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Maurer JJ, Cheng Y, Pedroso A, Thompson KK, Akter S, Kwan T, Morota G, Kinstler S, Porwollik S, McClelland M, Escalante-Semerena JC, Lee MD. Peeling back the many layers of competitive exclusion. Front Microbiol 2024; 15:1342887. [PMID: 38591029 PMCID: PMC11000858 DOI: 10.3389/fmicb.2024.1342887] [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: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 04/10/2024] Open
Abstract
Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard®) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log10Salmonella genomes/gram) was assessed ex vivo using a S. typhimurium reporter strain with fluorescent YFP and CFP gene fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities' response to Salmonella in chickens with low (≤5.85 Log10 genomes/g) or high (≥6.00 Log10 genomes/g) Salmonella colonization. The ex vivo experiment revealed a reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella's SPI-1 virulence genes and LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis were central to Salmonella metabolism co-cultured with either community, and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth in the exclusive community. There were significant differences in the cecal community's stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community, suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth through antagonism may be key to exclusion.
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Affiliation(s)
- John J. Maurer
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Adriana Pedroso
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Kasey K. Thompson
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Shamima Akter
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Tiffany Kwan
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Gota Morota
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Sydney Kinstler
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | | | - Margie D. Lee
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Su R, Fu H, Ding L, Fu B, He S, Ma H, Hu H, Ren H. Long-term impact of nano zero-valent iron on methanogenic activity, microbial community structure, and transcription activity in anaerobic wastewater treatment system. BIORESOURCE TECHNOLOGY 2024; 393:130028. [PMID: 37977494 DOI: 10.1016/j.biortech.2023.130028] [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: 07/28/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Nano zero-valent iron (NZVI) is commonly used in industrial wastewater treatment. However, its long-term impact mechanisms of metabolization in anaerobic systems are not well understood. This study investigated the effects of long-term and continuous addition of NZVI on methanogenic activity, microbial community, and transcription activity. The results demonstrated that low levels of NZVI (1000 mg/L) induced inhibition of methanogenesis after 80 days, while high levels of NZVI (5000 mg/L) immediately led to a sharp decrease of cumulative methane production and chemical oxygen demand removal, which arrived at a steady state (14.4 % of control and 17 %) after 30 days. NZVI adversely affected cell viability, adenosine triphosphate production, and fatty acid evolution of cell membranes played a crucial role in resisting chronic NZVI toxicity. Moreover, high NZVI levels hindered the transcription of key enzymes CoM and mcrA, while low NZVI levels maintained its high CoM and mcrA activity, but down-regulated the transcription of cdh and hdr. Besides, amino-utilizing bacteria was reduced under the high NZVI concentration, while low NZVI changed dominant genus with potential protein hydrolysis function from Candidatus Cloacamonas to Sedimentibacter. These results provide a guideline for proper NZVI utilization in wastewater treatment.
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Affiliation(s)
- Runhua Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Huimin Fu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Lili Ding
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Su He
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haijun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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3
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Bharathan G, Mundra S, Darwich DM, Saeed MM, Al Hafri ASA, Alsalmi MMSM, Maqsood S, Mudgil P, Fanning S, Srikumar S. Regulation of iron metabolism is critical for the survival of Salmonella Typhimurium in pasteurized milk. Food Microbiol 2023; 115:104326. [PMID: 37567619 DOI: 10.1016/j.fm.2023.104326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/13/2023]
Abstract
Salmonella is known to survive in raw/pasteurized milk and cause foodborne outbreaks. Lactoferrin, present in milk from all animal sources, is an iron-binding glycoprotein that limits the availability of iron to pathogenic bacteria. Despite the presence of lactoferrins, Salmonella can grow in milk obtained from different animal sources. However, the mechanism by which Salmonella overcomes iron scarcity induced by lactoferrin in milk is not evaluated yet. Salmonella employs the DNA binding transcriptional regulator Fur (ferric update regulator) to mediate iron uptake during survival in iron deplete conditions. To understand the importance of Fur in Salmonella milk growth, we profiled the growth of Salmonella Typhimurium Δfur (ST4/74Δfur) in both bovine and camel milk. ST4/74Δfur was highly inhibited in milk compared to wild-type ST4/74, confirming the importance of Fur mediated regulation of iron metabolism in Salmonella milk growth. We further studied the biology of ST4/74Δfur to understand the importance of iron metabolism in Salmonella milk survival. Using increasing concentrations of FeCl3, and the antibiotic streptonigrin we show that iron accumulates in the cytoplasm of ST4/74Δfur. We hypothesized that the accumulated iron could activate oxidative stress via Fenton's reaction leading to growth inhibition. However, the inhibition of ST4/74Δfur in milk was not due to Fenton's reaction, but due to the 'iron scarce' conditions of milk and microaerophilic incubation conditions which made the presence of the fur gene indispensable for Salmonella milk growth. Subsequently, survival studies of 14 other transcriptional mutants of ST4/74 in milk confirmed that RpoE-mediated response to extracytoplasmic stress is also important for the survival of Salmonella in milk. Though we have data only for fur and rpoE, many other Salmonella transcriptional factors could play important roles in the growth of Salmonella in milk, a theme for future research on Salmonella milk biology. Nevertheless, our data provide early insights into the biology of milk-associated Salmonella.
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Affiliation(s)
- Greeshma Bharathan
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Dania Mustafa Darwich
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Maitha Mohammad Saeed
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Ahad Saeed Ali Al Hafri
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | | | - Sajid Maqsood
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Priti Mudgil
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, D04 N2E5, Ireland
| | - Shabarinath Srikumar
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates.
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Totsline N, Kniel KE, Bais HP. Microgravity and evasion of plant innate immunity by human bacterial pathogens. NPJ Microgravity 2023; 9:71. [PMID: 37679341 PMCID: PMC10485020 DOI: 10.1038/s41526-023-00323-x] [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: 02/20/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Spaceflight microgravity and modeled-microgravity analogs (MMA) broadly alter gene expression and physiology in both pathogens and plants. Research elucidating plant and bacterial responses to normal gravity or microgravity has shown the involvement of both physiological and molecular mechanisms. Under true and simulated microgravity, plants display differential expression of pathogen-defense genes while human bacterial pathogens exhibit increased virulence, antibiotic resistance, stress tolerance, and reduced LD50 in animal hosts. Human bacterial pathogens including Salmonella enterica and E. coli act as cross-kingdom foodborne pathogens by evading and suppressing the innate immunity of plants for colonization of intracellular spaces. It is unknown if evasion and colonization of plants by human pathogens occurs under microgravity and if there is increased infection capability as demonstrated using animal hosts. Understanding the relationship between microgravity, plant immunity, and human pathogens could prevent potentially deadly outbreaks of foodborne disease during spaceflight. This review will summarize (1) alterations to the virulency of human pathogens under microgravity and MMA, (2) alterations to plant physiology and gene expression under microgravity and MMA, (3) suppression and evasion of plant immunity by human pathogens under normal gravity, (4) studies of plant-microbe interactions under microgravity and MMA. A conclusion suggests future study of interactions between plants and human pathogens under microgravity is beneficial to human safety, and an investment in humanity's long and short-term space travel goals.
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Affiliation(s)
- Noah Totsline
- Department of Plant and Soil Sciences, AP Biopharma, University of Delaware, Newark, DE, USA.
| | - Kalmia E Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA
| | - Harsh P Bais
- Department of Plant and Soil Sciences, AP Biopharma, University of Delaware, Newark, DE, USA
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5
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Ha N, Lee EJ. Manganese Transporter Proteins in Salmonella enterica serovar Typhimurium. J Microbiol 2023; 61:289-296. [PMID: 36862278 DOI: 10.1007/s12275-023-00027-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
The metal cofactors are essential for the function of many enzymes. The host restricts the metal acquisition of pathogens for their immunity and the pathogens have evolved many ways to obtain metal ions for their survival and growth. Salmonella enterica serovar Typhimurium also needs several metal cofactors for its survival, and manganese has been found to contribute to Salmonella pathogenesis. Manganese helps Salmonella withstand oxidative and nitrosative stresses. In addition, manganese affects glycolysis and the reductive TCA, which leads to the inhibition of energetic and biosynthetic metabolism. Therefore, manganese homeostasis is crucial for full virulence of Salmonella. Here, we summarize the current information about three importers and two exporters of manganese that have been identified in Salmonella. MntH, SitABCD, and ZupT have been shown to participate in manganese uptake. mntH and sitABCD are upregulated by low manganese concentration, oxidative stress, and host NRAMP1 level. mntH also contains a Mn2+-dependent riboswitch in its 5' UTR. Regulation of zupT expression requires further investigation. MntP and YiiP have been identified as manganese efflux proteins. mntP is transcriptionally activated by MntR at high manganese levels and repressed its activity by MntS at low manganese levels. Regulation of yiiP requires further analysis, but it has been shown that yiiP expression is not dependent on MntS. Besides these five transporters, there might be additional transporters that need to be identified.
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Affiliation(s)
- Nakyeong Ha
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
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6
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Saldaña-Ahuactzi Z, Knodler LA. FoxR is an AraC-like transcriptional regulator of ferrioxamine uptake in Salmonella enterica. Mol Microbiol 2022; 118:369-386. [PMID: 35970762 DOI: 10.1111/mmi.14970] [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: 03/23/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/07/2023]
Abstract
Salmonella enterica spp. produce siderophores to bind iron with high affinity and can also use three xenosiderophores secreted by other microorganisms, ferrichrome, coprogen, and ferrioxamine. Here we focused on FoxA, a TonB-dependent transporter of ferrioxamines. Adjacent to foxA is a gene annotated as a helix-turn-helix (HTH) domain-containing protein, SL0358 (foxR), in the Salmonella enterica serovar Typhimurium SL1344 genome. FoxR shares homology with transcriptional regulators belonging to the AraC/XylS family. foxR is syntenic with foxA in the Enterobacteriaceae family, suggesting their functional relatedness. Both foxA and foxR are repressed by the ferric uptake regulator (Fur) under iron-rich growth conditions. When iron is scarce, FoxR acts as a transcriptional activator of foxA by directly binding to its upstream regulatory region. A point mutation in the HTH domain of FoxR abolished this binding, as did mutation of a direct repeat motif in the foxA upstream regulatory region. Desferrioxamine (DFOE) enhanced FoxR protein stability and foxA transcription but did not affect the affinity of FoxR binding to the foxA regulatory region. In summary, we have identified FoxR as a new member of the AraC/XylS family that regulates xenosiderophore-mediated iron uptake by S. Typhimurium and likely other Enterobacteriaceae members.
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Affiliation(s)
- Zeus Saldaña-Ahuactzi
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Leigh A Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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7
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Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level. mSystems 2022; 7:e0149321. [PMID: 35913188 PMCID: PMC9426430 DOI: 10.1128/msystems.01493-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens could identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range, and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here, we present SalmoNet2, a major update to SalmoNet1, the first multilayered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory, and enzyme-enzyme interactions. The new version extends the number of Salmonella networks from 11 to 20. We now include a strain from the second species in the Salmonella genus, a strain from the Salmonella enterica subspecies arizonae and additional strains of importance from the subspecies enterica, including S. Typhimurium strain D23580, an epidemic multidrug-resistant strain associated with invasive nontyphoidal salmonellosis (iNTS). The database now uses strain specific metabolic models instead of a generalized model to highlight differences between strains. The update has increased the coverage of high-quality protein-protein interactions, and enhanced interoperability with other computational resources by adopting standardized formats. The resource website has been updated with tutorials to help researchers analyze their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/. IMPORTANCE Multilayered network databases collate interaction information from multiple sources, and are powerful both as a knowledge base and subject of analysis. Here, we present SalmoNet2, an integrated network resource containing protein-protein, transcriptional regulatory, and metabolic interactions for 20 Salmonella strains. Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high-quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyze their data using SalmoNet2.
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Uppalapati SR, Vazquez-Torres A. Manganese Utilization in Salmonella Pathogenesis: Beyond the Canonical Antioxidant Response. Front Cell Dev Biol 2022; 10:924925. [PMID: 35903545 PMCID: PMC9315381 DOI: 10.3389/fcell.2022.924925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
The metal ion manganese (Mn2+) is equally coveted by hosts and bacterial pathogens. The host restricts Mn2+ in the gastrointestinal tract and Salmonella-containing vacuoles, as part of a process generally known as nutritional immunity. Salmonella enterica serovar Typhimurium counteract Mn2+ limitation using a plethora of metal importers, whose expression is under elaborate transcriptional and posttranscriptional control. Mn2+ serves as cofactor for a variety of enzymes involved in antioxidant defense or central metabolism. Because of its thermodynamic stability and low reactivity, bacterial pathogens may favor Mn2+-cofactored metalloenzymes during periods of oxidative stress. This divalent metal catalyzes metabolic flow through lower glycolysis, reductive tricarboxylic acid and the pentose phosphate pathway, thereby providing energetic, redox and biosynthetic outputs associated with the resistance of Salmonella to reactive oxygen species generated in the respiratory burst of professional phagocytic cells. Combined, the oxyradical-detoxifying properties of Mn2+ together with the ability of this divalent metal cation to support central metabolism help Salmonella colonize the mammalian gut and establish systemic infections.
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Affiliation(s)
- Siva R. Uppalapati
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO, United States,*Correspondence: Siva R. Uppalapati, ; Andres Vazquez-Torres,
| | - Andres Vazquez-Torres
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO, United States,Veterans Affairs Eastern Colorado Health Care System, Denver, CO, United States,*Correspondence: Siva R. Uppalapati, ; Andres Vazquez-Torres,
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9
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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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Sakharova T, Mukhametov A, Bokov D. The role of divalent iron cations in the growth, adhesive properties and extracellular adaptation mechanisms of Propionibacterium sp. Saudi J Biol Sci 2022; 29:3642-3646. [PMID: 35844429 PMCID: PMC9280214 DOI: 10.1016/j.sjbs.2022.02.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/07/2022] [Accepted: 02/27/2022] [Indexed: 10/26/2022] Open
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Hill PWS, Moldoveanu AL, Sargen M, Ronneau S, Glegola-Madejska I, Beetham C, Fisher RA, Helaine S. The vulnerable versatility of Salmonella antibiotic persisters during infection. Cell Host Microbe 2021; 29:1757-1773.e10. [PMID: 34731646 DOI: 10.1016/j.chom.2021.10.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/23/2021] [Accepted: 10/08/2021] [Indexed: 11/30/2022]
Abstract
Tolerance and persistence are superficially similar phenomena by which bacteria survive bactericidal antibiotics. It is assumed that the same physiology underlies survival of individual tolerant and persistent bacteria. However, by comparing tolerance and persistence during Salmonella Typhimurium infection, we reveal that these two phenomena are underpinned by different bacterial physiologies. Multidrug-tolerant mutant Salmonella enter a near-dormant state protected from immune-mediated genotoxic damages. However, the numerous tolerant cells, optimized for survival, lack the capabilities necessary to initiate infection relapse following antibiotic withdrawal. In contrast, persisters retain an active state. This leaves them vulnerable to accumulation of macrophage-induced dsDNA breaks but concurrently confers the versatility to initiate infection relapse if protected by RecA-mediated DNA repair. Accordingly, recurrent, invasive, non-typhoidal Salmonella clinical isolates display hallmarks of persistence rather than tolerance during antibiotic treatment. Our study highlights the complex trade-off that antibiotic-recalcitrant Salmonella balance to act as a reservoir for infection relapse.
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Affiliation(s)
- Peter W S Hill
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
| | - Ana Laura Moldoveanu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Molly Sargen
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Séverin Ronneau
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Izabela Glegola-Madejska
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Catrin Beetham
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Robert A Fisher
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Sophie Helaine
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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12
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Analysis of six tonB gene homologs in Bacteroides fragilis revealed that tonB3 is essential for survival in experimental intestinal colonization and intra-abdominal infection. Infect Immun 2021; 90:e0046921. [PMID: 34662212 DOI: 10.1128/iai.00469-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic, anaerobic pathogen and commensal of the human large intestinal tract, Bacteroides fragilis strain 638R, contains six predicted TonB proteins, termed TonB1-6, four ExbBs orthologs, ExbB1-4, and five ExbDs orthologs, ExbD1-5. The inner membrane TonB/ExbB/ExbD complex harvests energy from the proton motive force (Δp) and the TonB C-terminal domain interacts with and transduces energy to outer membrane TonB-dependent transporters (TBDTs). However, TonB's role in activating nearly one hundred TBDTs for nutrient acquisition in B. fragilis during intestinal colonization and extraintestinal infection has not been established. In this study, we show that growth was abolished in the ΔtonB3 mutant when heme, vitamin B12, Fe(III)-ferrichrome, starch, mucin-glycans, or N-linked glycans were used as a substrate for growth in vitro. Genetic complementation of the ΔtonB3 mutant with the tonB3 gene restored growth on these substrates. The ΔtonB1, ΔtonB2, ΔtonB4, ΔtonB5, and ΔtonB6 single mutants did not show a growth defect. This indicates that there was no functional compensation for the lack of TonB3, and it demonstrates that TonB3, alone, drives the TBDTs involved in the transport of essential nutrients. The ΔtonB3 mutant had a severe growth defect in a mouse model of intestinal colonization compared to the parent strain. This intestinal growth defect was enhanced in the ΔtonB3 ΔtonB6 double mutant strain which completely lost its ability to colonize the mouse intestinal tract compared to the parent strain. The ΔtonB1, ΔtonB2, ΔtonB4, and ΔtonB5 mutants did not significantly affect intestinal colonization. Moreover, the survival of the ΔtonB3 mutant strain was completely eradicated in a rat model of intra-abdominal infection. Taken together, these findings show that TonB3 was essential for survival in vivo. The genetic organization of tonB1, tonB2, tonB4, tonB5, and tonB6 gene orthologs indicates that they may interact with periplasmic and nonreceptor outer membrane proteins, but the physiological relevance of this has not been defined. Because anaerobic fermentation metabolism yields a lower Δp than aerobic respiration and B. fragilis has a reduced redox state in its periplasmic space - in contrast to an oxidative environment in aerobes - it remains to be determined if the diverse system of TonB/ExbB/ExbD orthologs encoded by B. fragilis have an increased sensitivity to PMF (relative to aerobic bacteria) to allow for the harvesting of energy under anaerobic conditions.
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Pajarillo EAB, Lee E, Kang DK. Trace metals and animal health: Interplay of the gut microbiota with iron, manganese, zinc, and copper. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2021; 7:750-761. [PMID: 34466679 PMCID: PMC8379138 DOI: 10.1016/j.aninu.2021.03.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/27/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Metals such as iron, manganese, copper, and zinc are recognized as essential trace elements. These trace metals play critical roles in development, growth, and metabolism, participating in various metabolic processes by acting as cofactors of enzymes or providing structural support to proteins. Deficiency or toxicity of these metals can impact human and animal health, giving rise to a number of metabolic and neurological disorders. Proper breakdown, absorption, and elimination of these trace metals is a tightly regulated process that requires crosstalk between the host and these micronutrients. The gut is a complex system that serves as the interface between these components, but other factors that contribute to this delicate interaction are not well understood. The gut is home to trillions of microorganisms and microbial genes (the gut microbiome) that can regulate the metabolism and transport of micronutrients and contribute to the bioavailability of trace metals through their assimilation from food sources or by competing with the host. Furthermore, deficiency or toxicity of these metals can modulate the gut microenvironment, including microbiota, nutrient availability, stress, and immunity. Thus, understanding the role of the gut microbiota in the metabolism of manganese, iron, copper, and zinc, as well as in heavy metal deficiencies and toxicities, and vice versa, may provide insight into developing improved or alternative therapeutic strategies to address emerging health concerns. This review describes the current understanding of how the gut microbiome and trace metals interact and affect host health, particularly in pigs.
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Affiliation(s)
- Edward Alain B. Pajarillo
- Department of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee 32307, FL, USA
| | - Eunsook Lee
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
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14
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Powers TR, Haeberle AL, Predeus AV, Hammarlöf DL, Cundiff JA, Saldaña-Ahuactzi Z, Hokamp K, Hinton JCD, Knodler LA. Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica. PLoS Pathog 2021; 17:e1009280. [PMID: 34460873 PMCID: PMC8432900 DOI: 10.1371/journal.ppat.1009280] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 09/10/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis, S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract. S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived Salmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered by S. Typhimurium within the epithelial cytosol, and the bacterial genes required for cytosolic colonization, remain largely unknown. Here we have exploited the parallel colonization strategies of S. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes with cytosol-induced or vacuole-induced expression signatures. Using these genes as environmental biosensors, we defined that Salmonella is exposed to oxidative stress and iron and manganese deprivation in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimal S. Typhimurium replication in the cytosol, as well as entC, fepB, soxS, mntH and sitA. Virulence genes that are typically associated with extracellular bacteria, namely Salmonella pathogenicity island 1 (SPI1) and SPI4, showed increased expression in the cytosol compared to vacuole. Our study reveals that the cytosolic and vacuolar S. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. This archetypical vacuole-adapted pathogen therefore requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.
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Affiliation(s)
- TuShun R. Powers
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Amanda L. Haeberle
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Alexander V. Predeus
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Disa L. Hammarlöf
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jennifer A. Cundiff
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Zeus Saldaña-Ahuactzi
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Karsten Hokamp
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Leigh A. Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
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15
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Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 2021; 12:182-218. [PMID: 34499567 PMCID: PMC8632127 DOI: 10.1080/21541264.2021.1973865] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles - xenogeneic silencers and developmental regulators - and that many unrecognized potential NAPs exist in each bacterial species examined.
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Affiliation(s)
- Haley M. Amemiya
- University of Michigan Medical School, Ann Arbor, MI, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L. Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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16
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Cunrath O, Palmer JD. An overview of Salmonella enterica metal homeostasis pathways during infection. ACTA ACUST UNITED AC 2021; 2:uqab001. [PMID: 34250489 PMCID: PMC8264917 DOI: 10.1093/femsml/uqab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/19/2021] [Indexed: 12/14/2022]
Abstract
Nutritional immunity is a powerful strategy at the core of the battlefield between host survival and pathogen proliferation. A host can prevent pathogens from accessing biological metals such as Mg, Fe, Zn, Mn, Cu, Co or Ni, or actively intoxicate them with metal overload. While the importance of metal homeostasis for the enteric pathogen Salmonella enterica Typhimurium was demonstrated many decades ago, inconsistent results across various mouse models, diverse Salmonella genotypes, and differing infection routes challenge aspects of our understanding of this phenomenon. With expanding access to CRISPR-Cas9 for host genome manipulation, it is now pertinent to re-visit past results in the context of specific mouse models, identify gaps and incongruities in current knowledge landscape of Salmonella homeostasis, and recommend a straight path forward towards a more universal understanding of this historic host-microbe relationship.
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Affiliation(s)
- Olivier Cunrath
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Rd, Oxford, UK OX1 3SZ
| | - Jacob D Palmer
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Rd, Oxford, UK OX1 3SZ
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17
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Sousa Gerós A, Simmons A, Drakesmith H, Aulicino A, Frost JN. The battle for iron in enteric infections. Immunology 2020; 161:186-199. [PMID: 32639029 PMCID: PMC7576875 DOI: 10.1111/imm.13236] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Iron is an essential element for almost all living organisms, but can be extremely toxic in high concentrations. All organisms must therefore employ homeostatic mechanisms to finely regulate iron uptake, usage and storage in the face of dynamic environmental conditions. The critical step in mammalian systemic iron homeostasis is the fine regulation of dietary iron absorption. However, as the gastrointestinal system is also home to >1014 bacteria, all of which engage in their own programmes of iron homeostasis, the gut represents an anatomical location where the inter-kingdom fight for iron is never-ending. Here, we explore the molecular mechanisms of, and interactions between, host and bacterial iron homeostasis in the gastrointestinal tract. We first detail how mammalian systemic and cellular iron homeostasis influences gastrointestinal iron availability. We then focus on two important human pathogens, Salmonella and Clostridia; despite their differences, they exemplify how a bacterial pathogen must navigate and exploit this web of iron homeostasis interactions to avoid host nutritional immunity and replicate successfully. We then reciprocally explore how iron availability interacts with the gastrointestinal microbiota, and the consequences of this on mammalian physiology and pathogen iron acquisition. Finally, we address how understanding the battle for iron in the gastrointestinal tract might inform clinical practice and inspire new treatments for important diseases.
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Affiliation(s)
- Ana Sousa Gerós
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Translational Gastroenterology UnitJohn Radcliffe HospitalOxfordUK
| | - Alison Simmons
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Translational Gastroenterology UnitJohn Radcliffe HospitalOxfordUK
| | - Hal Drakesmith
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Anna Aulicino
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Translational Gastroenterology UnitJohn Radcliffe HospitalOxfordUK
| | - Joe N. Frost
- MRC Human Immunology UnitWeatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
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18
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Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors. Microorganisms 2020; 8:microorganisms8101622. [PMID: 33096715 PMCID: PMC7588896 DOI: 10.3390/microorganisms8101622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene transcription is the initial step in the complex process that controls gene expression within bacteria. Transcriptional control involves the joint effort of RNA polymerases and numerous other regulatory factors. Whether global or local, positive or negative, regulators play an essential role in the bacterial cell. For instance, some regulators specifically modify the transcription of virulence genes, thereby being indispensable to pathogenic bacteria. Here, we provide a comprehensive overview of important transcription factors and DNA-binding proteins described for the virulent bacterium Francisella tularensis, the causative agent of tularemia. This is an unexplored research area, and the poorly described networks of transcription factors merit additional experimental studies to help elucidate the molecular mechanisms of pathogenesis in this bacterium, and how they contribute to disease.
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19
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The Ferric Uptake Regulator Represses Type VI Secretion System Function by Binding Directly to the clpV Promoter in Salmonella enterica Serovar Typhimurium. Infect Immun 2019; 87:IAI.00562-19. [PMID: 31383745 DOI: 10.1128/iai.00562-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022] Open
Abstract
Type VI secretion systems (T6SSs) are highly conserved and complex protein secretion systems that deliver effector proteins into eukaryotic hosts or other bacteria. T6SSs are regulated precisely by a variety of regulatory systems, which enables bacteria to adapt to varied environments. A T6SS within Salmonella pathogenicity island 6 (SPI-6) is activated during infection, and it contributes to the pathogenesis, as well as interbacterial competition, of Salmonella enterica serovar Typhimurium (S. Typhimurium). However, the regulation of the SPI-6 T6SS in S. Typhimurium is not well understood. In this study, we found that the SPI-6 T6SS core gene clpV was significantly upregulated in response to the iron-depleted condition and during infection. The global ferric uptake regulator (Fur) was shown to repress the clpV expression in the iron-replete medium. Moreover, electrophoretic mobility shift and DNase I footprinting assays revealed that Fur binds directly to the clpV promoter region at multiple sites spanning the transcriptional start site. We also observed that the relieving of Fur-mediated repression on clpV contributed to the interbacterial competition activity and pathogenicity of S. Typhimurium. These findings provide insights into the direct regulation of Fur in the expression and functional activity of SPI-6 T6SS in S. Typhimurium and thus help to elucidate the mechanisms of bacterial adaptability and virulence.
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20
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21
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Sevilla E, Bes MT, González A, Peleato ML, Fillat MF. Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms. Antioxid Redox Signal 2019; 30:1651-1696. [PMID: 30073850 DOI: 10.1089/ars.2017.7442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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22
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Regulation of Iron Uptake by Fine-Tuning the Iron Responsiveness of the Iron Sensor Fur. Appl Environ Microbiol 2019; 85:AEM.03026-18. [PMID: 30824449 DOI: 10.1128/aem.03026-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/23/2019] [Indexed: 02/07/2023] Open
Abstract
Iron is one of most abundant environmental metal ions but is highly limited in organisms. It is an important metal ion as it facilitates various biological processes, including catalysis of metabolic enzymes and DNA biogenesis. In bacteria, the ferric uptake regulator (Fur) protein controls iron uptake by regulating genes coding for iron transporters in response to iron concentration. This iron response is ascribed to Fur's intrinsic affinity for iron because its binding to iron dictates its regulatory function. However, we now report that the pathogen Salmonella achieves a proper response of Fur to changes in environmental iron concentrations via EIIANtr (a nitrogen metabolic phosphotransferase system component). We establish that EIIANtr increases expression of iron transporter-coding genes under low-iron conditions (i.e., nanomolar ranges) in a Fur-dependent manner, which promotes Salmonella growth under such conditions. EIIANtr directly hampers Fur binding to DNA, thereby inducing expression of those genes. This regulation allows Salmonella to express Fur-regulated genes under low-iron conditions. Our findings reveal a potentially widespread control mechanism of bacterial iron uptake systems operating in response to iron availability.IMPORTANCE Iron is a fundamental metal ion for living organisms as it facilitates various biological processes. The ferric uptake regulator (Fur) protein controls iron homeostasis in various bacterial species. It is believed that Fur's iron-dependent regulatory action is sufficient for it to function as an iron sensor. However, we now establish that the bacterial pathogen Salmonella enables Fur to properly reflect changes in surrounding iron availability by fine-tuning its responsiveness to iron. This process requires a protein that hampers Fur DNA binding at low iron concentrations. In this way, Salmonella broadens the range of iron concentrations that Fur responds to. Our findings reveal a potentially widespread control mechanism of bacterial iron homeostasis.
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23
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Potts AH, Guo Y, Ahmer BMM, Romeo T. Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics. PLoS One 2019; 14:e0211430. [PMID: 30682134 PMCID: PMC6347204 DOI: 10.1371/journal.pone.0211430] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
To cause infection, Salmonella must survive and replicate in host niches that present dramatically different environmental conditions. This requires a flexible metabolism and physiology, responsive to conditions of the local milieu. The sequence specific RNA binding protein CsrA serves as a global regulator that governs gene expression required for pathogenicity, metabolism, biofilm formation, and motility in response to nutritional conditions. Its activity is determined by two noncoding small RNAs (sRNA), CsrB and CsrC, which sequester and antagonize this protein. Here, we used ribosome profiling and RNA-seq analysis to comprehensively examine the effects of CsrA on mRNA occupancy with ribosomes, a measure of translation, transcript stability, and the steady state levels of transcripts under in vitro SPI-1 inducing conditions, to simulate growth in the intestinal lumen, and under in vitro SPI-2-inducing conditions, to simulate growth in the Salmonella containing vacuole (SCV) of the macrophage. Our findings uncovered new roles for CsrA in controlling the expression of structural and regulatory genes involved in stress responses, metabolism, and virulence systems required for infection. We observed substantial variation in the CsrA regulon under the two growth conditions. In addition, CsrB/C sRNA levels were greatly reduced under the simulated intracellular conditions and were responsive to nutritional factors that distinguish the intracellular and luminal environments. Altogether, our results reveal CsrA to be a flexible regulator, which is inferred to be intimately involved in maintaining the distinct gene expression patterns associated with growth in the intestine and the macrophage.
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Affiliation(s)
- Anastasia H Potts
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States of America
| | - Yinping Guo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States of America
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States of America
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States of America
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24
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Wang Y, Jia B, Xu X, Zhang L, Wei C, Ou H, Cui Y, Shi C, Shi X. Comparative Genomic Analysis and Characterization of Two Salmonella enterica Serovar Enteritidis Isolates From Poultry With Notably Different Survival Abilities in Egg Whites. Front Microbiol 2018; 9:2111. [PMID: 30245675 PMCID: PMC6137255 DOI: 10.3389/fmicb.2018.02111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Salmonellaenterica serovar Enteritidis (Salmonella Enteritidis) is a globally important foodborne pathogen, and the contaminated chicken eggs are the major source of salmonellosis in humans. Salmonella Enteritidis strains are differentially susceptible to the hostile environment of egg whites. Strains with superior survival ability in egg whites are more likely to contaminate eggs and consequently infect humans. However, the genetic basis for this phenotype is unclear. We characterized two Salmonella Enteritidis strains isolated from chicken meat that had similar genetic backgrounds but large differences in survival ability in egg whites. Although genome comparisons indicated that the gene content and genomic synteny were highly conserved, variations including six insertions or deletions (INDELs) and 70 single nucleotide polymorphisms (SNPs) were observed between the two genomes. Of these, 38 variations including four INDELs and 34 non-synonymous SNPs (nsSNP) were annotated to result in amino acid substitutions or INDELs in coding proteins. These variations were located in 38 genes involved in lysozyme inhibition, vitamin biosynthesis, cell division and DNA damage response, osmotic and oxidative protection, iron-related functions, cell envelope maintenance, amino acid and carbohydrate metabolism, antimicrobial resistance, and type III secretion system. We carried out allelic replacements for two nsSNPs in bioC (biotin synthesis) and pliC (lysozyme inhibition), and two INDELs in ftsK and yqiJ (DNA damage response) by homologous recombination, and these replacements did not alter the bacterial survival ability in egg whites. However, the bacterial survival ability in egg whites was reduced when deletion mutation of the genes bioC and pliC occurred. This study provides initial correlations between observed genotypes and phenotypes and serves as an important caveat for further functional studies.
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Affiliation(s)
- Yanyan Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Ben Jia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuebin Xu
- Department of Microbiology, Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Lida Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Ou
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Cui
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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25
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Abstract
The adaptations that protect pathogenic microorganisms against the cytotoxicity of nitric oxide (NO) engendered in the immune response are incompletely understood. We show here that salmonellae experiencing nitrosative stress suffer dramatic losses of the nucleoside triphosphates ATP, GTP, CTP, and UTP while simultaneously generating a massive burst of the alarmone nucleotide guanosine tetraphosphate. RelA proteins associated with ribosomes overwhelmingly synthesize guanosine tetraphosphate in response to NO as a feedback mechanism to transient branched-chain amino acid auxotrophies. Guanosine tetraphosphate activates the transcription of valine biosynthetic genes, thereby reestablishing branched-chain amino acid biosynthesis that enables the translation of the NO-consuming flavohemoglobin Hmp. Guanosine tetraphosphate synthesized by RelA protects salmonellae from the metabolic stress inflicted by reactive nitrogen species generated in the mammalian host response. This research illustrates the importance of nucleotide metabolism in the adaptation of salmonellae to the nutritional stress imposed by NO released in the innate host response. Nitric oxide triggers dramatic drops in nucleoside triphosphates, the building blocks that power DNA replication; RNA transcription; translation; cell division; and the biosynthesis of fatty acids, lipopolysaccharide, and peptidoglycan. Concomitantly, this diatomic gas stimulates a burst of guanosine tetraphosphate. Global changes in nucleotide metabolism may contribute to the potent bacteriostatic activity of nitric oxide. In addition to inhibiting numerous growth-dependent processes, guanosine tetraphosphate positively regulates the transcription of branched-chain amino acid biosynthesis genes, thereby facilitating the translation of antinitrosative defenses that mediate recovery from nitrosative stress.
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26
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Gans J, Osborne J, Cheng J, Djapgne L, Oglesby-Sherrouse AG. Sequence-Specific Affinity Chromatography of Bacterial Small Regulatory RNA-Binding Proteins from Bacterial Cells. Methods Mol Biol 2018; 1737:341-350. [PMID: 29484602 DOI: 10.1007/978-1-4939-7634-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial small RNA molecules (sRNAs) are increasingly recognized as central regulators of bacterial stress responses and pathogenesis. In many cases, RNA-binding proteins are critical for the stability and function of sRNAs. Previous studies have adopted strategies to genetically tag an sRNA of interest, allowing isolation of RNA-protein complexes from cells. Here we present a sequence-specific affinity purification protocol that requires no prior genetic manipulation of bacterial cells, allowing isolation of RNA-binding proteins bound to native RNA molecules.
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Affiliation(s)
- Jonathan Gans
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Jonathan Osborne
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Juliet Cheng
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
| | - Louise Djapgne
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, MD, USA
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Das G, Das S, Dutta S, Ghosh I. In silico identification and characterization of stress and virulence associated repeats in Salmonella. Genomics 2017; 110:23-34. [PMID: 28827093 DOI: 10.1016/j.ygeno.2017.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/09/2017] [Accepted: 08/03/2017] [Indexed: 01/05/2023]
Abstract
So much genomic similarities yet causing different diseases, is like a paradox in Salmonella biology. Repeat is one of the probes that can explain such differences. Here, a comparative genomics approach is followed to identify and characterize repeats that might play role in adaptation and pathogenesis. Repeats are non-randomly distributed in the genomes except few typhoid causing strains. Perfect long repeats are rare compare to polymorphic ones and both are statistically consistent. Significant differences in repeat densities in stress related genes manifest its probable participation in survival and virulence. 573 and 1053 repeat loci have been identified which are exclusively associated with stress and virulent genes respectively. In Salmonella Typhi, an octameric VNTR locus is found in between acrD and yffB genes having more than 25 perfect copies across Salmonella Typhi but possesses only single copy in other serovars. This repeat can be used as a diagnostic probe for typhoid.
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Affiliation(s)
- Gourab Das
- School of Computational and Integrative Sciences, Jawaharlal Nehru University (JNU), New Mehrauli Road, Munirka, New Delhi, Delhi 110067, India
| | - Surojit Das
- National Institute of Cholera and Enteric Diseases (NICED), P-33, C.I.T. Road, Scheme XM, Beleghata, Kolkata 700010, India
| | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases (NICED), P-33, C.I.T. Road, Scheme XM, Beleghata, Kolkata 700010, India
| | - Indira Ghosh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University (JNU), New Mehrauli Road, Munirka, New Delhi, Delhi 110067, India.
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28
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Leclerc JM, Dozois CM, Daigle F. Salmonella enterica serovar Typhi siderophore production is elevated and Fur inactivation causes cell filamentation and attenuation in macrophages. FEMS Microbiol Lett 2017; 364:3958796. [PMID: 28859315 DOI: 10.1093/femsle/fnx147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serovars Typhi and Typhimurium are two closely related bacteria causing different types of infection in humans. Iron acquisition is considered essential for virulence. Siderophores are important iron chelators and production of enterobactin and salmochelins by these serovars was quantified. Overall, Salmonella Typhi produced higher levels of siderophores than Salmonella Typhimurium. The role of the global regulator Fur, involved in iron homeostasis, present and conserved in both these serovars, was then investigated. Deletion of the fur gene led to distinct phenotypes in these serovars. Defective growth in iron-rich and iron-limiting conditions and formation of filamentous cells was only observed in the S. Typhi fur mutant. Furthermore, Fur was required for optimal motility in both serovars, but motility was more reduced for the fur mutant of S. Typhi compared to S. Typhimurium. During interaction with human-cultured macrophages, Fur was more important for S. Typhi, as the fur mutant had severe defects in uptake and survival. Globally, these results demonstrate that Fur differentially affects the physiology and the virulence phenotypes of the two strains and is more critical for S. Typhi growth, morphology, motility and interaction with host cells than it is for S. Typhimurium.
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Affiliation(s)
- Jean-Mathieu Leclerc
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montreal, Quebec H3C 3J7, Canada
| | - Charles M Dozois
- INRS-Institut Armand-Frappier, 531 boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - France Daigle
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montreal, Quebec H3C 3J7, Canada
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29
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Zhang Q, Wan C, Li C, Bai X, Liu M, Liu S, Zhang Y. Evaluation of a quantitative real-time PCR for rapid detection of Riemerella Anatipestifer infection in birds. J Vet Med Sci 2017; 79:2057-2062. [PMID: 28781328 PMCID: PMC5745191 DOI: 10.1292/jvms.17-0227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To establish an accurate, rapid, and a quantifiable method for the detection of
Riemerella anatipestifer infection, a widespread infectious disease in
birds, we developed a TaqMan-based real-time PCR assay by using DtxR
gene-specific primers and a TaqMan probe. The standard curve established with a linear
correlation (R2) of 0.998 and efficiency of 99% between the Ct
value and the logarithm of the plasmid copy number. The reproducibility and specificity of
the real-time PCR assay were confirmed by using plasmids containing DtxR
genes or DNAs extracted from well-known bacteria or viruses causing duck diseases. The
real-time PCR assay was 100 times more sensitive than the conventional PCR. The results
reveal that the established real-time PCR assay might be a useful method for diagnosis and
quantitative detection of Riemerella anatipestifer in birds.
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Affiliation(s)
- Qingshan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Chenxi Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Xiaofei Bai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Ming Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yun Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
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30
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Baron F, Bonnassie S, Alabdeh M, Cochet MF, Nau F, Guérin-Dubiard C, Gautier M, Andrews SC, Jan S. Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses. Front Microbiol 2017; 8:829. [PMID: 28553268 PMCID: PMC5428311 DOI: 10.3389/fmicb.2017.00829] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022] Open
Abstract
Chicken egg white protects the embryo from bacterial invaders by presenting an assortment of antagonistic activities that combine together to both kill and inhibit growth. The key features of the egg white anti-bacterial system are iron restriction, high pH, antibacterial peptides and proteins, and viscosity. Salmonella enterica serovar Enteritidis is the major pathogen responsible for egg-borne infection in humans, which is partly explained by its exceptional capacity for survival under the harsh conditions encountered within egg white. However, at temperatures up to 42°C, egg white exerts a much stronger bactericidal effect on S. Enteritidis than at lower temperatures, although the mechanism of egg white-induced killing is only partly understood. Here, for the first time, the impact of exposure of S. Enteritidis to egg white under bactericidal conditions (45°C) is explored by global-expression analysis. A large-scale (18.7% of genome) shift in transcription is revealed suggesting major changes in specific aspects of S. Enteritidis physiology: induction of egg white related stress-responses (envelope damage, exposure to heat and alkalinity, and translation shutdown); shift in energy metabolism from respiration to fermentation; and enhanced micronutrient provision (due to iron and biotin restriction). Little evidence of DNA damage or redox stress was obtained. Instead, data are consistent with envelope damage resulting in cell death by lysis. A surprise was the high degree of induction of hexonate/hexuronate utilization genes, despite no evidence indicating the presence of these substrates in egg white.
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Affiliation(s)
- Florence Baron
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Sylvie Bonnassie
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- Science de la Vie et de la Terre, Université de Rennes IRennes, France
| | - Mariah Alabdeh
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Marie-Françoise Cochet
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Françoise Nau
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Catherine Guérin-Dubiard
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Michel Gautier
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | | | - Sophie Jan
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
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31
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Pakarian P, Pawelek PD. A novel set of vectors for Fur-controlled protein expression under iron deprivation in Escherichia coli. BMC Biotechnol 2016; 16:68. [PMID: 27619907 PMCID: PMC5020551 DOI: 10.1186/s12896-016-0298-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the presence of sufficient iron, the Escherichia coli protein Fur (Ferric Uptake Regulator) represses genes controlled by the Fur box, a consensus sequence near or within promoters of target genes. De-repression of Fur-controlled genes occurs upon iron deprivation. In the E. coli chromosome, there is a bidirectional intercistronic promoter region with two non-overlapping Fur boxes. This region controls Fur-regulated expression of entCEBAH in the clockwise direction and fepB in the anticlockwise direction. RESULTS We cloned the E. coli bidirectional fepB/entC promoter region into low-copy-number plasmid backbones (pACYC184 and pBR322) along with downstream sequences encoding epitope tags and a multiple cloning site (MCS) compatible with the bacterial adenylate cyclase two-hybrid (BACTH) system. The vector pFCF1 allows for iron-controlled expression of FLAG-tagged proteins, whereas the pFBH1 vector allows for iron-controlled expression of HA-tagged proteins. We showed that E. coli knockout strains transformed with pFCF1-entA, pFCF1-entE and pFBH1-entB express corresponding proteins with appropriate epitope tags when grown under iron restriction. Furthermore, transformants exhibited positive chrome azurol S (CAS) assay signals under iron deprivation, indicating that the transformants were functional for siderophore biosynthesis. Western blotting and growth studies in rich and iron-depleted media demonstrated that protein expression from these plasmids was under iron control. Finally, we produced the vector pFCF2, a pFCF1 derivative in which a kanamycin resistance (KanR) gene was engineered in the direction opposite of the MCS. The entA ORF was then subcloned into the pFCF2 MCS. Bidirectional protein expression in an iron-deprived pFCF2-entA transformant was confirmed using antibiotic selection, CAS assays and growth studies. CONCLUSIONS The vectors pFCF1, pFCF2, and pFBH1 have been shown to use the fepB/entC promoter region to control bidirectional in trans expression of epitope-tagged proteins in iron-depleted transformants. In the presence of intracellular iron, protein expression from these constructs was abrogated due to Fur repression. The compatibility of the pFCF1 and pFBH1 backbones allows for iron-controlled expression of multiple epitope-tagged proteins from a single co-transformant.
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Affiliation(s)
- Paknoosh Pakarian
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St., W., Montreal, QC, H4B 1R6, Canada
| | - Peter D Pawelek
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St., W., Montreal, QC, H4B 1R6, Canada. .,Groupe de Recherche Axé sur la Structure des Protéines (GRASP), Montreal, Canada.
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32
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McClure RS, Overall CC, McDermott JE, Hill EA, Markillie LM, McCue LA, Taylor RC, Ludwig M, Bryant DA, Beliaev AS. Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002. Nucleic Acids Res 2016; 44:8810-8825. [PMID: 27568004 PMCID: PMC5062996 DOI: 10.1093/nar/gkw737] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 08/05/2016] [Indexed: 12/29/2022] Open
Abstract
Cyanobacterial regulation of gene expression must contend with a genome organization that lacks apparent functional context, as the majority of cellular processes and metabolic pathways are encoded by genes found at disparate locations across the genome and relatively few transcription factors exist. In this study, global transcript abundance data from the model cyanobacterium Synechococcus sp. PCC 7002 grown under 42 different conditions was analyzed using Context-Likelihood of Relatedness (CLR). The resulting network, organized into 11 modules, provided insight into transcriptional network topology as well as grouping genes by function and linking their response to specific environmental variables. When used in conjunction with genome sequences, the network allowed identification and expansion of novel potential targets of both DNA binding proteins and sRNA regulators. These results offer a new perspective into the multi-level regulation that governs cellular adaptations of the fast-growing physiologically robust cyanobacterium Synechococcus sp. PCC 7002 to changing environmental variables. It also provides a methodological high-throughput approach to studying multi-scale regulatory mechanisms that operate in cyanobacteria. Finally, it provides valuable context for integrating systems-level data to enhance gene grouping based on annotated function, especially in organisms where traditional context analyses cannot be implemented due to lack of operon-based functional organization.
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Affiliation(s)
- Ryan S McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Christopher C Overall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Eric A Hill
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lye Meng Markillie
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lee Ann McCue
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ronald C Taylor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Marcus Ludwig
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Alexander S Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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33
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Colgan AM, Kröger C, Diard M, Hardt WD, Puente JL, Sivasankaran SK, Hokamp K, Hinton JCD. The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium. PLoS Genet 2016; 12:e1006258. [PMID: 27564394 PMCID: PMC5001712 DOI: 10.1371/journal.pgen.1006258] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/25/2016] [Indexed: 11/24/2022] Open
Abstract
We know a great deal about the genes used by the model pathogen Salmonella enterica serovar Typhimurium to cause disease, but less about global gene regulation. New tools for studying transcripts at the single nucleotide level now offer an unparalleled opportunity to understand the bacterial transcriptome, and expression of the small RNAs (sRNA) and coding genes responsible for the establishment of infection. Here, we define the transcriptomes of 18 mutants lacking virulence-related global regulatory systems that modulate the expression of the SPI1 and SPI2 Type 3 secretion systems of S. Typhimurium strain 4/74. Using infection-relevant growth conditions, we identified a total of 1257 coding genes that are controlled by one or more regulatory system, including a sub-class of genes that reflect a new level of cross-talk between SPI1 and SPI2. We directly compared the roles played by the major transcriptional regulators in the expression of sRNAs, and discovered that the RpoS (σ38) sigma factor modulates the expression of 23% of sRNAs, many more than other regulatory systems. The impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts is described, and we found 13 sRNAs that are co-regulated with SPI1 and SPI2 virulence genes. We report the first example of an sRNA, STnc1480, that is subject to silencing by H-NS and subsequent counter-silencing by PhoP and SlyA. The data for these 18 regulatory systems is now available to the bacterial research community in a user-friendly online resource, SalComRegulon. The transcriptional networks and the functions of small regulatory RNAs of Salmonella enterica serovar Typhimurium are being studied intensively. S. Typhimurium is becoming the ideal model pathogen for linking transcriptional and post-transcriptional gene regulation to bacterial virulence. Here, we systematically defined the regulatory factors responsible for controlling the expression of S. Typhimurium coding genes and sRNAs under infection-relevant growth conditions. As well as confirming published regulatory inputs for Salmonella pathogenicity islands, such as the positive role played by Fur in the expression of SPI1, we report, for the first time, the global impact of the FliZ, HilE and PhoB/R transcription factors and identify 124 sRNAs that belong to virulence-associated regulons. We found a subset of genes of known and unknown function that are regulated by both HilD and SsrB, highlighting the cross-talk mechanisms that control Salmonella virulence. An integrative analysis of the regulatory datasets revealed 5 coding genes of unknown function that may play novel roles in virulence. We hope that the SalComRegulon resource will be a dynamic database that will be constantly updated to inspire new hypothesis-driven experimentation, and will contribute to the construction of a comprehensive transcriptional network for S. Typhimurium.
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Affiliation(s)
- Aoife M. Colgan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Médéric Diard
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | | | - José L. Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Sathesh K. Sivasankaran
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Jay C. D. Hinton
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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34
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Acquisition of Iron Is Required for Growth of Salmonella spp. in Tomato Fruit. Appl Environ Microbiol 2015; 81:3663-70. [PMID: 25795672 DOI: 10.1128/aem.04257-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/14/2015] [Indexed: 11/20/2022] Open
Abstract
Salmonella remains a leading cause of bacterial food-borne disease, sickening millions each year. Although outbreaks of salmonellosis have traditionally been associated with contaminated meat products, recent years have seen numerous disease cases caused by the consumption of produce. Tomatoes have been specifically implicated, due to the ability of Salmonella spp. to enter the tomato fruit and proliferate within, making the decontamination of the raw product impossible. To investigate the genetic means by which Salmonella is able to survive and proliferate within tomatoes, we conducted a screen for bacterial genes of Salmonella enterica serovar Montevideo specifically induced after inoculation into ripe tomato fruit. Among these genes, we found 17 members of the previously described anaerobic Fur (ferric uptake regulator) regulon. Fur is a transcriptional and posttranscriptional regulator known to sense iron, suggesting the importance of this mineral to Salmonella within tomatoes. To test whether iron acquisition is essential for Salmonella growth in tomatoes, we tested a ΔfepDGC mutant, which lacks the ability to import iron-associated siderophores. This mutant grew significantly more poorly within tomatoes than did the wild type, but the growth defect of the mutant was fully reversed by the addition of exogenous iron, demonstrating the need for bacterial iron scavenging. Further, dependence upon iron was not apparent for Salmonella growing in filtered tomato juice, implicating the cellular fraction of the fruit as an important mediator of iron acquisition by the bacteria.
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35
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Rydenfelt M, Garcia HG, Cox RS, Phillips R. The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli. PLoS One 2014; 9:e114347. [PMID: 25549361 PMCID: PMC4280137 DOI: 10.1371/journal.pone.0114347] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/02/2014] [Indexed: 12/31/2022] Open
Abstract
The ability to regulate gene expression is of central importance for the adaptability of living organisms to changes in their external and internal environment. At the transcriptional level, binding of transcription factors (TFs) in the promoter region can modulate the transcription rate, hence making TFs central players in gene regulation. For some model organisms, information about the locations and identities of discovered TF binding sites have been collected in continually updated databases, such as RegulonDB for the well-studied case of E. coli. In order to reveal the general principles behind the binding-site arrangement and function of these regulatory architectures we propose a random promoter architecture model that preserves the overall abundance of binding sites to identify overrepresented binding site configurations. This model is analogous to the random network model used in the study of genetic network motifs, where regulatory motifs are identified through their overrepresentation with respect to a “randomly connected” genetic network. Using our model we identify TF pairs which coregulate operons in an overrepresented fashion, or individual TFs which act at multiple binding sites per promoter by, for example, cooperative binding, DNA looping, or through multiple binding domains. We furthermore explore the relationship between promoter architecture and gene expression, using three different genome-wide protein copy number censuses. Perhaps surprisingly, we find no systematic correlation between the number of activator and repressor binding sites regulating a gene and the level of gene expression. A position-weight-matrix model used to estimate the binding affinity of RNA polymerase (RNAP) to the promoters of activated and repressed genes suggests that this lack of correlation might in part be due to differences in basal transcription levels, with repressed genes having a higher basal activity level. This quantitative catalogue relating promoter architecture and function provides a first step towards genome-wide predictive models of regulatory function.
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Affiliation(s)
- Mattias Rydenfelt
- Department of Physics, California Institute of Technology, Pasadena, CA, United States of America
- Integrative Research Institute for the Life Sciences and Institute for Theoretical Biology, Humboldt University, Berlin, Germany
| | - Hernan G. Garcia
- Joseph-Henry Laboratories of Physics, Princeton University, Princeton, NJ, United States of America
| | - Robert Sidney Cox
- Department of Chemical Science and Engineering, Kobe University, Kobe, Japan
| | - Rob Phillips
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, United States of America
- Division of Biology, California Institute of Technology, Pasadena, CA, United States of America
- * E-mail:
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36
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Correia S, Nunes-Miranda JD, Pinto L, Santos HM, de Toro M, Sáenz Y, Torres C, Capelo JL, Poeta P, Igrejas G. Complete proteome of a quinolone-resistant Salmonella Typhimurium phage type DT104B clinical strain. Int J Mol Sci 2014; 15:14191-219. [PMID: 25196519 PMCID: PMC4159846 DOI: 10.3390/ijms150814191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 06/27/2014] [Accepted: 07/25/2014] [Indexed: 11/26/2022] Open
Abstract
Salmonellosis is one of the most common and widely distributed foodborne diseases. The emergence of Salmonella strains that are resistant to a variety of antimicrobials is a serious global public health concern. Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) is one of these emerging epidemic multidrug resistant strains. Here we collate information from the diverse and comprehensive range of experiments on Salmonella proteomes that have been published. We then present a new study of the proteome of the quinolone-resistant Se20 strain (phage type DT104B), recovered after ciprofloxacin treatment and compared it to the proteome of reference strain SL1344. A total of 186 and 219 protein spots were recovered from Se20 and SL1344 protein extracts, respectively, after two-dimensional gel electrophoresis. The signatures of 94% of the protein spots were successfully identified through matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). Three antimicrobial resistance related proteins, whose genes were previously detected by polymerase chain reaction (PCR), were identified in the clinical strain. The presence of these proteins, dihydropteroate synthase type-2 (sul2 gene), aminoglycoside resistance protein A (strA gene) and aminoglycoside 6'-N-acetyltransferase type Ib-cr4 (aac(6')-Ib-cr4 gene), was confirmed in the DT104B clinical strain. The aac(6')-Ib-cr4 gene is responsible for plasmid-mediated aminoglycoside and quinolone resistance. This is a preliminary analysis of the proteome of these two S. Typhimurium strains and further work is being developed to better understand how antimicrobial resistance is developing in this pathogen.
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Affiliation(s)
- Susana Correia
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Júlio D Nunes-Miranda
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Luís Pinto
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Hugo M Santos
- BIOSCOPE group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, 2829-516 Monte de Caparica, Portugal.
| | - María de Toro
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander 39011, Spain.
| | - Yolanda Sáenz
- Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, C/Piqueras 98, 26006 Logroño, La Rioja, Spain.
| | - Carmen Torres
- Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, C/Piqueras 98, 26006 Logroño, La Rioja, Spain.
| | - José Luis Capelo
- BIOSCOPE group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, 2829-516 Monte de Caparica, Portugal.
| | - Patrícia Poeta
- Centre of Studies of Animal and Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Gilberto Igrejas
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
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Stress response of Salmonella enterica serovar typhimurium to acidified nitrite. Appl Environ Microbiol 2014; 80:6373-82. [PMID: 25107963 DOI: 10.1128/aem.01696-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The antimicrobial action of the curing agent sodium nitrite (NaNO2), which is added as a preservative to raw meat products, depends on its conversion to nitric oxide and other reactive nitrogen species under acidic conditions. In this study, we used RNA sequencing to analyze the acidified-NaNO2 shock and adaptive responses of Salmonella enterica serovar Typhimurium, a frequent contaminant in raw meat, considering parameters relevant for the production of raw-cured sausages. Upon a 10-min exposure to 150 mg/liter NaNO2 in LB (pH 5.5) acidified with lactic acid, genes involved in nitrosative-stress protection, together with several other stress-related genes, were induced. In contrast, genes involved in translation, transcription, replication, and motility were downregulated. The induction of stress tolerance and the reduction of cell proliferation obviously promote survival under harsh acidified-NaNO2 stress. The subsequent adaptive response was characterized by upregulation of NsrR-regulated genes and iron uptake systems and by downregulation of genes involved in anaerobic respiratory pathways. Strikingly, amino acid decarboxylase systems, which contribute to acid tolerance, displayed increased transcript levels in response to acidified NaNO2. The induction of systems known to be involved in acid resistance indicates a nitrite-mediated increase in the level of acid stress. Deletion of cadA, which encodes lysine decarboxylase, resulted in increased sensitivity to acidified NaNO2. Intracellular pH measurements using a pH-sensitive green fluorescent protein (GFP) variant showed that the cytoplasmic pH of S. Typhimurium in LB medium (pH 5.5) is decreased upon the addition of NaNO2. This study provides the first evidence that intracellular acidification is an additional antibacterial mode of action of acidified NaNO2.
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38
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Condell O, Power KA, Händler K, Finn S, Sheridan A, Sergeant K, Renaut J, Burgess CM, Hinton JCD, Nally JE, Fanning S. Comparative analysis of Salmonella susceptibility and tolerance to the biocide chlorhexidine identifies a complex cellular defense network. Front Microbiol 2014; 5:373. [PMID: 25136333 PMCID: PMC4117984 DOI: 10.3389/fmicb.2014.00373] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/03/2014] [Indexed: 12/04/2022] Open
Abstract
Chlorhexidine is one of the most widely used biocides in health and agricultural settings as well as in the modern food industry. It is a cationic biocide of the biguanide class. Details of its mechanism of action are largely unknown. The frequent use of chlorhexidine has been questioned recently, amidst concerns that an overuse of this compound may select for bacteria displaying an altered susceptibility to antimicrobials, including clinically important anti-bacterial agents. We generated a Salmonella enterica serovar Typhimurium isolate (ST24(CHX)) that exhibited a high-level tolerant phenotype to chlorhexidine, following several rounds of in vitro selection, using sub-lethal concentrations of the biocide. This mutant showed altered suceptibility to a panel of clinically important antimicrobial compounds. Here we describe a genomic, transcriptomic, proteomic, and phenotypic analysis of the chlorhexidine tolerant S. Typhimurium compared with its isogenic sensitive progenitor. Results from this study describe a chlorhexidine defense network that functions in both the reference chlorhexidine sensitive isolate and the tolerant mutant. The defense network involved multiple cell targets including those associated with the synthesis and modification of the cell wall, the SOS response, virulence, and a shift in cellular metabolism toward anoxic pathways, some of which were regulated by CreB and Fur. In addition, results indicated that chlorhexidine tolerance was associated with more extensive modifications of the same cellular processes involved in this proposed network, as well as a divergent defense response involving the up-regulation of additional targets such as the flagellar apparatus and an altered cellular phosphate metabolism. These data show that sub-lethal concentrations of chlorhexidine induce distinct changes in exposed Salmonella, and our findings provide insights into the mechanisms of action and tolerance to this biocidal agent.
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Affiliation(s)
- Orla Condell
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College DublinBelfield, Dublin, Ireland
- European Program for Public Health Microbiology Training, European Centre for Disease Prevention and ControlStockholm, Sweden
| | - Karen A. Power
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College DublinBelfield, Dublin, Ireland
| | - Kristian Händler
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College DublinDublin, Ireland
| | - Sarah Finn
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College DublinBelfield, Dublin, Ireland
| | - Aine Sheridan
- Food Safety Department, Teagasc Food Research CentreAshtown, Dublin, Ireland
| | - Kjell Sergeant
- Department of Environment and Agrobiotechnologies (EVA), Centre de Recherche Public-Gabriel LippmannBelvaux, Luxembourg
| | - Jenny Renaut
- Department of Environment and Agrobiotechnologies (EVA), Centre de Recherche Public-Gabriel LippmannBelvaux, Luxembourg
| | | | - Jay C. D. Hinton
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College DublinDublin, Ireland
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Jarlath E. Nally
- School of Veterinary Medicine, University College DublinBelfield, Dublin, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College DublinBelfield, Dublin, Ireland
- Institute for Global Food Security, Queen's University BelfastBelfast, Northern Ireland
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39
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Ali MM, Newsom DL, González JF, Sabag-Daigle A, Stahl C, Steidley B, Dubena J, Dyszel JL, Smith JN, Dieye Y, Arsenescu R, Boyaka PN, Krakowka S, Romeo T, Behrman EJ, White P, Ahmer BMM. Fructose-asparagine is a primary nutrient during growth of Salmonella in the inflamed intestine. PLoS Pathog 2014; 10:e1004209. [PMID: 24967579 PMCID: PMC4072780 DOI: 10.1371/journal.ppat.1004209] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (Salmonella) is one of the most significant food-borne pathogens affecting both humans and agriculture. We have determined that Salmonella encodes an uptake and utilization pathway specific for a novel nutrient, fructose-asparagine (F-Asn), which is essential for Salmonella fitness in the inflamed intestine (modeled using germ-free, streptomycin-treated, ex-germ-free with human microbiota, and IL10-/- mice). The locus encoding F-Asn utilization, fra, provides an advantage only if Salmonella can initiate inflammation and use tetrathionate as a terminal electron acceptor for anaerobic respiration (the fra phenotype is lost in Salmonella SPI1- SPI2- or ttrA mutants, respectively). The severe fitness defect of a Salmonella fra mutant suggests that F-Asn is the primary nutrient utilized by Salmonella in the inflamed intestine and that this system provides a valuable target for novel therapies.
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Affiliation(s)
- Mohamed M. Ali
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - David L. Newsom
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Juan F. González
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Christopher Stahl
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Brandi Steidley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Judith Dubena
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Jessica L. Dyszel
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jenee N. Smith
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Yakhya Dieye
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Razvan Arsenescu
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Prosper N. Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Steven Krakowka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Tony Romeo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Edward J. Behrman
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Peter White
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Brian M. M. Ahmer
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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40
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Calderón PF, Morales EH, Acuña LG, Fuentes DN, Gil F, Porwollik S, McClelland M, Saavedra CP, Calderón IL. The small RNA RyhB homologs from Salmonella typhimurium participate in the response to S-nitrosoglutathione-induced stress. Biochem Biophys Res Commun 2014; 450:641-5. [PMID: 24937451 DOI: 10.1016/j.bbrc.2014.06.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 06/06/2014] [Indexed: 12/25/2022]
Abstract
Typically, the expression of sRNAs is activated in response to environmental stimuli in order to regulate gene expression through post-transcriptional mechanisms. In the present work we show that the Salmonellatyphimurium paralogous sRNAs RyhB-1 and RyhB-2 are induced in response to the nitrosating agent S-nitrosoglutathione (GSNO). Inactivation of these sRNAs decreased S. typhimurium resistance to GSNO and increased the levels of nitrosylated proteins. These results prompted us to evaluate a possible role of these sRNAs in nitrosative stress resistance. RNA profiling was used as a screen to identify novel RyhB-1 and RyhB-2 regulated targets. A subset of genes was filtered based on their potential role in the response to nitrosative stress and their expression was analyzed by quantitative RT-PCR in wild type, single and double mutant strains (ΔryhB1, ΔryhB2 and ΔryhB1 ΔryhB2) treated with GSNO. In response to GSNO RyhB-1 and RyhB-2 negatively regulate the expression of the genes cyoABC (cytochrome bo oxidase), cydB (cytochrome bd oxidase), cybC (cytochrome b-562), and positively regulate the nirBCD operon (nitrite reductase system). Together, these results suggest that RyhB-1 and RyhB-2 finely tune the expression of genes coding for cytochrome oxidases and the nitrate reductase system, allowing the cell to cope with GSNO-induced stress.
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Affiliation(s)
- Paulina F Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Eduardo H Morales
- Great Lakes Bioenergy Research Center and Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Lillian G Acuña
- Laboratorio de Ecofisiología Microbiana, Fundación Ciencia & Vida, Santiago, Chile.
| | - Danitza N Fuentes
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Fernando Gil
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - S Porwollik
- Department of Microbiology and Molecular Genetics, B240 Medical Sciences Building, University of California, Irvine, CA 92697, USA.
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, B240 Medical Sciences Building, University of California, Irvine, CA 92697, USA.
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Iván L Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
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41
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Bertrand RL. Lag phase-associated iron accumulation is likely a microbial counter-strategy to host iron sequestration: role of the ferric uptake regulator (fur). J Theor Biol 2014; 359:72-9. [PMID: 24929040 DOI: 10.1016/j.jtbi.2014.05.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 05/19/2014] [Accepted: 05/27/2014] [Indexed: 01/26/2023]
Abstract
Iron is an essential metal for almost all forms of life, but potentiates oxidative stress via Fenton catalysis. During microbial lag phase there is a rapid influx of iron with concomitant oxidative hypersensitivity. How and why iron accumulation occurs remains to be elucidated. Iron homeostasis in prokaryotes is mediated by the ferric uptake regulator (Fur), an iron-activated global regulator that controls intracellular iron levels by feedback inhibition with the metal. Herein it is postulated, based on the expression profiles of antioxidant enzymes within the Fur regulon as observed in wild type and Δfur mutants, that iron accumulation is mediated by a transitively low concentration of the Fur protein during lag phase. Vertebrate hosts sequester iron upon 'sensing' an infection in order to retard microbial proliferation through a process known as 'nutritional immunity'. It is herein argued that the purpose of iron accumulation is not principally a preparative step for the replicative phase, as suggested elsewhere, but an evolved behavior that counteracts host iron sequestration. This interpretation is supported by multiple clinical and animal studies that demonstrate that iron surplus in hosts advances progression and susceptibility to infection, and vice versa. Contextualizing iron accumulation as a counter-immune behavior adds impetus to the development of antibiotics targeting pathogenic modes of iron acquisition.
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Affiliation(s)
- Robert L Bertrand
- Department of Chemistry, University of Winnipeg, Winnipeg, MB, Canada R3B 2E9.
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42
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Transcriptome dynamics-based operon prediction in prokaryotes. BMC Bioinformatics 2014; 15:145. [PMID: 24884724 PMCID: PMC4235196 DOI: 10.1186/1471-2105-15-145] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 04/22/2014] [Indexed: 11/21/2022] Open
Abstract
Background Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. Results In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. Conclusion We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.
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43
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González A, Angarica VE, Sancho J, Fillat MF. The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes. Nucleic Acids Res 2014; 42:4833-46. [PMID: 24503250 PMCID: PMC4005646 DOI: 10.1093/nar/gku123] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handful of examples. In this article, we combine an in silico genome-wide predictive approach with experimental determinations to better define the FurA regulon. Predicted FurA-binding sites were identified upstream of 215 genes belonging to diverse functional categories including iron homeostasis, photosynthesis and respiration, heterocyst differentiation, oxidative stress defence and light-dependent signal transduction mechanisms, among others. The probabilistic model proved to be effective at discerning FurA boxes from non-cognate sequences, while subsequent electrophoretic mobility shift assay experiments confirmed the in vitro specific binding of FurA to at least 20 selected predicted targets. Gene-expression analyses further supported the dual role of FurA as transcriptional modulator that can act both as repressor and as activator. In either role, the in vitro affinity of the protein to its target sequences is strongly dependent on metal co-regulator and reducing conditions, suggesting that FurA couples in vivo iron homeostasis and the response to oxidative stress to major physiological processes in cyanobacteria.
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Affiliation(s)
- Andrés González
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain and Unidad Asociada BIFI-IQFR (CSIC), 28006 Madrid, Spain
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44
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Foley SL, Johnson TJ, Ricke SC, Nayak R, Danzeisen J. Salmonella pathogenicity and host adaptation in chicken-associated serovars. Microbiol Mol Biol Rev 2013; 77:582-607. [PMID: 24296573 PMCID: PMC3973385 DOI: 10.1128/mmbr.00015-13] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.
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45
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Calderón IL, Morales EH, Collao B, Calderón PF, Chahuán CA, Acuña LG, Gil F, Saavedra CP. Role of Salmonella Typhimurium small RNAs RyhB-1 and RyhB-2 in the oxidative stress response. Res Microbiol 2013; 165:30-40. [PMID: 24239962 DOI: 10.1016/j.resmic.2013.10.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/04/2013] [Indexed: 11/26/2022]
Abstract
As part of the response to specific stress conditions, bacteria express small molecules of non-coding RNA which maintain cellular homeostasis by regulating gene expression, commonly at the post-transcriptional level. Among these, in Salmonella enterica sv. Typhimurium, the paralog small non-coding RNAs RyhB-1 and RyhB-2 play an important role in iron homeostasis. In addition, in the present work, we show that RyhB-1 and RyhB-2 also participate in the response to hydrogen peroxide (H2O2). Deletion of RyhB-1 and/or RyhB-2 resulted in increased levels of intracellular reactive oxygen species, protein carbonylation and an altered NADH/NAD(+) ratio. Analyses of the transcriptional profiles of ryhB-1 and ryhB-2 by northern blot and qRT-PCR showed that they are induced in response to H2O2 in an OxyR-dependent manner. By using lacZ-fusions and electrophoretic mobility shift assays, we confirmed the requirement of OxyR for inducing expression of both ryhB-1 and ryhB-2. Taken together, our results support a model in which, in response to peroxide treatment, ryhB-1 and ryhB-2 are upregulated by OxyR through direct interaction with their promoter region.
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Affiliation(s)
- Iván L Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Eduardo H Morales
- Great Lakes Bioenergy Research Center and Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bernardo Collao
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Paulina F Calderón
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Catalina A Chahuán
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Lillian G Acuña
- Laboratorio de Ecofisiología Microbiana, Fundación Ciencia & Vida, Santiago, Chile.
| | - Fernando Gil
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
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46
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Ferric uptake regulator-dependent antinitrosative defenses in Salmonella enterica serovar Typhimurium pathogenesis. Infect Immun 2013; 82:333-40. [PMID: 24166960 DOI: 10.1128/iai.01201-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Herein we report an important role for the ferric uptake regulator (Fur) in the resistance of Salmonella enterica serovar Typhimurium to the reactive nitrogen species produced by inducible nitric oxide (NO) synthase in an NRAMP1(r) murine model of acute systemic infection. The expression of fur protected Salmonella grown under normoxic and hypoxic conditions against the bacteriostatic activity of NO. The hypersusceptibility of fur-deficient Salmonella to the cytotoxic actions of NO coincides with a marked repression of respiratory activity and the reduced ability of the bacteria to detoxify NO. A fur mutant Salmonella strain contained reduced levels of the terminal quinol oxidases of the electron transport chain. Addition of the heme precursor δ-aminolevulinic acid restored the cytochrome content, respiratory activity, NO consumption, and wild-type growth in bacteria undergoing nitrosative stress. The innate antinitrosative defenses regulated by Fur added to the adaptive response associated with the NO-detoxifying activity of the flavohemoprotein Hmp. Our investigations indicate that, in addition to playing a critical role in iron homeostasis, Fur is an important antinitrosative determinant of Salmonella pathogenesis.
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47
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Yang XW, He Y, Xu J, Xiao X, Wang FP. The regulatory role of ferric uptake regulator (Fur) during anaerobic respiration of Shewanella piezotolerans WP3. PLoS One 2013; 8:e75588. [PMID: 24124499 PMCID: PMC3790847 DOI: 10.1371/journal.pone.0075588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/16/2013] [Indexed: 12/02/2022] Open
Abstract
Ferric uptake regulator (Fur) is a global regulator that controls bacterial iron homeostasis. In this study, a fur deletion mutant of the deep-sea bacterium Shewanella piezotolerans WP3 was constructed. Physiological studies revealed that the growth rate of this mutant under aerobic conditions was only slightly lower than that of wild type (WT), but severe growth defects were observed under anaerobic conditions when different electron acceptors (EAs) were provided. Comparative transcriptomic analysis demonstrated that Fur is involved not only in classical iron homeostasis but also in anaerobic respiration. Fur exerted pleiotropic effects on the regulation of anaerobic respiration by controlling anaerobic electron transport, the heme biosynthesis system, and the cytochrome c maturation system. Biochemical assays demonstrated that levels of c-type cytochromes were lower in the fur mutant, consistent with the transcriptional profiling. Transcriptomic analysis and electrophoretic mobility shift assays revealed a primary regulation network for Fur in WP3. These results suggest that Fur may act as a sensor for anoxic conditions to trigger and influence the anaerobic respiratory system.
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Affiliation(s)
- Xin-Wei Yang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Ying He
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Jiao Tong University, Shanghai, PR China
- * E-mail:
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48
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Troxell B, Hassan HM. Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria. Front Cell Infect Microbiol 2013; 3:59. [PMID: 24106689 PMCID: PMC3788343 DOI: 10.3389/fcimb.2013.00059] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/16/2022] Open
Abstract
In the ancient anaerobic environment, ferrous iron (Fe2+) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe3+) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe3+, bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe3+. However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe2+ as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.
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Affiliation(s)
- Bryan Troxell
- Department of Immunology and Microbiology, Indiana University School of Medicine Indianapolis, IN, USA
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da Silva Neto JF, Lourenço RF, Marques MV. Global transcriptional response of Caulobacter crescentus to iron availability. BMC Genomics 2013; 14:549. [PMID: 23941329 PMCID: PMC3751524 DOI: 10.1186/1471-2164-14-549] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 08/09/2013] [Indexed: 01/22/2023] Open
Abstract
Background In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. Results In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility. Conclusions Using a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms.
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Affiliation(s)
- José F da Silva Neto
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av Prof Lineu Prestes 1374, 05508-000 São Paulo, Brazil.
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Wallrodt I, Jelsbak L, Thorndahl L, Thomsen LE, Lemire S, Olsen JE. The putative thiosulfate sulfurtransferases PspE and GlpE contribute to virulence of Salmonella Typhimurium in the mouse model of systemic disease. PLoS One 2013; 8:e70829. [PMID: 23940650 PMCID: PMC3733917 DOI: 10.1371/journal.pone.0070829] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/22/2013] [Indexed: 11/30/2022] Open
Abstract
The phage-shock protein PspE and GlpE of the glycerol 3-phosphate regulon of Salmonella enterica serovar Typhimurium are predicted to belong to the class of thiosulfate sulfurtransferases, enzymes that traffic sulfur between molecules. In the present study we demonstrated that the two genes contribute to S. Typhimurium virulence, as a glpE and pspE double deletion strain showed significantly decreased virulence in a mouse model of systemic infection. However, challenge of cultured epithelial cells and macrophages did not reveal any virulence-associated phenotypes. We hypothesized that their contribution to virulence could be in sulfur metabolism or by contributing to resistance to nitric oxide, oxidative stress, or cyanide detoxification. In vitro studies demonstrated that glpE but not pspE was important for resistance to H2O2. Since the double mutant, which was the one affected in virulence, was not affected in this assay, we concluded that resistance to oxidative stress and the virulence phenotype was most likely not linked. The two genes did not contribute to nitric oxid stress, to synthesis of essential sulfur containing amino acids, nor to detoxification of cyanide. Currently, the precise mechanism by which they contribute to virulence remains elusive.
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Affiliation(s)
- Inke Wallrodt
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lotte Jelsbak
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lotte Thorndahl
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line E. Thomsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sebastien Lemire
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - John E. Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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