymerase chain reaction, confocal laser scanning microscopy, and field-emission scanning electron microscopy were utilized to analyze the effects of peppermint oil treatment on the bacteria and their biofilm. Results showed that peppermint oil (1/2× minimum inhibitory concentration [MIC], MIC, and 2× MIC) substantially lessened biofilm formation, with high bactericidal properties. A minimum of 2.5-log to a maximum of around 5-log reduction was attained, with the highest sensitivity shown by V. parahaemolyticus. Morphological experiments revealed degradation of the biofilm structure, followed by some dead cells with broken membranes. Thus, this study established the possibility of using peppermint oil to combat key foodborne and food spoilage pathogens in the food processing environment.
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Affiliation(s)
- Md Ashrafudoulla
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Republic of Korea
| | | | - Minsu Song
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Republic of Korea
| | | | - Shanjida Shaila
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Republic of Korea
| | - Duk Hyun Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Republic of Korea
| | - Shamsun Nahar
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Republic of Korea
| | - Sazzad Hossen Toushik
- Department of Biochemistry & Microbiology, School of Health & Life Sciences, North South University, Dhaka, Bangladesh
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, Corvallis, Oregon, USA
| | - Sang-Do Ha
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Republic of Korea
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30
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Kelbrick M, Hesse E, O' Brien S. Cultivating antimicrobial resistance: how intensive agriculture ploughs the way for antibiotic resistance. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001384. [PMID: 37606636 PMCID: PMC10482381 DOI: 10.1099/mic.0.001384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
Antimicrobial resistance (AMR) is a growing threat to public health, global food security and animal welfare. Despite efforts in antibiotic stewardship, AMR continues to rise worldwide. Anthropogenic activities, particularly intensive agriculture, play an integral role in the dissemination of AMR genes within natural microbial communities - which current antibiotic stewardship typically overlooks. In this review, we examine the impact of anthropogenically induced temperature fluctuations, increased soil salinity, soil fertility loss, and contaminants such as metals and pesticides on the de novo evolution and dissemination of AMR in the environment. These stressors can select for AMR - even in the absence of antibiotics - via mechanisms such as cross-resistance, co-resistance and co-regulation. Moreover, anthropogenic stressors can prime bacterial physiology against stress, potentially widening the window of opportunity for the de novo evolution of AMR. However, research to date is typically limited to the study of single isolated bacterial species - we lack data on how intensive agricultural practices drive AMR over evolutionary timescales in more complex microbial communities. Furthermore, a multidisciplinary approach to fighting AMR is urgently needed, as it is clear that the drivers of AMR extend far beyond the clinical environment.
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Affiliation(s)
- Matthew Kelbrick
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Elze Hesse
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Siobhán O' Brien
- Department of Microbiology, Moyne Institute for Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Republic of Ireland
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31
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Maharjan RP, Sullivan GJ, Adams F, Shah B, Hawkey J, Delgado N, Semenec L, Dinh H, Li L, Short F, Parkhill J, Paulsen I, Barquist L, Eijkelkamp B, Cain A. DksA is a conserved master regulator of stress response in Acinetobacter baumannii. Nucleic Acids Res 2023; 51:6101-6119. [PMID: 37158230 PMCID: PMC10325922 DOI: 10.1093/nar/gkad341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific stress responses of well-studied Gram-negative pathogens like Escherichia coli are controlled by alternative sigma factors, archetypically RpoS. The deadly hospital pathogen Acinetobacter baumannii is notoriously resistant to environmental stresses, yet it lacks RpoS, and the molecular mechanisms driving this incredible stress tolerance remain poorly defined. Here, using functional genomics, we identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in A. baumannii. Transcriptomics, phenomics and in vivo animal studies revealed that DksA controls ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization in a niche-specific manner. Phylogenetically, DksA was highly conserved and well-distributed across Gammaproteobacteria, with 96.6% containing DksA, spanning 88 families. This study lays the groundwork for understanding DksA as a major regulator of general stress response and virulence in this important pathogen.
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Affiliation(s)
- Ram P Maharjan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Felise G Adams
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Bhumika S Shah
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Victoria, Australia
| | - Natasha Delgado
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Liping Li
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Francesca L Short
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080Würzburg, Germany
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
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32
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Castro VS, Ngo S, Stanford K. Influence of temperature and pH on induction of Shiga toxin Stx1a in Escherichia coli. Front Microbiol 2023; 14:1181027. [PMID: 37485504 PMCID: PMC10359099 DOI: 10.3389/fmicb.2023.1181027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Shiga toxin-producing strains represent pathogenic group that is of concern in food production. The present study evaluated forty-eight E. coli isolates (11 with intact stx gene, while remaining isolates presented only stx-fragments) for Shiga toxin production. The four most expressive stx-producers (O26, O103, O145, and O157) were selected to evaluate effects of pH (3.5, 4.5, and 7) and temperature (35, 40, and 50°C). After determining acid stress effects in media on Stx-induction, we mimicked "in natura" conditions using milk, apple, and orange juices. Only isolates that showed the presence of intact stx gene (11/48) produced Shiga toxin. In addition, acid pH had a role in down-regulating the production of Shiga toxin, in both lactic acid and juices. In contrast, non-lethal heating (40°C), when in neutral pH and milk was a favorable environment to induce Shiga toxin. Lastly, two isolates (O26 and O103) showed a higher capacity to produce Shiga toxin and were included in a genomic cluster with other E. coli involved in worldwide foodborne outbreaks. The induction of this toxin when subjected to 40°C may represent a potential risk to the consumer, since the pathogenic effect of oral ingestion of Shiga toxin has already been proved in an animal model.
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Abstract
Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.
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Affiliation(s)
- Ryan Buchser
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Phillip Sweet
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
| | - Aparna Anantharaman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
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Hajiagha MN, Kafil HS. Efflux pumps and microbial biofilm formation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105459. [PMID: 37271271 DOI: 10.1016/j.meegid.2023.105459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/06/2023]
Abstract
Biofilm-related infections are resistant forms of pathogens that are regarded as a medical problem, particularly due to the spread of multiple drug resistance. One of the factors associated with biofilm drug resistance is the presence of various types of efflux pumps in bacteria. Efflux pumps also play a role in biofilm formation by influencing Physical-chemical interactions, mobility, gene regulation, quorum sensing (QS), extracellular polymeric substances (EPS), and toxic compound extrusion. According to the findings of studies based on efflux pump expression analysis, their role in the anatomical position within the biofilm will differ depending on the biofilm formation stage, encoding gene expression level, the type and concentration of substrate. In some cases, the function of the efflux pumps can overlap with each other, so it seems necessary to accurate identify the efflux pumps of biofilm-forming bacteria along with their function in this process. Such studies will help to choose treatment strategy, at least in combination with antibiotics. Furthermore, if the goal of treatment is an efflux pump manipulation, we should not limit it to inhibition.
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Affiliation(s)
- Mahdyeh Neghabi Hajiagha
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Holý O, Parra-Flores J, Bzdil J, Cabal-Rosel A, Daza-Prieto B, Cruz-Córdova A, Xicohtencatl-Cortes J, Rodríguez-Martínez R, Acuña S, Forsythe S, Ruppitsch W. Screening of Antibiotic and Virulence Genes from Whole Genome Sequenced Cronobacter sakazakii Isolated from Food and Milk-Producing Environments. Antibiotics (Basel) 2023; 12:antibiotics12050851. [PMID: 37237754 DOI: 10.3390/antibiotics12050851] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The objective of this study was to use whole-genome sequencing (WGS) to screen for genes encoding for antibiotic resistance, fitness and virulence in Cronobacter sakazakii strains that had been isolated from food and powdered-milk-producing environments. Virulence (VGs) and antibiotic-resistance genes (ARGs) were detected with the Comprehensive Antibiotic Resistance Database (CARD) platform, ResFinder and PlasmidFinder tools. Susceptibility testing was performed using disk diffusion. Fifteen presumptive strains of Cronobacter spp. were identified by MALDI-TOF MS and ribosomal-MLST. Nine C. sakazakii strains were found in the meningitic pathovar ST4: two were ST83 and one was ST1. The C. sakazakii ST4 strains were further distinguished using core genome MLST based on 3678 loci. Almost all (93%) strains were resistant to cephalotin and 33% were resistant to ampicillin. In addition, 20 ARGs, mainly involved in regulatory and efflux antibiotics, were detected. Ninety-nine VGs were detected that encoded for OmpA, siderophores and genes involved in metabolism and stress. The IncFIB (pCTU3) plasmid was detected, and the prevalent mobile genetic elements (MGEs) were ISEsa1, ISEc52 and ISEhe3. The C. sakazakii isolates analyzed in this study harbored ARGs and VGs, which could have contributed to their persistence in powdered-milk-producing environments, and increase the risk of infection in susceptible population groups.
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Affiliation(s)
- Ondrej Holý
- Science and Research Center, Faculty of Health Sciences, Palacký University Olomouc, 77515 Olomouc, Czech Republic
| | - Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán 3800708, Chile
| | - Jaroslav Bzdil
- Ptacy s.r.o., Valasska Bystrice 194, 75627 Valasska Bystrice, Czech Republic
| | - Adriana Cabal-Rosel
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria
| | - Beatriz Daza-Prieto
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria
| | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Ricardo Rodríguez-Martínez
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Sergio Acuña
- Department of Food Engineering, Universidad del Bío-Bío, Chillán 3800708, Chile
| | - Stephen Forsythe
- FoodMicrobe.com Ltd., Adams Hill, Keyworth, Nottinghamshire NG12 5GY, UK
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria
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Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. RESEARCH SQUARE 2023:rs.3.rs-2729651. [PMID: 37090546 PMCID: PMC10120744 DOI: 10.21203/rs.3.rs-2729651/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced twelve RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations resulted in large shifts in the fear vs. greed tradeoff, likely through destabilizing the rpoB-rpoC interface. RpoS and GAD regulons drive the fear response while ribosomal proteins and the ppGpp regulon underlie greed. Growth rate selection pressure during ALE results in endpoint strains that often have RNAP mutations, with synergistic mutations reflective of particular conditions. A phylogenetic analysis found the tradeoff in numerous bacteria species. The results suggest that the fear vs. greed tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.
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Affiliation(s)
- Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
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Grassmann AA, Tokarz R, Golino C, McLain MA, Groshong AM, Radolf JD, Caimano MJ. BosR and PlzA reciprocally regulate RpoS function to sustain Borrelia burgdorferi in ticks and mammals. J Clin Invest 2023; 133:e166710. [PMID: 36649080 PMCID: PMC9974103 DOI: 10.1172/jci166710] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The RNA polymerase alternative σ factor RpoS in Borrelia burgdorferi (Bb), the Lyme disease pathogen, is responsible for programmatic-positive and -negative gene regulation essential for the spirochete's dual-host enzootic cycle. RpoS is expressed during tick-to-mammal transmission and throughout mammalian infection. Although the mammalian-phase RpoS regulon is well described, its counterpart during the transmission blood meal is unknown. Here, we used Bb-specific transcript enrichment by tick-borne disease capture sequencing (TBDCapSeq) to compare the transcriptomes of WT and ΔrpoS Bb in engorged nymphs and following mammalian host-adaptation within dialysis membrane chambers. TBDCapSeq revealed dramatic changes in the contours of the RpoS regulon within ticks and mammals and further confirmed that RpoS-mediated repression is specific to the mammalian-phase of Bb's enzootic cycle. We also provide evidence that RpoS-dependent gene regulation, including repression of tick-phase genes, is required for persistence in mice. Comparative transcriptomics of engineered Bb strains revealed that the Borrelia oxidative stress response regulator (BosR), a noncanonical Fur family member, and the cyclic diguanosine monophosphate (c-di-GMP) effector PlzA reciprocally regulate the function of RNA polymerase complexed with RpoS. BosR is required for RpoS-mediated transcription activation and repression in addition to its well-defined role promoting transcription of rpoS by the RNA polymerase alternative σ factor RpoN. During transmission, ligand-bound PlzA antagonizes RpoS-mediated repression, presumably acting through BosR.
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Affiliation(s)
| | - Rafal Tokarz
- Center for Infection and Immunity and
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Caroline Golino
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | | | - Ashley M. Groshong
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
- Department of Molecular Biology and Biophysics
- Department of Genetics and Genome Sciences, and
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics
- Department of Molecular Biology and Biophysics
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Evans CR, Smiley MK, Thio SA, Wei M, Price-Whelan A, Min W, Dietrich LE. Spatial heterogeneity in biofilm metabolism elicited by local control of phenazine methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528762. [PMID: 36824979 PMCID: PMC9949047 DOI: 10.1101/2023.02.15.528762] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Within biofilms, gradients of electron acceptors such as oxygen stimulate the formation of physiological subpopulations. This heterogeneity can enable cross-feeding and promote drug resilience, features of the multicellular lifestyle that make biofilm-based infections difficult to treat. The pathogenic bacterium Pseudomonas aeruginosa produces pigments called phenazines that can support metabolic activity in hypoxic/anoxic biofilm subzones, but these compounds also include methylated derivatives that are toxic to their producer under some conditions. Here, we uncover roles for the global regulators RpoS and Hfq/Crc in controlling the beneficial and detrimental effects of methylated phenazines in biofilms. Our results indicate that RpoS controls phenazine methylation by modulating activity of the carbon catabolite repression pathway, in which the Hfq/Crc complex inhibits translation of the phenazine methyltransferase PhzM. We find that RpoS indirectly inhibits expression of CrcZ, a small RNA that binds to and sequesters Hfq/Crc, specifically in the oxic subzone of P. aeruginosa biofilms. Deletion of rpoS or crc therefore leads to overproduction of methylated phenazines, which we show leads to increased metabolic activity-an apparent beneficial effect-in hypoxic/anoxic subpopulations within biofilms. However, we also find that biofilms lacking Crc show increased sensitivity to an exogenously added methylated phenazine, indicating that the increased metabolic activity in this mutant comes at a cost. Together, these results suggest that complex regulation of PhzM allows P. aeruginosa to simultaneously exploit the benefits and limit the toxic effects of methylated phenazines.
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Affiliation(s)
| | - Marina K. Smiley
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Sean Asahara Thio
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10025
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10025
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Dorman CJ. Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations. Mol Microbiol 2023; 119:19-28. [PMID: 36565252 PMCID: PMC10108321 DOI: 10.1111/mmi.15014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/25/2022]
Abstract
Transcription is a noisy and stochastic process that produces sibling-to-sibling variations in physiology across a population of genetically identical cells. This pattern of diversity reflects, in part, the burst-like nature of transcription. Transcription bursting has many causes and a failure to remove the supercoils that accumulate in DNA during transcription elongation is an important contributor. Positive supercoiling of the DNA ahead of the transcription elongation complex can result in RNA polymerase stalling if this DNA topological roadblock is not removed. The relaxation of these positive supercoils is performed by the ATP-dependent type II topoisomerases DNA gyrase and topoisomerase IV. Interference with the action of these topoisomerases involving, inter alia, topoisomerase poisons, fluctuations in the [ATP]/[ADP] ratio, and/or the intervention of nucleoid-associated proteins with GapR-like or YejK-like activities, may have consequences for the smooth operation of the transcriptional machinery. Antibiotic-tolerant (but not resistant) persister cells are among the phenotypic outliers that may emerge. However, interference with type II topoisomerase activity can have much broader consequences, making it an important epigenetic driver of physiological diversity in the bacterial population.
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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Bacillus subtilis Stressosome Sensor Protein Sequences Govern the Ability To Distinguish among Environmental Stressors and Elicit Different σ B Response Profiles. mBio 2022; 13:e0200122. [PMID: 36409125 PMCID: PMC9765535 DOI: 10.1128/mbio.02001-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteria use a variety of systems to sense stress and mount an appropriate response to ensure fitness and survival. Bacillus subtilis uses stressosomes-cytoplasmic multiprotein complexes-to sense environmental stressors and enact the general stress response by activating the alternative sigma factor σB. Each stressosome includes 40 RsbR proteins, representing four paralogous (RsbRA, RsbRB, RsbRC, and RsbRD) putative stress sensors. Population-level analyses suggested that the RsbR paralogs are largely redundant, while our prior work using microfluidics-coupled fluorescence microscopy uncovered differences among the RsbR paralogs' σB response profiles with respect to timing and intensity when facing an identical stressor. Here, we use a similar approach to address the question of whether the σB responses mediated by each paralog differ in the presence of different environmental stressors: can they distinguish among stressors? Wild-type cells (with all four paralogs) and RsbRA-only cells activate σB with characteristic transient response timing irrespective of stressor but show various response magnitudes. However, cells with other individual RsbR paralogs show distinct timing and magnitude in their responses to ethanol, salt, oxidative, and acid stress, implying that RsbR proteins can distinguish among stressors. Experiments with hybrid fusion proteins comprising the N-terminal half of one paralog and the C-terminal half of another argue that the N-terminal identity influences response magnitude and that determinants in both halves of RsbRA are important for its stereotypical transient σB response timing. IMPORTANCE Bacterial survival depends on appropriate responses to diverse stressors. The general stress-response system in the environmental model bacterium Bacillus subtilis is constantly poised for an immediate response and uses unusual stress-sensing protein complexes called stressosomes. Stressosomes typically contain four different types of putative sensing protein. We asked whether each type of sensor has a distinct role in mediating response dynamics to different environmental stressors. We find that one sensor type always mediates a transient response, while the others show distinct response magnitude and timing to different stressors. We also find that a transient response is exceptional, as several engineered hybrid proteins did not show strong transient responses. Our work reveals functional distinctions among subunits of the stressosome complex and represents a step toward understanding how the general stress response of B. subtilis ensures its survival in natural environmental settings.
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M S, N RP, Rajendrasozhan S. Bacterial redox response factors in the management of environmental oxidative stress. World J Microbiol Biotechnol 2022; 39:11. [PMID: 36369499 DOI: 10.1007/s11274-022-03456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Bacteria evolved to survive in the available environmental chemosphere via several cellular mechanisms. A rich pool of antioxidants and stress regulators plays a significant role in the survival of bacteria in unfavorable environmental conditions. Most of the microbes exhibit resistant phenomena in toxic environment niches. Naturally, bacteria possess efficient thioredoxin reductase, glutaredoxin, and peroxiredoxin redox systems to handle environmental oxidative stress. Further, an array of transcriptional regulators senses the oxidative stress conditions. Transcription regulators, such as OxyR, SoxRS, PerR, UspA, SsrB, MarA, OhrR, SarZ, etc., sense and transduce bacterial oxidative stress responses. The redox-sensitive transcription regulators continuously recycle the utilized antioxidant enzymes during oxidative stress. These regulators promote the expression of antioxidant enzymes such as superoxide dismutase, catalase, and peroxides that overcome oxidative insults. Therefore, the transcriptional regulations maintain steady-state activities of antioxidant enzymes representing the resistance against host cell/environmental oxidative insults. Further, the redox system provides reducing equivalents to synthesize biomolecules, thereby contributing to cellular repair mechanisms. The inactive transcriptional regulators in the undisturbed cells are activated by oxidative stress. The oxidized transcriptional regulators modulate the expression of antioxidant and cellular repair enzymes to survive in extreme environmental conditions. Therefore, targeting these antioxidant systems and response regulators could alter cellular redox homeostasis. This review presents the mechanisms of different redox systems that favor bacterial survival in extreme environmental oxidative stress conditions.
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Affiliation(s)
- Sudharsan M
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, Chidambaram, Tamil Nadu, 608 002, India
| | - Rajendra Prasad N
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, Chidambaram, Tamil Nadu, 608 002, India.
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Regulatory Interplay between RNase III and Antisense RNAs in E. coli: the Case of AsflhD and FlhD, Component of the Master Regulator of Motility. mBio 2022; 13:e0098122. [PMID: 36000733 PMCID: PMC9600491 DOI: 10.1128/mbio.00981-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to respond to ever-changing environmental cues, bacteria display resilient regulatory mechanisms controlling gene expression. At the post-transcriptional level, this is achieved by a combination of RNA-binding proteins, such as ribonucleases (RNases), and regulatory RNAs, including antisense RNAs (asRNAs). Bound to their complementary mRNA, asRNAs are primary targets for the double-strand-specific endoribonuclease, RNase III. Taking advantage of our own and previously published transcriptomic data sets obtained in strains inactivated for RNase III, we selected several candidate asRNAs and confirmed the existence of RNase III-sensitive asRNAs for crp, ompR, phoP, and flhD genes, all encoding global regulators of gene expression in Escherichia coli. Using FlhD, a component of the master regulator of motility (FlhD4C2), as our model, we demonstrate that the asRNA AsflhD, transcribed from the coding sequence of flhD, is involved in the fine-tuning of flhD expression and thus participates in the control of motility.
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The stress sigma factor σS/RpoS counteracts Fur repression of genes involved in iron and manganese metabolism and modulates the ionome of Salmonella enterica serovar Typhimurium. PLoS One 2022; 17:e0265511. [PMID: 35358211 PMCID: PMC8970401 DOI: 10.1371/journal.pone.0265511] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of quiescent cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have previously identified sRNAs genes positively controlled by σS in Salmonella, including the two paralogous sRNA genes, ryhB1 and ryhB2/isrE. Expression of ryhB1 and ryhB2 is repressed by the ferric uptake regulator Fur when iron is available. In this study, we show that σS alleviates Fur-mediated repression of the ryhB genes and of additional Fur target genes. Moreover, σS induces transcription of the manganese transporter genes mntH and sitABCD and prevents their repression, not only by Fur, but also by the manganese-responsive regulator MntR. These findings prompted us to evaluate the impact of a ΔrpoS mutation on the Salmonella ionome. Inductively coupled plasma mass spectrometry analyses revealed a significant effect of the ΔrpoS mutation on the cellular concentration of manganese, magnesium, cobalt and potassium. In addition, transcriptional fusions in several genes involved in the transport of these ions were regulated by σS. This study suggests that σS controls fluxes of ions that might be important for the fitness of quiescent cells. Consistent with this hypothesis, the ΔrpoS mutation extended the lag phase of Salmonella grown in rich medium supplemented with the metal ion chelator EDTA, and this effect was abolished when magnesium, but not manganese or iron, was added back. These findings unravel the importance of σS and magnesium in the regrowth potential of quiescent cells.
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Bowlin MQ, Long AR, Huffines JT, Gray MJ. The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001185. [PMID: 35482529 PMCID: PMC10233264 DOI: 10.1099/mic.0.001185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.
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Affiliation(s)
- Marvin Q. Bowlin
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Abagail Renee Long
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joshua T. Huffines
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Jeffrey Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Wölflingseder M, Tutz S, Fengler VH, Schild S, Reidl J. Regulatory Interplay of RpoS and RssB Controls Motility and Colonization in Vibrio cholerae. Int J Med Microbiol 2022; 312:151555. [DOI: 10.1016/j.ijmm.2022.151555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/27/2022] [Accepted: 04/12/2022] [Indexed: 11/28/2022] Open
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Bhowmik P, Rajagopal S, Hmar RV, Singh P, Saxena P, Amar P, Thomas T, Ravishankar R, Nagaraj S, Katagihallimath N, Sarangapani RK, Ramachandran V, Datta S. Validated In Silico Model for Biofilm Formation in Escherichia coli. ACS Synth Biol 2022; 11:713-731. [PMID: 35025506 DOI: 10.1021/acssynbio.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using Escherichia coli as the representative biofilm former, we report here the development of an in silico model built by simulating events that transform a free-living bacterial entity into self-encased multicellular biofilms. Published literature on ∼300 genes associated with pathways involved in biofilm formation was curated, static maps were created, and suitably interconnected with their respective metabolites using ordinary differential equations. Precise interplay of genetic networks that regulate the transitory switching of bacterial growth pattern in response to environmental changes and the resultant multicomponent synthesis of the extracellular matrix were appropriately represented. Subsequently, the in silico model was analyzed by simulating time-dependent changes in the concentration of components by using the R and python environment. The model was validated by simulating and verifying the impact of key gene knockouts (KOs) and systematic knockdowns on biofilm formation, thus ensuring the outcomes were comparable with the reported literature. Similarly, specific gene KOs in laboratory and pathogenic E. coli were constructed and assessed. MiaA, YdeO, and YgiV were found to be crucial in biofilm development. Furthermore, qRT-PCR confirmed the elevation of expression in biofilm-forming clinical isolates. Findings reported in this study offer opportunities for identifying biofilm inhibitors with applications in multiple industries. The application of this model can be extended to the health care sector specifically to develop novel adjunct therapies that prevent biofilms in medical implants and reduce emergence of biofilm-associated resistant polymicrobial-chronic infections. The in silico framework reported here is open source and accessible for further enhancements.
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Affiliation(s)
- Purnendu Bhowmik
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Sreenath Rajagopal
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Rothangamawi Victoria Hmar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Purnima Singh
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Pragya Saxena
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Prakruthi Amar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Teby Thomas
- St. John’s Research Institute, Bengaluru, Karnataka 560034, India
| | - Rajani Ravishankar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Savitha Nagaraj
- St. John’s Medical College, Bengaluru, Karnataka 560034, India
| | - Nainesh Katagihallimath
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Ramanujan Kadambi Sarangapani
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Vasanthi Ramachandran
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
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Li B, Hou C, Ju X, Feng Y, Ye ZQ, Xiao Y, Gu M, Fu C, Wei C, You C. Gain of Spontaneous clpX Mutations Boosting Motility via Adaption to Environments in Escherichia coli. Front Bioeng Biotechnol 2021; 9:772397. [PMID: 34900963 PMCID: PMC8652233 DOI: 10.3389/fbioe.2021.772397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
Motility is finely regulated and is crucial to bacterial processes including colonization and biofilm formation. There is a trade-off between motility and growth in bacteria with molecular mechanisms not fully understood. Hypermotile Escherichia coli could be isolated by evolving non-motile cells on soft agar plates. Most of the isolates carried mutations located upstream of the flhDC promoter region, which upregulate the transcriptional expression of the master regulator of the flagellum biosynthesis, FlhDC. Here, we identified that spontaneous mutations in clpX boosted the motility of E. coli largely, inducing several folds of changes in swimming speed. Among the mutations identified, we further elucidated the molecular mechanism underlying the ClpXV78F mutation on the regulation of E. coli motility. We found that the V78F mutation affected ATP binding to ClpX, resulting in the inability of the mutated ClpXP protease to degrade FlhD as indicated by both structure modeling and in vitro protein degradation assays. Moreover, our proteomic data indicated that the ClpXV78F mutation elevated the stability of known ClpXP targets to various degrees with FlhD as one of the most affected. In addition, the specific tag at the C-terminus of FlhD being recognized for ClpXP degradation was identified. Finally, our transcriptome data characterized that the enhanced expression of the motility genes in the ClpXV78F mutations was intrinsically accompanied by the reduced expression of stress resistance genes relating to the reduced fitness of the hypermotile strains. A similar pattern was observed for previously isolated hypermotile E. coli strains showing high expression of flhDC at the transcriptional level. Hence, clpX appears to be a hot locus comparable to the upstream of the flhDC promoter region evolved to boost bacterial motility, and our finding provides insight into the reduced fitness of the hypermotile bacteria.
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Affiliation(s)
- Bingyu Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China.,Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chaofan Hou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Xian Ju
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Yong Feng
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Zhi-Qiang Ye
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yunzhu Xiao
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Mingyao Gu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chaoliang Wei
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen, China
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
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Abram F, Arcari T, Guerreiro D, O'Byrne CP. Evolutionary trade-offs between growth and survival: The delicate balance between reproductive success and longevity in bacteria. Adv Microb Physiol 2021; 79:133-162. [PMID: 34836610 DOI: 10.1016/bs.ampbs.2021.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
All living cells strive to allocate cellular resources in a way that promotes maximal evolutionary fitness. While there are many competing demands for resources the main decision making process centres on whether to proceed with growth and reproduction or to "hunker down" and invest in protection and survival (or to strike an optimal balance between these two processes). The transcriptional programme active at any given time largely determines which of these competing processes is dominant. At the top of the regulatory hierarchy are the sigma factors that commandeer the transcriptional machinery and determine which set of promoters are active at any given time. The regulatory inputs controlling their activity are therefore often highly complex, with multiple layers of regulation, allowing relevant environmental information to produce the most beneficial response. The tension between growth and survival is also evident in the developmental programme necessary to promote biofilm formation, which is typically associated with low growth rates and enhanced long-term survival. Nucleotide second messengers and energy pools (ATP/ADP levels) play critical roles in determining the fate of individual cells. Regulatory small RNAs frequently play important roles in the decision making processes too. In this review we discuss the trade-off that exists between reproduction and persistence in bacteria and discuss some of the recent advances in this fascinating field.
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Affiliation(s)
- Florence Abram
- Microbiology & Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Talia Arcari
- Microbiology & Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Duarte Guerreiro
- Microbiology & Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Conor P O'Byrne
- Microbiology & Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Ireland.
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Abstract
Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5' leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.
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Affiliation(s)
- Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA; .,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA;
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Felletti M, Romilly C, Wagner EGH, Jonas K. A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability. eLife 2021; 10:71611. [PMID: 34524083 PMCID: PMC8443254 DOI: 10.7554/elife.71611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/15/2021] [Indexed: 01/01/2023] Open
Abstract
The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.
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Affiliation(s)
- Michele Felletti
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Cédric Romilly
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Kristina Jonas
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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