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Chubiz LM. The Mar, Sox, and Rob Systems. EcoSal Plus 2023; 11:eesp00102022. [PMID: 37220096 PMCID: PMC10729928 DOI: 10.1128/ecosalplus.esp-0010-2022] [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: 09/14/2022] [Accepted: 03/03/2023] [Indexed: 01/28/2024]
Abstract
Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.
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Affiliation(s)
- Lon M. Chubiz
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, USA
- Biochemistry and Biotechnology Program, University of Missouri–St. Louis, St. Louis, Missouri, USA
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Nogueira R, Cabo ML, García-Sanmartín L, Sánchez-Ruiloba L, Rodríguez-Herrera JJ. Risk factor-based clustering of Listeria monocytogenes in food processing environments using principal component analysis. Food Res Int 2023; 170:112989. [PMID: 37316020 DOI: 10.1016/j.foodres.2023.112989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
Listeria monocytogenes has a range of strategies that allow it to persist as biofilms in food processing environments (FPE), making it a pathogen of concern to the food industry. The properties of these biofilms are highly variable among strains, and this significantly affects the risk of food contamination. The present study therefore aims to conduct a proof-of-concept study to cluster strains of L. monocytogenes by risk potential using principal component analysis, a multivariate approach. A set of 22 strains, isolated from food processing environments, were typed by serogrouping and pulsed-field gel electrophoresis, showing a relatively high diversity. They were characterized in terms of several biofilm properties that might pose a potential risk of food contamination. The properties studied were tolerance to benzalkonium chloride (BAC), the structural parameters of biofilms (biomass, surface area, maximum and average thickness, surface to biovolume ratio and roughness coefficient) measured by confocal laser scanning microscopy and (3) transfer of biofilm cells to smoked salmon. The PCA correlation circle revealed that the tolerance of biofilms to BAC was positively correlated with roughness, but negatively with biomass parameters. On the contrary, cell transfers were not related to three-dimensional structural parameters, which suggests the role of other variables yet unexplored. Additionally, hierarchical clustering grouped strains into three different clusters. One of them included the strains with high tolerance to BAC and roughness. Another one consisted of strains with enhanced transfer ability, whereas the third cluster contained those that stood out for the thickness of biofilms. The present study represents a novel and effective way to classify L. monocytogenes strains according to biofilm properties that condition the potential risk of reaching the consumer through food contamination. It would thus allow the selection of strains representative of different worst-case scenarios for future studies in support of QMRA and decision-making analysis.
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Affiliation(s)
- Raquel Nogueira
- Laboratory of Microbiology and Technology of Marine Products (MICROTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Marta López Cabo
- Laboratory of Microbiology and Technology of Marine Products (MICROTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Lucía García-Sanmartín
- Laboratory of Microbiology and Technology of Marine Products (MICROTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Lucía Sánchez-Ruiloba
- Optical Microscopy and Image Analysis Facility, Scientific-Technical Support Unit, Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - Juan José Rodríguez-Herrera
- Laboratory of Microbiology and Technology of Marine Products (MICROTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain.
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Strategies to Enhance the Biosynthesis of Monounsaturated Fatty Acids in Escherichia coli. BIOTECHNOL BIOPROC E 2023. [DOI: 10.1007/s12257-022-0295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Sharma P, Mondal K, Kumar S, Tamang S, Najar IN, Das S, Thakur N. RNA thermometers in bacteria: Role in thermoregulation. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194871. [DOI: 10.1016/j.bbagrm.2022.194871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 04/09/2023]
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Grivokostopoulos NC, Makariti IP, Tsadaris S, Skandamis PN. Impact of population density and stress adaptation on the internalization of Salmonella in leafy greens. Food Microbiol 2022; 106:104053. [PMID: 35690446 DOI: 10.1016/j.fm.2022.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022]
Abstract
Salmonella enterica is capable of entering the interior of leafy greens and establishing in the apoplastic area, a phenomenon known as internalization. The ability of internalized bacteria to evade common disinfection practices poses a well-established risk. Our aim was to study the effect of: i) inoculum size and ii) prior adaptation of Salmonella to sublethal stresses, on the internalization of the pathogen in four leafy vegetables. Spinach, lettuce, arugula and chicory were inoculated, by immersion for 2 min at room temperature with: i) Salmonella Enteritidis at 3.0, 4.0, 5.0, 6.0, 7.0 log CFU/mL and ii) non-adapted or adapted S. Enteritidis to acid (in TSB with 1% glucose, incubated for 24 h at 37 °C), cold (in TSB for 7 days at 4 °C), starvation (0.85% NaCl of pH 6.6, 48 h at 37 °C) or desiccation (1.5 h at 42 °C, 4 days at 21 °C) stress at appx 3.5 log CFU/mL). Inoculated leafy greens were subsequently stored at 5 °C and 20 °C for 2 h and 48 h (n = 2 × 2). Population of internalized Salmonella, after surface decontamination with 1% w/v AgNO3, was assessed on selective media. Even the lowest initial bacterial inoculum was adequate for internalization of Salmonella to occur in leafy vegetables. Non-adapted Salmonella inoculum of 7.0 (maximum) and 3.0 log CFU/mL (lowest inoculation level tested) after short storage (2 h) resulted in 3.7-4.3 and 1.3-1.5 log CFU/g internalized bacterial population, respectively. Colonization (including both attachment and internalization processes), as well as internalization process, were positively correlated to initial inoculum level. These processes reached a different plateau beyond which, no further increase in internalization was observed. Adaptation of the pathogen to mild stresses enhanced internalization (P < 0.05), with desiccation- and acid-adapted Salmonella demonstrating the highest internalization capacity, regardless of the vegetable and storage temperature. These findings could contribute to further elucidation of colonization capacity of Salmonella in leafy vegetables and assist in selecting the proper conditions that contribute to the prevention of fresh produce contamination with Salmonella.
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Affiliation(s)
- N C Grivokostopoulos
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - I P Makariti
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - S Tsadaris
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - P N Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece.
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Fatkhullin BF, Gabdulkhakov AG, Yusupov MM. Is RsfS a Hibernation Factor or a Ribosome Biogenesis Factor? BIOCHEMISTRY. BIOKHIMIIA 2022; 87:500-510. [PMID: 35790407 DOI: 10.1134/s0006297922060025] [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: 12/31/2021] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Solving the structures of bacterial, archaeal, and eukaryotic ribosomes by crystallography and cryo-electron microscopy has given an impetus for studying intracellular regulatory proteins affecting various stages of protein translation. Among them are ribosome hibernation factors, which have been actively investigated during the last decade. These factors are involved in the regulation of protein biosynthesis under stressful conditions. The main role of hibernation factors is the reduction of energy consumption for protein biosynthesis and preservation of existing functional ribosomes from degradation, which increases cell survival under unfavorable conditions. Despite a broad interest in this topic, only a few articles have been published on the ribosomal silencing factor S (RsfS). According to the results of these studies, RsfS can be assigned to the group of hibernation factors. However, recent structural studies of the 50S ribosomal subunit maturation demonstrated that RsfS has the features inherent to biogenesis factors for example, ability to bind to the immature ribosomal subunit (similar to the RsfS mitochondrial ortholog MALSU1, mitochondrial assembly of ribosomal large subunit 1). In this review, we summarized the information on the function and structural features RsfS, as well as compared RsfS with MALSU1 in order to answer the emerging question on whether RsfS is a hibernation factor or a ribosome biogenesis factor. We believe that this review might promote future studies of the RsfS-involving molecular mechanisms, which so far remain completely unknown.
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Affiliation(s)
- Bulat F Fatkhullin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
- Institute of Genetics and Molecular and Cellular Biology, Illkirsch-Graffenstaden, F-67400, France
| | - Azat G Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Marat M Yusupov
- Institute of Genetics and Molecular and Cellular Biology, Illkirsch-Graffenstaden, F-67400, France
- Laboratory of Structural Analyze of Biomacromolecules, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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Tabla R, Gómez A, Rebollo JE, Molina F, Roa I. Effectiveness of a bacteriophage cocktail in reducing cheese early blowing caused by Escherichia coli. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Genomics and transcriptomics analyses provide insights into the cold adaptation strategies of an Antarctic bacterium, Cryobacterium sp. SO1. Polar Biol 2021. [DOI: 10.1007/s00300-021-02883-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Rodríguez-Verdugo A, Lozano-Huntelman N, Cruz-Loya M, Savage V, Yeh P. Compounding Effects of Climate Warming and Antibiotic Resistance. iScience 2020; 23:101024. [PMID: 32299057 PMCID: PMC7160571 DOI: 10.1016/j.isci.2020.101024] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/11/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria have evolved diverse mechanisms to survive environments with antibiotics. Temperature is both a key factor that affects the survival of bacteria in the presence of antibiotics and an environmental trait that is drastically increasing due to climate change. Therefore, it is timely and important to understand links between temperature changes and selection of antibiotic resistance. This review examines these links by synthesizing results from laboratories, hospitals, and environmental studies. First, we describe the transient physiological responses to temperature that alter cellular behavior and lead to antibiotic tolerance and persistence. Second, we focus on the link between thermal stress and the evolution and maintenance of antibiotic resistance mutations. Finally, we explore how local and global changes in temperature are associated with increases in antibiotic resistance and its spread. We suggest that a multidisciplinary, multiscale approach is critical to fully understand how temperature changes are contributing to the antibiotic crisis.
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Affiliation(s)
| | - Natalie Lozano-Huntelman
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mauricio Cruz-Loya
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Van Savage
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Pamela Yeh
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; Santa Fe Institute, Santa Fe, NM 87501, USA.
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Sawasato K, Sekiya Y, Nishiyama K. Two‐step induction ofcdsApromoters leads to upregulation of the glycolipidMPIase at cold temperature. FEBS Lett 2019; 593:1711-1723. [DOI: 10.1002/1873-3468.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Katsuhiro Sawasato
- The United Graduate School of Agricultural Sciences Iwate University Morioka Japan
| | - Yusei Sekiya
- Department of Biological Chemistry and Food Science Faculty of Agriculture Iwate University Morioka Japan
| | - Ken‐ichi Nishiyama
- The United Graduate School of Agricultural Sciences Iwate University Morioka Japan
- Department of Biological Chemistry and Food Science Faculty of Agriculture Iwate University Morioka Japan
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Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM. Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica. Cell Stress Chaperones 2019; 24:351-368. [PMID: 30649671 PMCID: PMC6439030 DOI: 10.1007/s12192-019-00969-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - Shazilah Kamaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor Darul Ehsan, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection. Infect Immun 2018; 86:IAI.00388-18. [PMID: 30082479 DOI: 10.1128/iai.00388-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs) and urolithiasis. The transcriptional regulator MrpJ inversely modulates two critical aspects of P. mirabilis UTI progression: fimbria-mediated attachment and flagellum-mediated motility. Transcriptome data indicated a network of virulence-associated genes under MrpJ's control. Here, we identify the direct gene regulon of MrpJ and its contribution to P. mirabilis pathogenesis, leading to the discovery of novel virulence targets. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was used for the first time in a CAUTI pathogen to probe for in vivo direct targets of MrpJ. Selected MrpJ-regulated genes were mutated and assessed for their contribution to UTI using a mouse model. ChIP-seq revealed a palindromic MrpJ binding sequence and 78 MrpJ-bound regions, including binding sites upstream of genes involved in motility, fimbriae, and a type VI secretion system (T6SS). A combinatorial mutation approach established the contribution of three fimbriae (fim8A, fim14A, and pmpA) to UTI and a new pathogenic role for the T6SS in UTI progression. In conclusion, this study (i) establishes the direct gene regulon and an MrpJ consensus binding site and (ii) led to the discovery of new virulence genes in P. mirabilis UTI, which could be targeted for therapeutic intervention of CAUTI.
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Crozier L, Hedley PE, Morris J, Wagstaff C, Andrews SC, Toth I, Jackson RW, Holden NJ. Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts. Front Microbiol 2016; 7:1088. [PMID: 27462311 PMCID: PMC4940412 DOI: 10.3389/fmicb.2016.01088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 12/11/2022] Open
Abstract
Verocytotoxigenic Escherichia coli (VTEC) can contaminate crop plants, potentially using them as secondary hosts, which can lead to food-borne infection. Currently, little is known about the influence of the specific plant species on the success of bacterial colonization. As such, we compared the ability of the VTEC strain, E. coli O157:H7 'Sakai,' to colonize the roots and leaves of four leafy vegetables: spinach (Spinacia oleracea), lettuce (Lactuca sativa), vining green pea (Pisum sativum), and prickly lettuce (Lactuca serriola), a wild relative of domesticated lettuce. Also, to determine the drivers of the initial response on interaction with plant tissue, the whole transcriptome of E. coli O157:H7 Sakai was analyzed following exposure to plant extracts of varying complexity (spinach leaf lysates or root exudates, and leaf cell wall polysaccharides from spinach or lettuce). Plant extracts were used to reduce heterogeneity inherent in plant-microbe interactions and remove the effect of plant immunity. This dual approach provided information on the initial adaptive response of E. coli O157:H7 Sakai to the plant environment together with the influence of the living plant during bacterial establishment and colonization. Results showed that both the plant tissue type and the plant species strongly influence the short-term (1 h) transcriptional response to extracts as well as longer-term (10 days) plant colonization or persistence. We show that propagation temperature (37 vs. 18°C) has a major impact on the expression profile and therefore pre-adaptation of bacteria to a plant-relevant temperature is necessary to avoid misleading temperature-dependent wholescale gene-expression changes in response to plant material. For each of the plant extracts tested, the largest group of (annotated) differentially regulated genes were associated with metabolism. However, large-scale differences in the metabolic and biosynthetic pathways between treatment types indicate specificity in substrate utilization. Induction of stress-response genes reflected the apparent physiological status of the bacterial genes in each extract, as a result of glutamate-dependent acid resistance, nutrient stress, or translational stalling. A large proportion of differentially regulated genes are uncharacterized (annotated as hypothetical), which could indicate yet to be described functional roles associated with plant interaction for E. coli O157:H7 Sakai.
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Affiliation(s)
- Louise Crozier
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Carol Wagstaff
- School of Chemistry, Food and Pharmacy, The University of ReadingReading, UK
| | - Simon C. Andrews
- School of Biological Sciences, The University of ReadingReading, UK
| | - Ian Toth
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | | | - Nicola J. Holden
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
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