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Zhong X, Liu F, Liang T, Lu R, Shi M, Zhou X, Yang M. The two-component system TtrRS boosts Vibrio parahaemolyticus colonization by exploiting sulfur compounds in host gut. PLoS Pathog 2024; 20:e1012410. [PMID: 39038066 DOI: 10.1371/journal.ppat.1012410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024] Open
Abstract
One of the greatest challenges encountered by enteric pathogens is responding to rapid changes of nutrient availability in host. However, the mechanisms by which pathogens sense gastrointestinal signals and exploit available host nutrients for proliferation remain largely unknown. Here, we identified a two-component system in Vibrio parahaemolyticus, TtrRS, which senses environmental tetrathionate and subsequently activates the transcription of the ttrRS-ttrBCA-tsdBA gene cluster to promote V. parahaemolyticus colonization of adult mice. We demonstrated that TsdBA confers the ability of thiosulfate oxidation to produce tetrathionate which is sensed by TtrRS. TtrRS autoregulates and directly activates the transcription of the ttrBCA and tsdBA gene clusters. Activated TtrBCA promotes bacterial growth under micro-aerobic conditions by inducing the reduction of both tetrathionate and thiosulfate. TtrBCA and TsdBA activation by TtrRS is important for V. parahaemolyticus to colonize adult mice. Therefore, TtrRS and their target genes constitute a tetrathionate-responsive genetic circuit to exploit the host available sulfur compounds, which further contributes to the intestinal colonization of V. parahaemolyticus.
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Affiliation(s)
- Xiaojun Zhong
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Fuwen Liu
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Tianqi Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Ranran Lu
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Mengting Shi
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Xiujuan Zhou
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
| | - Menghua Yang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Hangzhou, China
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Sutar AA, Dashpute RS, Shinde YD, Mukherjee S, Chowdhury C. A Systemic Review on Fitness and Survival of Salmonella in Dynamic Environment and Conceivable Ways of Its Mitigation. Indian J Microbiol 2024; 64:267-286. [PMID: 39011015 PMCID: PMC11246371 DOI: 10.1007/s12088-023-01176-4] [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: 06/01/2023] [Accepted: 12/05/2023] [Indexed: 07/17/2024] Open
Abstract
Gastroenteritis caused by non-typhoidal Salmonella still prevails resulting in several recent outbreaks affecting many people worldwide. The presence of invasive non-typhoidal Salmonella is exemplified by several characteristic symptoms and their severity relies on prominent risk factors. The persistence of this pathogen can be attributed to its broad host range, complex pathogenicity and virulence and adeptness in survival under challenging conditions inside the host. Moreover, a peculiar aid of the ever-changing climatic conditions grants this organism with remarkable potential to survive within the environment. Abusive use of antibiotics for the treatment of gastroenteritis has led to the emergence of multiple drug resistance, making the infections difficult to treat. This review emphasizes the importance of early detection of Salmonella, along with strategies for accomplishing it, as well as exploring alternative treatment approaches. The exceptional characteristics exhibited by Salmonella, like strategies of infection, persistence, and survival parallelly with multiple drug resistance, make this pathogen a prominent concern to human health.
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Affiliation(s)
- Ajit A Sutar
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Rohit S Dashpute
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Yashodhara D Shinde
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
| | - Srestha Mukherjee
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
| | - Chiranjit Chowdhury
- Biochemical Sciences Division, CSIR- National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MH 411008 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Hernández Villamizar S, Chica Cárdenas LA, Morales Mancera LT, Vives Florez MJ. Anaerobiosis, a neglected factor in phage-bacteria interactions. Appl Environ Microbiol 2023; 89:e0149123. [PMID: 37966212 PMCID: PMC10734468 DOI: 10.1128/aem.01491-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Many parameters affect phage-bacteria interaction. Some of these parameters depend on the environment in which the bacteria are present. Anaerobiosis effect on phage infection in facultative anaerobic bacteria has not yet been studied. The absence of oxygen triggers metabolic changes in facultative bacteria and this affects phage infection and viral life cycle. Understanding how an anaerobic environment can alter the behavior of phages during infection is relevant for the phage therapy success.
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Wang XG, Zou ZP, Du Y, Ye BC, Zhou Y. Construction of an Engineered Escherichia coli with Efficient Chemotactic and Metabolizing Ability toward Tetrathionate. ACS Synth Biol 2023; 12:3414-3423. [PMID: 37939253 DOI: 10.1021/acssynbio.3c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The emergence of genetically engineered bacteria has provided a new means for the diagnosis and treatment of diseases. However, in vivo applications of these engineered bacteria are hindered by their inefficient accumulation in areas of inflammation. In this study, we constructed an engineered Escherichia coli (E. coli) for directional migration toward tetrathionate (a biomarker of gut inflammation), which is regulated by the TtrSR two-component system (TCS) from Shewanella baltica OS195 (S. baltica). Specifically, we removed endogenous cheZ to control the motility of E. coli. Moreover, we introduced the reductase gene cluster (ttrBCA) from Salmonella enterica serotype typhimurium (S. typhimurium), a major pathogen causing gut inflammation, into E. coli to metabolize tetrathionate. The resulting strain was tested for its motility along the gradients of tetrathionate; the engineered strain exhibits tropism to tetrathionate compared with the original strain. Furthermore, the engineered E. coli could only restore its smooth swimming ability when tetrathionate existed. With these modifications enabling tetrathionate-mediated chemotactic and metabolizing activity, this strategy with therapeutic elements will provide a great potential opportunity for target treatment of various diseases by swapping the corresponding genetic circuits.
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Affiliation(s)
- Xin-Ge Wang
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Zhen-Ping Zou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Yue Du
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Ying Zhou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
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Nava-Galeana J, Núñez C, Bustamante VH. Proteomic analysis reveals the global effect of the BarA/SirA-Csr regulatory cascade in Salmonella Typhimurium grown in conditions that favor the expression of invasion genes. J Proteomics 2023; 286:104960. [PMID: 37451358 DOI: 10.1016/j.jprot.2023.104960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
In many bacteria, the BarA/SirA and Csr regulatory systems control expression of genes encoding a wide variety of cellular functions. The BarA/SirA two-component system induces the expression of CsrB and CsrC, two small non-coding RNAs that sequester CsrA, a protein that binds to target mRNAs and thus negatively or positively regulates their expression. BarA/SirA and CsrB/C induce expression of the Salmonella Pathogenicity Island 1 (SPI-1) genes required for Salmonella invasion of host cells. To further investigate the regulatory role of the BarA/SirA and Csr systems in Salmonella, we performed LC-MS/MS proteomic analysis using the WT S. Typhimurium strain and its derived ΔsirA and ΔcsrB ΔcsrC mutants grown in SPI-1-inducing conditions. The expression of 164 proteins with a wide diversity, or unknown, functions was significantly affected positively or negatively by the absence of SirA and/or CsrB/C. Interestingly, 19 proteins were identified as new targets for SirA-CsrB/C. Our results support that SirA and CsrB/C act in a cascade fashion to regulate gene expression in S. Typhimurium in the conditions tested. Notably, our results show that SirA-CsrB/C-CsrA controls expression of proteins required for the replication of Salmonella in the intestinal lumen, in an opposite way to its control exerted on the SPI-1 proteins. SIGNIFICANCE: The BarA/SirA and Csr global regulatory systems control a wide range of cellular processes, including the expression of virulence genes. For instance, in Salmonella, BarA/SirA and CsrB/C positively regulate expression of the SPI-1 genes, which are required for Salmonella invasion to host cells. In this study, by performing a proteomic analysis, we identified 164 proteins whose expression was positively or negatively controlled by SirA and CsrB/C in SPI-1-inducing conditions, including 19 new possible targets of these systems. Our results support the action of SirA and CsrB/C in a cascade fashion to control different cellular processes in Salmonella. Interestingly, our data indicate that SirA-CsrB/C-CsrA controls inversely the expression of proteins required for invasion of the intestinal epithelium and for replication in the intestinal lumen, which suggests a role for this regulatory cascade as a molecular switch for Salmonella virulence. Thus, our study further expands the insight into the regulatory mechanisms governing the virulence and physiology of an important pathogen.
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Affiliation(s)
- Jessica Nava-Galeana
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
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Nava-Galeana J, Yakhnin H, Babitzke P, Bustamante VH. CsrA Positively and Directly Regulates the Expression of the pdu, pocR, and eut Genes Required for the Luminal Replication of Salmonella Typhimurium. Microbiol Spectr 2023; 11:e0151623. [PMID: 37358421 PMCID: PMC10433801 DOI: 10.1128/spectrum.01516-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/26/2023] [Indexed: 06/27/2023] Open
Abstract
Enteric pathogens, such as Salmonella, have evolved to thrive in the inflamed gut. Genes located within the Salmonella pathogenicity island 1 (SPI-1) mediate the invasion of cells from the intestinal epithelium and the induction of an intestinal inflammatory response. Alternative electron acceptors become available in the inflamed gut and are utilized by Salmonella for luminal replication through the metabolism of propanediol and ethanolamine, using the enzymes encoded by the pdu and eut genes. The RNA-binding protein CsrA inhibits the expression of HilD, which is the central transcriptional regulator of the SPI-1 genes. Previous studies suggest that CsrA also regulates the expression of the pdu and eut genes, but the mechanism for this regulation is unknown. In this work, we show that CsrA positively regulates the pdu genes by binding to the pocR and pduA transcripts as well as the eut genes by binding to the eutS transcript. Furthermore, our results show that the SirA-CsrB/CsrC-CsrA regulatory cascade controls the expression of the pdu and eut genes mediated by PocR or EutR, which are the positive AraC-like transcriptional regulators for the pdu and eut genes, respectively. By oppositely regulating the expression of genes for invasion and for luminal replication, the SirA-CsrB/CsrC-CsrA regulatory cascade could be involved in the generation of two Salmonella populations that cooperate for intestinal colonization and transmission. Our study provides new insight into the regulatory mechanisms that govern Salmonella virulence. IMPORTANCE The regulatory mechanisms that control the expression of virulence genes are essential for bacteria to infect hosts. Salmonella has developed diverse regulatory mechanisms to colonize the host gut. For instance, the SirA-CsrB/CsrC-CsrA regulatory cascade controls the expression of the SPI-1 genes, which are required for this bacterium to invade intestinal epithelium cells and for the induction of an intestinal inflammatory response. In this study, we determine the mechanisms by which the SirA-CsrB/CsrC-CsrA regulatory cascade controls the expression of the pdu and eut genes, which are necessary for the replication of Salmonella in the intestinal lumen. Thus, our data, together with the results of previous reports, indicate that the SirA-CsrB/CsrC-CsrA regulatory cascade has an important role in the intestinal colonization by Salmonella.
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Affiliation(s)
- Jessica Nava-Galeana
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Víctor H. Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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7
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Alegbeleye O, Sant'Ana AS. Survival of Salmonella spp. under varying temperature and soil conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 884:163744. [PMID: 37142008 DOI: 10.1016/j.scitotenv.2023.163744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023]
Abstract
Soils can serve as suitable reservoirs for or barriers against microbial contamination of water resources and plant produce. The magnitude of water or food contamination risks through soil depends on several factors, including the survival potential of microorganisms in the soil. This study assessed and compared the survival/persistence of 14 Salmonella spp. strains in loam and sandy soils at 5, 10, 20, 25, 30, 35, 37 °C and under uncontrolled ambient temperature conditions in Campinas Sao Paulo. The ambient temperature ranged from 6 °C (minimum) to 36 °C (maximum). Bacterial population densities were determined by the conventional culture method (plate counts) and monitored for 216 days. Statistical differences among the test parameters were determined by Analysis of Variance, while relationships between temperature and soil type were evaluated using Pearson correlation analysis. Similarly, relationships between time and temperature for survival of the various strains were evaluated using Pearson correlation analysis. Results obtained indicate that temperature and soil type influence the survival of Salmonella spp. in soils. All 14 strains survived for up to 216 days in the organic-rich loam soil under at least three of the temperature conditions evaluated. However, comparatively lower survival rates were recorded in sandy soil, especially at lower temperature. The optimum temperature for survival varied among the strains, where some survived best at 5 °C and others between 30 and 37 °C. Under uncontrolled temperature conditions, the Salmonella strains survived better in loam than in sandy soils. Bacterial growth over post inoculation storage period was overall more impressive in loam soil. In general, the results indicate that temperature and soil type can interact to influence the survival of Salmonella spp. strains in soil. For the survival of some strains, there were significant correlations between soil type and temperature, while for some others, no significant relationship between soil and temperature was determined. A similar trend was observed for the correlation between time and temperature.
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Affiliation(s)
- Oluwadara Alegbeleye
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
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Cabrera JM, Saraiva MMS, Rodrigues Alves LB, Monte DFM, Vasconcelos RO, Freitas Neto OC, Berchieri Junior A. Salmonella enterica serovars in absence of ttrA and pduA genes enhance the cell immune response during chick infections. Sci Rep 2023; 13:595. [PMID: 36631563 PMCID: PMC9834210 DOI: 10.1038/s41598-023-27741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Salmonella spp. is one of the major foodborne pathogens responsible for causing economic losses to the poultry industry and bringing consequences for public health as well. Both the pathogen survival ability in the intestinal environment during inflammation as well as their relationship with the host immune system, play a key role during infections in poultry. The objective of this study was to quantify the presence of the macrophages and CD4+/CD8+ cells populations using the immunohistochemistry technique, in commercial lineages of chickens experimentally infected by wild-type and mutant strains of Salmonella Enteritidis and Salmonella Typhimurium lacking ttrA and pduA genes. Salmonella Enteritidis ∆ttrA∆pduA triggered a higher percentage of the stained area than the wild-type, with exception of light laying hens. Salmonella Typhimurium wild-type strain and Salmonella Typhimurium ∆ttrA∆pduA infections lead to a similar pattern in which, at 1 and 14 dpi, the caecal tonsils and ileum of birds showed a more expressive stained area compared to 3 and 7 dpi. In all lineages studied, prominent infiltration of macrophages in comparison with CD4+ and CD8+ cells was observed. Overall, animals infected by the mutant strain displayed a positively stained area higher than the wild-type. Deletions in both ttrA and pduA genes resulted in a more intense infiltration of macrophages and CD4+ and CD8+ cells in the host birds, suggesting no pathogen attenuation, even in different strains of Salmonella.
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Affiliation(s)
- Julia M. Cabrera
- grid.410543.70000 0001 2188 478XSao Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900 Brazil
| | - Mauro M. S. Saraiva
- grid.410543.70000 0001 2188 478XSao Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900 Brazil ,grid.5254.60000 0001 0674 042XDepartment of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Frederiksberg, Denmark
| | - Lucas B. Rodrigues Alves
- grid.410543.70000 0001 2188 478XSao Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900 Brazil
| | - Daniel F. M. Monte
- grid.410543.70000 0001 2188 478XSao Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900 Brazil
| | - Rosemeri O. Vasconcelos
- grid.410543.70000 0001 2188 478XSao Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900 Brazil
| | - Oliveiro C. Freitas Neto
- grid.8430.f0000 0001 2181 4888Federal University of Minas Gerais (UFMG), Veterinary School, Belo Horizonte, MG 31270-901 Brazil
| | - Angelo Berchieri Junior
- grid.410543.70000 0001 2188 478XSao Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900 Brazil
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Boulanger EF, Sabag-Daigle A, Baniasad M, Kokkinias K, Schwieters A, Wrighton KC, Wysocki VH, Ahmer BMM. Sugar-Phosphate Toxicities Attenuate Salmonella Fitness in the Gut. J Bacteriol 2022; 204:e0034422. [PMID: 36383008 PMCID: PMC9765134 DOI: 10.1128/jb.00344-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
Pathogens are becoming resistant to antimicrobials at an increasing rate, and novel therapeutic strategies are needed. Using Salmonella as a model, we have investigated the induction of sugar-phosphate toxicity as a potential therapeutic modality. The approach entails providing a nutrient while blocking the catabolism of that nutrient, resulting in the accumulation of a toxic intermediate. We hypothesize that this build-up will decrease the fitness of the organism during infection given nutrient availability. We tested this hypothesis using mutants lacking one of seven genes whose mutation is expected to cause the accumulation of a toxic metabolic intermediate. The araD, galE, rhaD, glpD, mtlD, manA, and galT mutants were then provided the appropriate sugars, either in vitro or during gastrointestinal infection of mice. All but the glpD mutant had nutrient-dependent growth defects in vitro, suggestive of sugar-phosphate toxicity. During gastrointestinal infection of mice, five mutants had decreased fitness. Providing the appropriate nutrient in the animal's drinking water was required to cause fitness defects with the rhaD and manA mutants and to enhance the fitness defect of the araD mutant. The galE and mtlD mutants were severely attenuated regardless of the nutrient being provided in the drinking water. Homologs of galE are widespread among bacteria and in humans, rendering the specific targeting of bacterial pathogens difficult. However, the araD, mtlD, and rhaD genes are not present in humans, appear to be rare in most phyla of bacteria, and are common in several genera of Enterobacteriaceae, making the encoded enzymes potential narrow-spectrum therapeutic targets. IMPORTANCE Bacterial pathogens are becoming increasingly resistant to antibiotics. There is an urgent need to identify novel drug targets and therapeutic strategies. In this work we have assembled and characterized a collection of mutations in our model pathogen, Salmonella enterica, that block a variety of sugar utilization pathways in such a way as to cause the accumulation of a toxic sugar-phosphate. Mutations in three genes, rhaD, araD, and mtlD, dramatically decrease the fitness of Salmonella in a mouse model of gastroenteritis, suggesting that RhaD, AraD, and MtlD may be good narrow-spectrum drug targets. The induction of sugar-phosphate toxicities may be a therapeutic strategy that is broadly relevant to other bacterial and fungal pathogens.
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Affiliation(s)
- Erin F. Boulanger
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Maryam Baniasad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Katherine Kokkinias
- Department of Soil and Crop Science, Colorado State University, Ft. Collins, Colorado, USA
| | - Andrew Schwieters
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C. Wrighton
- Department of Soil and Crop Science, Colorado State University, Ft. Collins, Colorado, USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Brian M. M. Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
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10
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Cohn AR, Orsi RH, Carroll LM, Liao J, Wiedmann M, Cheng RA. Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle. Front Microbiol 2022; 13:1005215. [PMID: 36532462 PMCID: PMC9748477 DOI: 10.3389/fmicb.2022.1005215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023] Open
Abstract
Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro's infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.
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Affiliation(s)
- Alexa R. Cohn
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Renato H. Orsi
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Laura M. Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Rachel A. Cheng
- Department of Food Science, Cornell University, Ithaca, NY, United States
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11
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Adsit FG, Randall TA, Locklear J, Kurtz DM. The emergence of the tetrathionate reductase operon in the Escherichia coli/Shigella pan-genome. Microbiologyopen 2022; 11:e1333. [PMID: 36479628 PMCID: PMC9638481 DOI: 10.1002/mbo3.1333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Escherichia coli pathogenic variants (pathovars) are generally characterized by defined virulence traits and are susceptible to the evolution of hybridized identities due to the considerable plasticity of the E. coli genome. We have isolated a strain from a purified diet intended for research animals that further demonstrates the ability of E. coli to acquire novel genetic elements leading potentially to emergent new pathovars. Utilizing next generation sequencing to obtain a whole genome profile, we report an atypical strain of E. coli, EcoFA807-17, possessing a tetrathionate reductase (ttr) operon, which enables the utilization of tetrathionate as an electron acceptor, thus facilitating respiration in anaerobic environments such as the mammalian gut. The ttr operon is a potent virulence factor for several enteric pathogens, most prominently Salmonella enterica. However, the presence of chromosomally integrated tetrathionate reductase genes does not appear to have been previously reported in wild-type E. coli or Shigella. Accordingly, it is possible that the appearance of this virulence factor may signal the evolution of new mechanisms of pathogenicity in E. coli and Shigella and may potentially alter the effectiveness of existing assays using tetrathionate reductase as a unique marker for the detection of Salmonella enterica.
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Affiliation(s)
- Floyd G. Adsit
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Thomas A. Randall
- Integrative BioinformaticsNational Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Jacqueline Locklear
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - David M. Kurtz
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
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12
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Costa FG, Escalante-Semerena JC. Localization and interaction studies of the Salmonella enterica ethanolamine ammonia-lyase (EutBC), its reactivase (EutA), and the EutT corrinoid adenosyltransferase. Mol Microbiol 2022; 118:191-207. [PMID: 35785499 PMCID: PMC9481676 DOI: 10.1111/mmi.14962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Abstract
Some prokaryotes compartmentalize select metabolic capabilities. Salmonella enterica subspecies enterica serovar Typhimurium LT2 (hereafter S. Typhimurium) catabolizes ethanolamine (EA) within a proteinaceous compartment that we refer to as the ethanolamine utilization (Eut) metabolosome. EA catabolism is initiated by the adenosylcobalamin (AdoCbl)-dependent ethanolamine ammonia-lyase (EAL), which deaminates EA via an adenosyl radical mechanism to yield acetaldehyde plus ammonia. This adenosyl radical can be quenched, requiring the replacement of AdoCbl by the ATP-dependent EutA reactivase. During growth on ethanolamine, S. Typhimurium synthesizes AdoCbl from cobalamin (Cbl) using the ATP:Co(I)rrinoid adenosyltransferase (ACAT) EutT. It is known that EAL localizes to the metabolosome, however, prior to this work, it was unclear where EutA and EutT localized, and whether they interacted with EAL. Here, we provide evidence that EAL, EutA, and EutT localize to the Eut metabolosome, and that EutA interacts directly with EAL. We did not observe interactions between EutT and EAL nor between EutT and the EutA/EAL complex. However, growth phenotypes of a ΔeutT mutant strain show that EutT is critical for efficient ethanolamine catabolism. This work provides a preliminary understanding of the dynamics of AdoCbl synthesis and its uses within the Eut metabolosome.
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Affiliation(s)
- Flavia G. Costa
- Department of Microbiology, University of Georgia, Athens, GA, USA 30602
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13
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Góes V, Monte DFM, Saraiva MDMS, Maria de Almeida A, Cabrera JM, Rodrigues Alves LB, Ferreira TS, Lima TSD, Benevides VP, Barrow PA, Freitas Neto OCD, Berchieri A. Salmonella Heidelberg side-step gene loss of respiratory requirements in chicken infection model. Microb Pathog 2022; 171:105725. [PMID: 36007847 DOI: 10.1016/j.micpath.2022.105725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/15/2022] [Accepted: 08/14/2022] [Indexed: 11/27/2022]
Abstract
Among the important recent observations involving anaerobic respiration was that an electron acceptor produced as a result of an inflammatory response to Salmonella Typhimurium generates a growth advantage over the competing microbiota in the lumen. In this regard, anaerobically, salmonellae can oxidize thiosulphate (S2O32-) converting it into tetrathionate (S4O62-), the process by which it is encoded by ttr gene cluster (ttrSRttrBCA). Another important pathway under aerobic or anaerobic conditions is the 1,2-propanediol-utilization mediated by the pdu gene cluster that promotes Salmonella expansion during colitis. Therefore, we sought to compare in this study, whether Salmonella Heidelberg strains lacking the ttrA, ttrApduA, and ttrACBSR genes experience a disadvantage during cecal colonization in broiler chicks. In contrast to expectations, we found that the gene loss in S. Heidelberg potentially confers an increase in fitness in the chicken infection model. These data argue that S. Heidelberg may trigger an alternative pathway involving the use of an alternative electron acceptor, conferring a growth advantage for S. Heidelberg in chicks.
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Affiliation(s)
- Vinícius Góes
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel F M Monte
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil.
| | | | - Adriana Maria de Almeida
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Julia Memrava Cabrera
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Lucas Bocchini Rodrigues Alves
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Taísa Santiago Ferreira
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Tulio Spina de Lima
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Valdinete P Benevides
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Surrey, Guildford, GU2 7AL, United Kingdom
| | - Oliveiro Caetano de Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Angelo Berchieri
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil.
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14
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Abstract
Changes in the composition of the gut microbiota are associated with many human diseases. So far, however, we have failed to define homeostasis or dysbiosis by the presence or absence of specific microbial species. The composition and function of the adult gut microbiota is governed by diet and host factors that regulate and direct microbial growth. The host delivers oxygen and nitrate to the lumen of the small intestine, which selects for bacteria that use respiration for energy production. In the colon, by contrast, the host limits the availability of oxygen and nitrate, which results in a bacterial community that specializes in fermentation for growth. Although diet influences microbiota composition, a poor diet weakens host control mechanisms that regulate the microbiota. Hence, quantifying host parameters that control microbial growth could help define homeostasis or dysbiosis and could offer alternative strategies to remediate dysbiosis.
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Affiliation(s)
- Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
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15
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Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes. mSystems 2022; 7:e0035922. [PMID: 35703535 PMCID: PMC9426584 DOI: 10.1128/msystems.00359-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the ability of microbiome members to respond to changes in the environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas-related phylotypes belonging to two different species, including a novel species, “Candidatus Endozoicomonas penghunesis” 4G, whose chromosome-level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species had different potentials to scavenge reactive oxygen species, suggesting potential differences in responding to the environment. Differential capabilities of dominant members of the microbiome to respond to environmental change can (i) provide distinct advantages or disadvantages to coral hosts when subjected to changing environmental conditions and (ii) have positive or negative implications for future reefs. IMPORTANCE The coral microbiome has been known to play a crucial role in host health. In recent years, we have known that the coral microbiome changes in response to external stressors and that coral hosts structure their microbiome in a host-specific manner. However, an important internal factor, the ability of microbiome members to respond to change, has been often neglected. In this study, we combine metabarcoding, culturing, and genomics to delineate the differential ability of two dominant Endozoicomonas species, including a novel “Ca. Endozoicomonas penghunesis” 4G, to respond to change in the environment following a reciprocal transplant experiment.
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16
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Yang M, Wenner N, Dykes GF, Li Y, Zhu X, Sun Y, Huang F, Hinton JCD, Liu LN. Biogenesis of a bacterial metabolosome for propanediol utilization. Nat Commun 2022; 13:2920. [PMID: 35614058 PMCID: PMC9132943 DOI: 10.1038/s41467-022-30608-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial metabolosomes are a family of protein organelles in bacteria. Elucidating how thousands of proteins self-assemble to form functional metabolosomes is essential for understanding their significance in cellular metabolism and pathogenesis. Here we investigate the de novo biogenesis of propanediol-utilization (Pdu) metabolosomes and characterize the roles of the key constituents in generation and intracellular positioning of functional metabolosomes. Our results demonstrate that the Pdu metabolosome undertakes both "Shell first" and "Cargo first" assembly pathways, unlike the β-carboxysome structural analog which only involves the "Cargo first" strategy. Shell and cargo assemblies occur independently at the cell poles. The internal cargo core is formed through the ordered assembly of multiple enzyme complexes, and exhibits liquid-like properties within the metabolosome architecture. Our findings provide mechanistic insight into the molecular principles driving bacterial metabolosome assembly and expand our understanding of liquid-like organelle biogenesis.
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Affiliation(s)
- Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Yan Li
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Xiaojun Zhu
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.
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17
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Microbial Diversity and Sulfur Cycling in an Early Earth Analogue: From Ancient Novelty to Modern Commonality. mBio 2022; 13:e0001622. [PMID: 35258328 PMCID: PMC9040765 DOI: 10.1128/mbio.00016-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Life emerged and diversified in the absence of molecular oxygen. The prevailing anoxia and unique sulfur chemistry in the Paleo-, Meso-, and Neoarchean and early Proterozoic eras may have supported microbial communities that differ from those currently thriving on the earth’s surface. Zodletone spring in southwestern Oklahoma represents a unique habitat where spatial sampling could substitute for geological eras namely, from the anoxic, surficial light-exposed sediments simulating a preoxygenated earth to overlaid water column where air exposure simulates oxygen intrusion during the Neoproterozoic era. We document a remarkably diverse microbial community in the anoxic spring sediments, with 340/516 (65.89%) of genomes recovered in a metagenomic survey belonging to 200 bacterial and archaeal families that were either previously undescribed or that exhibit an extremely rare distribution on the current earth. Such diversity is underpinned by the widespread occurrence of sulfite, thiosulfate, tetrathionate, and sulfur reduction and the paucity of sulfate reduction machineries in these taxa. Hence, these processes greatly expand lineages mediating reductive sulfur-cycling processes in the tree of life. An analysis of the overlaying oxygenated water community demonstrated the development of a significantly less diverse community dominated by well-characterized lineages and a prevalence of oxidative sulfur-cycling processes. Such a transition from ancient novelty to modern commonality underscores the profound impact of the great oxygenation event on the earth’s surficial anoxic community. It also suggests that novel and rare lineages encountered in current anaerobic habitats could represent taxa that once thrived in an anoxic earth but have failed to adapt to earth’s progressive oxygenation.
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18
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Chen K, Liu Y, Li M, Liu L, Yu Q, Wu L. Amelioration of enteric dysbiosis by polyoxotungstates in mice gut. J Inorg Biochem 2021; 226:111654. [PMID: 34740036 DOI: 10.1016/j.jinorgbio.2021.111654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 12/15/2022]
Abstract
Here we show that Preyssler-type polyoxotungstates (Preyssler-type POTs, [NaP5W30O110]-14) complexed with peptides can prevent the dysbiotic expansion of anaerobic bacteria of the Enterobacteriaceae family. In a dextran sulfate sodium (DSS)-induced colitis model, symptom remission of C57BL/6 J mice with colitis is achieved by orally treated with POT complexes. Ten days of daily administration of POT complexes reduces 5% body weight loss and the mRNA levels of proinflammatory markers (77% reduction for Il6, 73% reduction for Tnf, 91% reduction for Cxcl1) in the caecum and proximal colon. Bacterial population analysis reveals that these Enterobacteriaceae population in the caecal content decline by one order of magnitude after administration of POT complexes. POT complexes exert anti-inflammatory effects indirectly on the host immune system by inhibition of malignant expansion of anaerobic Enterobacteriaceae during gut inflammation. Furthermore, POTs show negligible effect on bacterial growth in vitro, healthy mice and their microbiota composition under homeostatic conditions. Rationally designed POT complexes will provide distinctive approach to improve enteric bacteria dysbiosis-associated gut inflammation by balancing bacterial communities.
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Affiliation(s)
- Kun Chen
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China.
| | - Yuan Liu
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Mu Li
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Lu Liu
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Qiang Yu
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Long Wu
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou, Hainan, 570228, China.
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19
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Cohn AR, Orsi RH, Carroll LM, Chen R, Wiedmann M, Cheng RA. Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars. Front Microbiol 2021; 12:730411. [PMID: 34721328 PMCID: PMC8552914 DOI: 10.3389/fmicb.2021.730411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 01/18/2023] Open
Abstract
The zoonotic pathogen Salmonella enterica includes >2,600 serovars, which differ in the range of hosts they infect and the severity of disease they cause. To further elucidate the mechanisms behind these differences, we performed transcriptomic comparisons of nontyphoidal Salmonella (NTS) serovars with the model for NTS pathogenesis, S. Typhimurium. Specifically, we used RNA-seq to characterize the understudied NTS serovars S. Javiana and S. Cerro, representing a serovar frequently attributed to human infection via contact with amphibians and reptiles, and a serovar primarily associated with cattle, respectively. Whole-genome sequence (WGS) data were utilized to ensure that strains characterized with RNA-seq were representative of their respective serovars. RNA extracted from representative strains of each serovar grown to late exponential phase in Luria-Bertani (LB) broth showed that transcript abundances of core genes were significantly higher (p<0.001) than those of accessory genes for all three serovars. Inter-serovar comparisons identified that transcript abundances of genes in Salmonella Pathogenicity Island (SPI) 1 were significantly higher in both S. Javiana and S. Typhimurium compared to S. Cerro. Together, our data highlight potential transcriptional mechanisms that may facilitate S. Cerro and S. Javiana survival in and adaptation to their respective hosts and impact their ability to cause disease in others. Furthermore, our analyses demonstrate the utility of omics approaches in advancing our understanding of the diversity of metabolic and virulence mechanisms of different NTS serovars.
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Affiliation(s)
- Alexa R Cohn
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Laura M Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ruixi Chen
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY, United States
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20
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Prentice MB. Bacterial microcompartments and their role in pathogenicity. Curr Opin Microbiol 2021; 63:19-28. [PMID: 34107380 DOI: 10.1016/j.mib.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/26/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
Catabolic bacterial microcompartments (BMC), or metabolosomes, are self-assembling structures formed by enzymes enclosed by porous protein shells. They provide a specialised environment inside bacterial cells separating a short catabolic pathway with reactive or toxic intermediates from the cytoplasm. Substrates for microcompartment metabolism like ethanolamine and 1,2-propanediol are constantly produced in the human intestine by bacterial metabolism of food or host cell components. Enteric pathogens gain a competitive advantage in the intestine by metabolising these substrates, an advantage enhanced by the host inflammatory response. They exploit the intestinal specificity of signature metabolosome substrates by adopting substrate sensors and regulators encoded by BMC operons for governance of non-metabolic processes in pathogenesis. In turn, products of microcompartment metabolism regulate the host immune system.
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Affiliation(s)
- Michael B Prentice
- Department of Pathology, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland.
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21
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Hughes ER, Winter MG, Alves da Silva L, Muramatsu MK, Jimenez AG, Gillis CC, Spiga L, Chanin RB, Santos RL, Zhu W, Winter SE. Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation. eLife 2021; 10:e58609. [PMID: 34085924 PMCID: PMC8177889 DOI: 10.7554/elife.58609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.
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Affiliation(s)
| | - Maria G Winter
- Department of Microbiology, UT SouthwesternDallasUnited States
| | - Laice Alves da Silva
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Angel G Jimenez
- Department of Microbiology, UT SouthwesternDallasUnited States
| | | | - Luisella Spiga
- Department of Microbiology, UT SouthwesternDallasUnited States
| | | | - Renato L Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Wenhan Zhu
- Department of Microbiology, UT SouthwesternDallasUnited States
| | - Sebastian E Winter
- Department of Microbiology, UT SouthwesternDallasUnited States
- Department of Immunology, UT SouthwesternDallasUnited States
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22
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Pokhrel A, Kang SY, Schmidt-Dannert C. Ethanolamine bacterial microcompartments: from structure, function studies to bioengineering applications. Curr Opin Microbiol 2021; 62:28-37. [PMID: 34034083 DOI: 10.1016/j.mib.2021.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022]
Abstract
Two decades of structural and functional studies have revealed functions, structures and diversity of bacterial microcompartments. The protein-based organelles encapsulate diverse metabolic pathways in semipermeable, icosahedral or pseudo-icosahedral shells. One of the first discovered and characterized microcompartments are those involved in ethanolamine degradation. This review will summarize their function and assembly along with shared and unique characteristics with other microcompartment types. The modularity and self-assembling properties of their shell proteins make them valuable targets for bioengineering. Advances and prospects for shell protein engineering in vivo and in vitro for synthetic biology and biotechnology applications will be discussed.
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Affiliation(s)
- Anaya Pokhrel
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Sun-Young Kang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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23
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Saraiva MMS, Rodrigues Alves LB, Monte DFM, Ferreira TS, Benevides VP, Barbosa FO, Freitas Neto OC, Almeida AM, Barrow PA, Berchieri Junior A. Deciphering the role of ttrA and pduA genes for Salmonella enterica serovars in a chicken infection model. Avian Pathol 2021; 50:1-12. [PMID: 33779420 DOI: 10.1080/03079457.2021.1909703] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Salmonella enterica serovars use self-induced intestinal inflammation to increase electron acceptor availability and to obtain a growth advantage in the host gut. There is evidence suggesting that the ability of Salmonella to use tetrathionate and 1,2-propanediol provides an advantage in murine infection. Thus, we present here the first study to evaluate both systemic infection and faecal excretion in commercial poultry challenged by Salmonella Enteritidis (SE) and S. Typhimurium (STM) harbouring deletions in ttrA and pduA genes, which are crucial to the metabolism of tetrathionate and 1,2-propanediol, respectively. Mutant strains were excreted at higher rates when compared to the wild-type strains. The highest rates were observed with white egg-layer and brown egg-layer chicks (67.5%), and broiler chicks (56.7%) challenged by SEΔttrAΔpduA, and brown egg-layer chicks (64.8%) challenged by STMΔttrAΔpduA. SEΔttrAΔpduA presented higher bacterial counts in the liver and spleen of the three chicken lineages and caecal contents from the broiler chickens, whereas STMΔttrAΔpduA presented higher counts in the liver and spleen of the broiler and brown-egg chickens for 28 days post-infection (P < 0.05). The ttrA and pduA genes do not appear to be major virulence determinants in faecal excretion or invasiveness for SE and STM in chickens. RESEARCH HIGHLIGHTSttrA and pudA do not impair gut colonization or systemic infection in chicks.Mutant strains were present in higher numbers in broilers than in laying chicks.Mutants of SE and STM showed greater pathogenicity in broiler chicks than layers.
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Affiliation(s)
- M M S Saraiva
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - L B Rodrigues Alves
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - D F M Monte
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - T S Ferreira
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - V P Benevides
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - F O Barbosa
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - O C Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - A M Almeida
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - P A Barrow
- School of Veterinary Medicine and Science, University of Surrey, Guildford, UK
| | - A Berchieri Junior
- Laboratory of Avian Pathology, Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
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Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes. mSystems 2021; 6:6/2/e01349-20. [PMID: 33850044 PMCID: PMC8547011 DOI: 10.1128/msystems.01349-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ethanolamine (EA) is a valuable microbial carbon and nitrogen source derived from cell membranes. EA catabolism is suggested to occur in a cellular metabolic subsystem called a bacterial microcompartment (BMC), and the activation of EA utilization (eut) genes is linked to bacterial pathogenesis. Despite reports showing that the activation of eut is regulated by a vitamin B12-binding riboswitch and that upregulation of eut genes occurs in mice, it remains unknown whether EA catabolism is BMC dependent in Listeria monocytogenes Here, we provide evidence for BMC-dependent anaerobic EA utilization via metabolic analysis, proteomics, and electron microscopy. First, we show vitamin B12-induced activation of the eut operon in L. monocytogenes coupled to the utilization of EA, thereby enabling growth. Next, we demonstrate BMC formation connected with EA catabolism with the production of acetate and ethanol in a molar ratio of 2:1. Flux via the ATP-generating acetate branch causes an apparent redox imbalance due to the reduced regeneration of NAD+ in the ethanol branch resulting in a surplus of NADH. We hypothesize that the redox imbalance is compensated by linking eut BMCs to anaerobic flavin-based extracellular electron transfer (EET). Using L. monocytogenes wild-type, BMC mutant, and EET mutant strains, we demonstrate an interaction between BMCs and EET and provide evidence for a role of Fe3+ as an electron acceptor. Taken together, our results suggest an important role of BMC-dependent EA catabolism in L. monocytogenes growth in anaerobic environments like the human gastrointestinal tract, with a crucial role for the flavin-based EET system in redox balancing.IMPORTANCE Listeria monocytogenes is a foodborne pathogen causing severe illness, and as such, it is crucial to understand the molecular mechanisms contributing to pathogenicity. One carbon source that allows L. monocytogenes to grow in humans is ethanolamine (EA), which is derived from phospholipids present in eukaryotic cell membranes. It is hypothesized that EA utilization occurs in bacterial microcompartments (BMCs), self-assembling subcellular proteinaceous structures and analogs of eukaryotic organelles. Here, we demonstrate that BMC-driven utilization of EA in L. monocytogenes results in increased energy production essential for anaerobic growth. However, exploiting BMCs and the encapsulated metabolic pathways also requires the balancing of oxidative and reductive pathways. We now provide evidence that L. monocytogenes copes with this by linking BMC activity to flavin-based extracellular electron transfer (EET) using iron as an electron acceptor. Our results shed new light on an important molecular mechanism that enables L. monocytogenes to grow using host-derived phospholipid degradation products.
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de Pina LC, da Silva FSH, Galvão TC, Pauer H, Ferreira RBR, Antunes LCM. The role of two-component regulatory systems in environmental sensing and virulence in Salmonella. Crit Rev Microbiol 2021; 47:397-434. [PMID: 33751923 DOI: 10.1080/1040841x.2021.1895067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adaptation to environments with constant fluctuations imposes challenges that are only overcome with sophisticated strategies that allow bacteria to perceive environmental conditions and develop an appropriate response. The gastrointestinal environment is a complex ecosystem that is home to trillions of microorganisms. Termed microbiota, this microbial ensemble plays important roles in host health and provides colonization resistance against pathogens, although pathogens have evolved strategies to circumvent this barrier. Among the strategies used by bacteria to monitor their environment, one of the most important are the sensing and signalling machineries of two-component systems (TCSs), which play relevant roles in the behaviour of all bacteria. Salmonella enterica is no exception, and here we present our current understanding of how this important human pathogen uses TCSs as an integral part of its lifestyle. We describe important aspects of these systems, such as the stimuli and responses involved, the processes regulated, and their roles in virulence. We also dissect the genomic organization of histidine kinases and response regulators, as well as the input and output domains for each TCS. Lastly, we explore how these systems may be promising targets for the development of antivirulence therapeutics to combat antibiotic-resistant infections.
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Affiliation(s)
- Lucindo Cardoso de Pina
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Biociências, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil
| | | | - L Caetano M Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil.,Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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26
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Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. Infect Immun 2021; 89:IAI.00606-20. [PMID: 33361201 DOI: 10.1128/iai.00606-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/10/2020] [Indexed: 11/20/2022] Open
Abstract
The Enteritidis and Dublin serovars of Salmonella enterica are phylogenetically closely related yet differ significantly in host range and virulence. S Enteritidis is a broad-host-range serovar that commonly causes self-limited gastroenteritis in humans, whereas S Dublin is a cattle-adapted serovar that can infect humans, often resulting in invasive extraintestinal disease. The mechanism underlying the higher invasiveness of S Dublin remains undetermined. In this work, we quantitatively compared the proteomes of clinical isolates of each serovar grown under gut-mimicking conditions. Compared to S Enteritidis, the S Dublin proteome was enriched in proteins linked to response to several stress conditions, such as those encountered during host infection, as well as to virulence. The S Enteritidis proteome contained several proteins related to central anaerobic metabolism pathways that were undetected in S Dublin. In contrast to what has been observed in other extraintestinal serovars, most of the coding genes for these pathways are not degraded in S Dublin. Thus, we provide evidence that S Dublin metabolic functions may be much more affected than previously reported based on genomic studies. Single and double null mutants in stress response proteins Dps, YciF, and YgaU demonstrate their relevance to S Dublin invasiveness in a murine model of invasive salmonellosis. All in all, this work provides a basis for understanding interserovar differences in invasiveness and niche adaptation, underscoring the relevance of using proteomic approaches to complement genomic studies.
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Possible Involvement of a Tetrathionate Reductase Homolog in Dissimilatory Arsenate Reduction by Anaeromyxobacter sp. Strain PSR-1. Appl Environ Microbiol 2020; 86:AEM.00829-20. [PMID: 32978134 DOI: 10.1128/aem.00829-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/15/2020] [Indexed: 11/20/2022] Open
Abstract
Anaeromyxobacter sp. strain PSR-1, a dissimilatory arsenate [As(V)]-reducing bacterium, can utilize As(V) as a terminal electron acceptor for anaerobic respiration. A previous draft genome analysis revealed that strain PSR-1 lacks typical respiratory As(V) reductase genes (arrAB), which suggested the involvement of another protein in As(V) respiration. Dissimilatory As(V) reductase activity of strain PSR-1 was induced under As(V)-respiring conditions and was localized predominantly in the periplasmic fraction. The activity was visualized by partially denaturing gel electrophoresis, and liquid chromatography-tandem mass spectrometry analysis identified proteins involved in the active band. Among these proteins, a protein annotated as molybdopterin-dependent oxidoreductase (PSR1_00330) exhibited the highest sequence coverage, 76%. Phylogenetic analysis revealed that this protein was a homolog of tetrathionate reductase catalytic subunit TtrA. However, the crude extract of strain PSR-1 did not show significant tetrathionate reductase enzyme activity. Comparative proteomic analysis revealed that the protein PSR1_00330 and a homolog of tetrathionate reductase electron transfer subunit TtrB (PSR1_00329) were expressed abundantly and specifically under As(V)-respiring conditions, respectively. The genes encoding PSR1_00330 and PSR1_00329 formed an operon-like structure along with a gene encoding a c-type cytochrome (cyt c), and their transcription was upregulated under As(V)-respiring conditions. These results suggest that the protein PSR1_00330, which lacks tetrathionate reductase activity, functions as a dissimilatory As(V) reductase in strain PSR-1. Considering the wide distribution of TtrA homologs among bacteria and archaea, they may play a hitherto unknown role along with conventional respiratory As(V) reductase (Arr) in the biogeochemical cycling of arsenic in nature.IMPORTANCE Dissimilatory As(V)-reducing prokaryotes play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. Generally, such prokaryotes reduce As(V) by means of a respiratory As(V) reductase designated Arr. However, some dissimilatory As(V)-reducing prokaryotes such as Anaeromyxobacter sp. strain PSR-1 lack genes encoding Arr, suggesting the involvement of other protein in As(V) reduction. In this study, using multiple proteomic and transcriptional analyses, it was found that the dissimilatory As(V) reductase of strain PSR-1 was a protein closely related to the tetrathionate reductase catalytic subunit (TtrA). Tetrathionate reductase is known to play a role in anaerobic respiration of Salmonella on tetrathionate, but strain PSR-1 showed neither growth on tetrathionate nor significant tetrathionate reductase enzyme activity. These results suggest the possibility that TtrA homologs encoded in a wide variety of archaeal and bacterial genomes might function as dissimilatory As(V) reductases.
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Clarithromycin Exerts an Antibiofilm Effect against Salmonella enterica Serovar Typhimurium rdar Biofilm Formation and Transforms the Physiology towards an Apparent Oxygen-Depleted Energy and Carbon Metabolism. Infect Immun 2020; 88:IAI.00510-20. [PMID: 32839186 DOI: 10.1128/iai.00510-20] [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: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 11/20/2022] Open
Abstract
Upon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection toward various forms of environmental stresses to individual cells. Thus, bacterial cells within biofilms become tolerant against antimicrobials and the immune system. In the present study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry, and rough) biofilm formation of the gastrointestinal pathogen Salmonella enterica serovar Typhimurium ATCC 14028 (Nalr) at a 1.56 μM subinhibitory concentration in standing culture and dissolved cell aggregates at 15 μM in a microaerophilic environment, suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such as csgB and adrA to be concomitantly downregulated. Although fliA and other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifted the cells toward an apparent oxygen- and energy-depleted status, whereby the metabolism that channels into oxidative phosphorylation was downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and l-arginine catabolism, potentially also to prevent cytosolic acidification, was upregulated. This analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.
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Burin R, Shah DH. Global transcriptional profiling of tyramine and d-glucuronic acid catabolism in Salmonella. Int J Med Microbiol 2020; 310:151452. [PMID: 33091748 DOI: 10.1016/j.ijmm.2020.151452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Salmonella has evolved various metabolic pathways to scavenge energy from the metabolic byproducts of the host gut microbiota, however, the precise metabolic byproducts and pathways utilized by Salmonella remain elusive. Previously we reported that Salmonella can proliferate by deriving energy from two metabolites that naturally occur in the host as gut microbial metabolic byproducts, namely, tyramine (TYR, an aromatic amine) and d-glucuronic acid (DGA, a hexuronic acid). Salmonella Pathogenicity Island 13 (SPI-13) plays a critical role in the ability of Salmonella to derive energy from TYR and DGA, however the catabolic pathways of these two micronutrients in Salmonella are poorly defined. The objective of this study was to identify the specific genetic components and construct the regulatory circuits for the TYR and DGA catabolic pathways in Salmonella. To accomplish this, we employed TYR and DGA-induced global transcriptional profiling and gene functional network analysis approaches. We report that TYR induced differential expression of 319 genes (172 up-regulated and 157 down-regulated) when Salmonella was grown in the presence of TYR as a sole energy source. These included the genes originally predicted to be involved in the classical TYR catabolic pathway. TYR also induced expression of majority of genes involved in the acetaldehyde degradation pathway and aided identification of a few new genes that are likely involved in alternative pathway for TYR catabolism. In contrast, DGA induced differential expression of 71 genes (58 up-regulated and 13 down-regulated) when Salmonella was grown in the presence of DGA as a sole energy source. These included the genes originally predicted to be involved in the classical pathway and a few new genes likely involved in the alternative pathway for DGA catabolism. Interestingly, DGA also induced expression of SPI-2 T3SS, suggesting that DGA may also influence nutritional virulence of Salmonella. In summary, this is the first report describing the global transcriptional profiling of TYR and DGA catabolic pathways of Salmonella. This study will contribute to the better understanding of the role of TYR and DGA in metabolic adaptation and virulence of Salmonella.
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Affiliation(s)
- Raquel Burin
- Department of Veterinary Microbiology and Pathology, United States
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, United States; Paul Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, 99164-7040, United States.
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30
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Stewart KL, Stewart AM, Bobik TA. Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0025-2019. [PMID: 33030141 PMCID: PMC7552817 DOI: 10.1128/ecosalplus.esp-0025-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.
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Affiliation(s)
- Katie L. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Andrew M. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Thomas A. Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
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Abstract
The ability to detect disease early and deliver precision therapy would be transformative for the treatment of human illnesses. To achieve these goals, biosensors that can pinpoint when and where diseases emerge are needed. Rapid advances in synthetic biology are enabling us to exploit the information-processing abilities of living cells to diagnose disease and then treat it in a controlled fashion. For example, living sensors could be designed to precisely sense disease biomarkers, such as by-products of inflammation, and to respond by delivering targeted therapeutics in situ. Here, we provide an overview of ongoing efforts in microbial biosensor design, highlight translational opportunities, and discuss challenges for enabling sense-and-respond precision medicines.
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Affiliation(s)
- Maria Eugenia Inda
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Timothy K. Lu
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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32
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Chowdhury C, Bobik TA. Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella. MICROBIOLOGY-SGM 2020; 165:1355-1364. [PMID: 31674899 DOI: 10.1099/mic.0.000872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that consist of metabolic enzymes encapsulated within a protein shell. The function of MCPs is to optimize metabolic pathways by increasing reaction rates and sequestering toxic pathway intermediates. A substantial amount of effort has been directed toward engineering synthetic MCPs as intracellular nanoreactors for the improved production of renewable chemicals. A key challenge in this area is engineering protein shells that allow the entry of desired substrates. In this study, we used site-directed mutagenesis of the PduT shell protein to remove its central iron-sulfur cluster and create openings (pores) in the shell of the Pdu MCP that have varied chemical properties. Subsequently, in vivo and in vitro studies were used to show that PduT-C38S and PduT-C38A variants increased the diffusion of 1,2-propanediol, propionaldehyde, NAD+ and NADH across the shell of the MCP. In contrast, PduT-C38I and PduT-C38W eliminated the iron-sulfur cluster without altering the permeability of the Pdu MCP, suggesting that the side-chains of C38I and C38W occluded the opening formed by removal of the iron-sulfur cluster. Thus, genetic modification offers an approach to engineering the movement of larger molecules (such as NAD/H) across MCP shells, as well as a method for blocking transport through trimeric bacterial microcompartment (BMC) domain shell proteins.
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Affiliation(s)
- Chiranjit Chowdhury
- Present address: Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Campus, Sector-125, Noida, UP-201313, India.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
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Ormsby MJ, Johnson SA, Carpena N, Meikle LM, Goldstone RJ, McIntosh A, Wessel HM, Hulme HE, McConnachie CC, Connolly JPR, Roe AJ, Hasson C, Boyd J, Fitzgerald E, Gerasimidis K, Morrison D, Hold GL, Hansen R, Walker D, Smith DGE, Wall DM. Propionic Acid Promotes the Virulent Phenotype of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. Cell Rep 2020; 30:2297-2305.e5. [PMID: 32075765 PMCID: PMC7034058 DOI: 10.1016/j.celrep.2020.01.078] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 08/09/2019] [Accepted: 01/22/2020] [Indexed: 02/07/2023] Open
Abstract
Propionic acid (PA) is a bacterium-derived intestinal antimicrobial and immune modulator used widely in food production and agriculture. Passage of Crohn's disease-associated adherent-invasive Escherichia coli (AIEC) through a murine model, in which intestinal PA levels are increased to mimic the human intestine, leads to the recovery of AIEC with significantly increased virulence. Similar phenotypic changes are observed outside the murine model when AIEC is grown in culture with PA as the sole carbon source; such PA exposure also results in AIEC that persists at 20-fold higher levels in vivo. RNA sequencing identifies an upregulation of genes involved in biofilm formation, stress response, metabolism, membrane integrity, and alternative carbon source utilization. PA exposure also increases virulence in a number of E. coli isolates from Crohn's disease patients. Removal of PA is sufficient to reverse these phenotypic changes. Our data indicate that exposure to PA results in AIEC resistance and increased virulence in its presence.
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Affiliation(s)
- Michael J Ormsby
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Síle A Johnson
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Nuria Carpena
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Lynsey M Meikle
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Robert J Goldstone
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Anne McIntosh
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Hannah M Wessel
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Heather E Hulme
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Ceilidh C McConnachie
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - James P R Connolly
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Conor Hasson
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Joseph Boyd
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Eamonn Fitzgerald
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Douglas Morrison
- Scottish Universities Environmental Research Centre, University of Glasgow, Glasgow G75 0QF, UK
| | - Georgina L Hold
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, 1345 Govan Road, Glasgow G51 4TF, UK
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Daniel M Wall
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK.
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Montano J, Rossidivito G, Torreano J, Porwollik S, Sela Saldinger S, McClelland M, Melotto M. Salmonella enterica Serovar Typhimurium 14028s Genomic Regions Required for Colonization of Lettuce Leaves. Front Microbiol 2020; 11:6. [PMID: 32038592 PMCID: PMC6993584 DOI: 10.3389/fmicb.2020.00006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/03/2020] [Indexed: 11/24/2022] Open
Abstract
Contamination of edible produce leaves with human bacterial pathogens has been associated with serious disease outbreaks and has become a major public health concern affecting all aspects of the market, from farmers to consumers. While pathogen populations residing on the surface of ready-to-eat produce can be potentially removed through thorough washing, there is no disinfection technology available that effectively eliminates internal bacterial populations. By screening 303 multi-gene deletion (MGD) mutants of Salmonella enterica serovar Typhimurium (STm) 14028s, we were able to identify ten genomic regions that play a role in opening the stomatal pore of lettuce leaves. The major metabolic functions of the deleted regions are associated with sensing the environment, bacterium movement, transport through the bacterial membrane, and biosynthesis of surface appendages. Interestingly, at 21 days post inoculation, seven of these mutants showed increased population titers inside the leaf, two mutants showed similar titers as the wild type bacterium, whereas one mutant with a large deletion that includes the Salmonella pathogenicity island 2 (SPI-2) showed significantly impaired persistence in the leaf apoplast. These findings suggest that not all the genomic regions required for initiation of leaf colonization (i.e., epiphytic behavior and tissue penetration) are essential for continuing bacterial survival as an endophyte. We also observed that mutants lacking either SPI-1 (Mut3) or SPI-2 (Mut9) induce callose deposition levels comparable to those of the wild type STm 14028s; therefore, these islands do not seem to affect this lettuce defense mechanism. However, the growth of Mut9, but not Mut3, was significantly impaired in the leaf apoplastic wash fluid (AWF) suggesting that the STm persistence in the apoplast may be linked to nutrient acquisition capabilities or overall bacterial fitness in this niche, which are dependent on the gene(s) deleted in the Mut9 strain. The genetic basis of STm colonization of leaves investigated in this study provides a foundation from which to develop mitigation tactics to enhance food safety.
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Affiliation(s)
- Jeanine Montano
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Plant Pathology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Gabrielle Rossidivito
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Joseph Torreano
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Shlomo Sela Saldinger
- Microbial Food Safety Research Unit, Department of Food Science, Agricultural Research Organization, Volcani Center, Rishon LeTsiyon, Israel
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Sengupta A, Wu J, Seffernick JT, Sabag-Daigle A, Thomsen N, Chen TH, Capua AD, Bell CE, Ahmer BMM, Lindert S, Wysocki VH, Gopalan V. Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase. J Mol Biol 2019; 431:4497-4513. [PMID: 31493410 DOI: 10.1016/j.jmb.2019.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 01/18/2023]
Abstract
Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including the terminal FraB deglycase. Salmonella mutants lacking FraB are highly attenuated in mouse models of inflammation due to the toxic build-up of the substrate 6-phosphofructose-aspartate (6-P-F-Asp). This toxicity makes Salmonella FraB an appealing drug target, but there is currently little experimental information about its catalytic mechanism. Therefore, we sought to test our postulated mechanism for the FraB-catalyzed deglycation of 6-P-F-Asp (via an enaminol intermediate) to glucose-6-phosphate and aspartate. A FraB homodimer model generated by RosettaCM was used to build substrate-docked structures that, coupled with sequence alignment of FraB homologs, helped map a putative active site. Five candidate active-site residues-including three expected to participate in substrate binding-were mutated individually and characterized. Native mass spectrometry and ion mobility were used to assess collision cross sections and confirm that the quaternary structure of the mutants mirrored the wild type, and that there are two active sites/homodimer. Our biochemical studies revealed that FraB Glu214Ala, Glu214Asp, and His230Ala were inactive in vitro, consistent with deprotonated-Glu214 and protonated-His230 serving as a general base and a general acid, respectively. Glu214Ala or His230Ala introduced into the Salmonella chromosome by CRISPR/Cas9-mediated genome editing abolished growth on F-Asn. Results from our computational and experimental approaches shed light on the catalytic mechanism of Salmonella FraB and of phosphosugar deglycases in general.
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Affiliation(s)
- Anindita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Jikang Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Nicholas Thomsen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Tien-Hao Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Angela Di Capua
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Charles E Bell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1. Appl Environ Microbiol 2019; 85:AEM.00763-19. [PMID: 31101608 DOI: 10.1128/aem.00763-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
The reduction of arsenate [As(V)] to arsenite [As(III)] by dissimilatory As(V)-reducing bacteria, such as Geobacter spp., may play a significant role in arsenic release from anaerobic sediments into groundwater. The biochemical and molecular mechanisms by which these bacteria cope with this toxic element remain unclear. In this study, the expression of several genes involved in arsenic respiration (arr) and resistance (ars) was determined using Geobacter sp. strain OR-1, the only cultured Geobacter strain capable of As(V) respiration. In addition, proteins expressed differentially under As(V)-respiring conditions were identified by semiquantitative proteomic analysis. Dissimilatory As(V) reductase (Arr) of strain OR-1 was localized predominantly in the periplasmic space, and the transcription of its gene (arrA) was upregulated under As(V)-respiring conditions. The transcription of the detoxifying As(V) reductase gene (arsC) was also upregulated, but its induction required 500 times higher concentration of As(III) (500 μM) than did the arrA gene. Comparative proteomic analysis revealed that in addition to the Arr and Ars proteins, proteins involved in the following processes were upregulated under As(V)-respiring conditions: (i) protein folding and assembly for rescue of proteins with oxidative damage, (ii) DNA replication and repair for restoration of DNA breaks, (iii) anaplerosis and gluconeogenesis for sustainable energy production and biomass formation, and (iv) protein and nucleotide synthesis for the replacement of damaged proteins and nucleotides. These results suggest that strain OR-1 copes with arsenic stress by orchestrating pleiotropic processes that enable this bacterium to resist and actively metabolize arsenic.IMPORTANCE Dissimilatory As(V)-reducing bacteria, such as Geobacter spp., play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. However, the biochemical and molecular mechanisms by which these bacteria cope with arsenic toxicity remain unclear. In this study, it was found that both respiratory and detoxifying As(V) reductases of a dissimilatory As(V)-reducing bacterium, Geobacter sp. strain OR-1, were upregulated under As(V)-respiring conditions. In addition, various proteins expressed specifically or more abundantly in strain OR-1 under arsenic stress were identified. Strain OR-1 actively metabolizes arsenic while orchestrating various metabolic processes that repair oxidative damage caused by arsenic. Such information is useful in assessing and identifying possible countermeasures for the prevention of microbial arsenic release in nature.
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Lengfelder I, Sava IG, Hansen JJ, Kleigrewe K, Herzog J, Neuhaus K, Hofmann T, Sartor RB, Haller D. Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis. Front Immunol 2019; 10:1420. [PMID: 31281321 PMCID: PMC6596359 DOI: 10.3389/fimmu.2019.01420] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10−/−) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10−/− mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (ΔeutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10−/− mice. However, replacement of the E. faecalis wild type bacteria by a ΔeutVW mutant in SIHUMI-colonized IL-10−/− mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10−/− mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis toward a protective function.
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Affiliation(s)
- Isabella Lengfelder
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Irina G Sava
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Jonathan J Hansen
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany
| | - Jeremy Herzog
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.,ZIEL Core Facility Microbiome, Technische Universität München, Freising, Germany
| | - Thomas Hofmann
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - R Balfour Sartor
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
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Ormsby MJ, Logan M, Johnson SA, McIntosh A, Fallata G, Papadopoulou R, Papachristou E, Hold GL, Hansen R, Ijaz UZ, Russell RK, Gerasimidis K, Wall DM. Inflammation associated ethanolamine facilitates infection by Crohn's disease-linked adherent-invasive Escherichia coli. EBioMedicine 2019; 43:325-332. [PMID: 31036531 PMCID: PMC6557746 DOI: 10.1016/j.ebiom.2019.03.071] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The predominance of specific bacteria such as adherent-invasive Escherichia coli (AIEC) within the Crohn's disease (CD) intestine remains poorly understood with little evidence uncovered to support a selective pressure underlying their presence. Intestinal ethanolamine is however readily accessible during periods of intestinal inflammation, and enables pathogens to outcompete the host microbiota under such circumstances. METHODS Quantitative RT-PCR (qRT-PCR) to determine expression of genes central to ethanolamine metabolism; transmission electron microscopy to detect presence of bacterial microcompartments (MCPs); in vitro infections of both murine and human macrophage cell lines examining intracellular replication of the AIEC-type strain LF82 and clinical E. coli isolates in the presence of ethanolamine; determination of E. coli ethanolamine utilization (eut) operon transcription in faecal samples from healthy patients, patients with active CD and the same patients in remission following treatment. RESULTS Growth on the intestinal short chain fatty acid propionic acid (PA) stimulates significantly increased transcription of the eut operon (fold change relative to glucose: >16.9; p-value <.01). Additionally ethanolamine was accessible to intra-macrophage AIEC and stimulated significant increases in growth intracellularly when it was added extracellularly at concentrations comparable to those in the human intestine. Finally, qRT-PCR indicated that expression of the E. coli eut operon was increased in children with active CD compared to healthy controls (fold change increase: >4.72; P < .02). After clinical remission post-exclusive enteral nutrition treatment, the same CD patients exhibited significantly reduced eut expression (Pre vs Post fold change decrease: >15.64; P < .01). INTERPRETATION Our data indicates a role for ethanolamine metabolism in selecting for AIEC that are consistently overrepresented in the CD intestine. The increased E. coli metabolism of ethanolamine seen in the intestine during active CD, and its decrease during remission, indicates ethanolamine use may be a key factor in shaping the intestinal microbiome in CD patients, particularly during times of inflammation. FUND: This work was funded by Biotechnology and Biological Sciences Research Council (BBSRC) grants BB/K008005/1 & BB/P003281/1 to DMW; by a Tenovus Scotland grant to MJO; by Glasgow Children's Hospital Charity, Nestle Health Sciences, Engineering and Physical Sciences Research Council (EPSRC) and Catherine McEwan Foundation grants awarded to KG; and by a Natural Environment Research Council (NERC) fellowship (NE/L011956/1) to UZI. The IBD team at the Royal Hospital for Children, Glasgow are supported by the Catherine McEwan Foundation and Yorkhill IBD fund. RKR and RH are supported by NHS Research Scotland Senior fellowship awards.
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Affiliation(s)
- Michael J Ormsby
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Michael Logan
- School of Engineering, University of Glasgow, Glasgow, Rankine Building, 79-85 Oakfield Ave, Glasgow G12 8LT, United Kingdom
| | - Síle A Johnson
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Anne McIntosh
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Ghaith Fallata
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Rodanthi Papadopoulou
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
| | - Eleftheria Papachristou
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
| | - Georgina L Hold
- Microbiome Research Centre, St George and Sutherland Clinical School, UNSW, Australia
| | - Richard Hansen
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, 1345 Govan Road, Glasgow G51 4TF, United Kingdom
| | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, Rankine Building, 79-85 Oakfield Ave, Glasgow G12 8LT, United Kingdom
| | - Richard K Russell
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, 1345 Govan Road, Glasgow G51 4TF, United Kingdom
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
| | - Daniel M Wall
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom.
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Buckley A, MacGregor B, Teske A. Identification, Expression and Activity of Candidate Nitrite Reductases From Orange Beggiatoaceae, Guaymas Basin. Front Microbiol 2019; 10:644. [PMID: 30984153 PMCID: PMC6449678 DOI: 10.3389/fmicb.2019.00644] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/14/2019] [Indexed: 11/13/2022] Open
Abstract
Orange filamentous Beggiatoaceae form massive microbial mats on hydrothermal sediments in Guaymas Basin; these bacteria are considered to oxidize sulfide with nitrate and nitrite as electron acceptors. From a previously analyzed genome of an orange Beggiatoaceae filament, three candidate genes for enzymes with nitrite-reducing function - an orange octaheme cytochrome, a nirS nitrite reductase, and a nitrite/tetrathionate-reducing octaheme cytochrome - were cloned and expressed in Escherichia coli. The expressed and purified orange cytochrome showed reduced nitrite-reducing activity compared to the multifunctional native protein obtained from microbial mats. The nirS gene product showed in vitro but no in-gel nitrite-reducing activity; and the nitrite/tetrathionate-reducing octaheme cytochrome was capable of reducing both nitrite and tetrathionate in vitro. Phylogenetic analysis shows that the orange Beggiatoaceae nirS, in contrast to the other candidate nitrite reductases, does not form monophyletic lineages with its counterparts in other large sulfur-oxidizing bacteria, and most likely represents a recent acquisition by lateral gene transfer. The nitrite/tetrathionate-reducing enzyme of the orange Beggiatoaceae is related to nitrite- and tetrathionate reductases harbored predominantly by Gammaproteobacteria, including obligate endosymbionts of hydrothermal vent tubeworms. Thus, the orange Guaymas Basin Beggiatoaceae have a repertoire of at least three different functional enzymes for nitrite reduction. By demonstrating the unusual diversity of enzymes with a potential role in nitrite reduction, we show that bacteria in highly dynamic, sulfide-rich hydrothermal vent habitats adapt to these conditions that usually prohibit nitrate and nitrite reduction. In the case of the orange Guaymas Beggiatoaceae, classical denitrification appears to be replaced by different multifunctional enzymes for nitrite and tetrathionate reduction; the resulting ecophysiological flexibility provides a new key to the dominance of these Beggiatoaceae in hydrothermal hot spots.
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Affiliation(s)
- Andrew Buckley
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Barbara MacGregor
- Department of Earth Sciences, College of Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Spiga L, Winter SE. Using Enteric Pathogens to Probe the Gut Microbiota. Trends Microbiol 2019; 27:243-253. [DOI: 10.1016/j.tim.2018.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/08/2018] [Accepted: 11/19/2018] [Indexed: 12/23/2022]
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Characterization of a Glycyl Radical Enzyme Bacterial Microcompartment Pathway in Rhodobacter capsulatus. J Bacteriol 2019; 201:JB.00343-18. [PMID: 30510145 DOI: 10.1128/jb.00343-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
Bacterial microcompartments (BMCs) are large (∼100-nm) protein shells that encapsulate enzymes, their substrates, and cofactors for the purposes of increasing metabolic reaction efficiency and protecting cells from toxic intermediates. The best-studied microcompartment is the carbon-fixing carboxysome that encapsulates ribulose-1,5-bisphosphate carboxylase and carbonic anhydrase. Other well-known BMCs include the Pdu and Eut BMCs, which metabolize 1,2-propanediol and ethanolamine, respectively, with vitamin B12-dependent diol dehydratase enzymes. Recent bioinformatic analyses identified a new prevalent type of BMC, hypothesized to utilize vitamin B12-independent glycyl radical enzymes to metabolize substrates. Here we use genetic and metabolic analyses to undertake in vivo characterization of the newly identified glycyl radical enzyme microcompartment 3 (GRM3) class of microcompartment clusters. Transcriptome sequencing analyses showed that the microcompartment gene cluster in the genome of the purple photosynthetic bacterium Rhodobacter capsulatus was expressed under dark anaerobic respiratory conditions in the presence of 1,2-propanediol. High-performance liquid chromatography and gas chromatography-mass spectrometry analyses showed that enzymes coded by this cluster metabolized 1,2-propanediol into propionaldehyde, propanol, and propionate. Surprisingly, the microcompartment pathway did not protect these cells from toxic propionaldehyde under the conditions used in this study, with buildup of this intermediate contributing to arrest of cell growth. We further show that expression of microcompartment genes is regulated by a two-component system located downstream of the microcompartment cluster.IMPORTANCE BMCs are protein shells that are designed to compartmentalize enzymatic reactions that require either sequestration of a substrate or the sequestration of toxic intermediates. Due to their ability to compartmentalize reactions, BMCs have also become attractive targets for bioengineering novel enzymatic reactions. Despite these useful features, little is known about the biochemistry of newly identified classes of BMCs. In this study, we have undertaken genetic and in vivo metabolic analyses of the newly identified GRM3 gene cluster.
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Contribution of the Cpx envelope stress system to metabolism and virulence regulation in Salmonella enterica serovar Typhimurium. PLoS One 2019; 14:e0211584. [PMID: 30716090 PMCID: PMC6361445 DOI: 10.1371/journal.pone.0211584] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/16/2019] [Indexed: 11/19/2022] Open
Abstract
The Cpx-envelope stress system regulates the expression of virulence factors in many Gram-negative pathogens. In Salmonella enterica serovar Typhimurium deletion of the sensor kinase CpxA but not of the response regulator CpxR results in the down regulation of the key regulator for invasion, HilA encoded by the Salmonella pathogenicity island 1 (SPI-1). Here, we provide evidence that cpxA deletion interferes with dephosphorylation of CpxR resulting in increased levels of active CpxR and consequently in misregulation of target genes. 14 potential operons were identified to be under direct control of CpxR. These include the virulence determinants ecotin, the omptin PgtE, and the SPI-2 regulator SsrB. The Tat-system and the PocR regulator that together promote anaerobic respiration of tetrathionate on 1,2-propanediol are also under direct CpxR control. Notably, 1,2-propanediol represses hilA expression. Thus, our work demonstrates for the first time the involvement of the Cpx system in a complex network mediating metabolism and virulence function.
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Guo Y, Cui X, Ou L, Isowaki C, Masuda Y, Honjoh KI, Miyamoto T. Effects of Sucrose on Heat Resistance and Gene Expression in <i>Salmonella</i> Typhimurium. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2019. [DOI: 10.3136/fstr.25.903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yue Guo
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University
| | - Xiaowen Cui
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University
| | - Liushu Ou
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University
| | - Chika Isowaki
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University
| | - Yoshimitsu Masuda
- Division of Food Science and Biotechnology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University
| | - Ken-ichi Honjoh
- Division of Food Science and Biotechnology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University
| | - Takahisa Miyamoto
- Division of Food Science and Biotechnology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University
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Sorbara MT, Pamer EG. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them. Mucosal Immunol 2019; 12:1-9. [PMID: 29988120 PMCID: PMC6312114 DOI: 10.1038/s41385-018-0053-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 02/08/2023]
Abstract
The communities of bacteria that reside in the intestinal tract are in constant competition within this dynamic and densely colonized environment. At homeostasis, the equilibrium that exists between these species and strains is shaped by their metabolism and also by pathways of active antagonism, which drive competition with related and unrelated strains. Importantly, these normal activities contribute to colonization resistance by the healthy microbiota, which includes the ability to prevent the expansion of potential pathogens. Disruption of the microbiota, resulting from, for example, inflammation or antibiotic use, can reduce colonization resistance. Pathogens that engraft following disruption of the microbiota are often adapted to expand into newly created niches and compete in an altered gut environment. In this review, we examine both the interbacterial mechanisms of colonization resistance and the strategies of pathogenic strains to exploit gaps in colonization resistance.
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Affiliation(s)
- Matthew T. Sorbara
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G. Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
- Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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A Bacterial Microcompartment Is Used for Choline Fermentation by Escherichia coli 536. J Bacteriol 2018; 200:JB.00764-17. [PMID: 29507086 DOI: 10.1128/jb.00764-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/23/2018] [Indexed: 01/16/2023] Open
Abstract
Bacterial choline degradation in the human gut has been associated with cancer and heart disease. In addition, recent studies found that a bacterial microcompartment is involved in choline utilization by Proteus and Desulfovibrio species. However, many aspects of this process have not been fully defined. Here, we investigate choline degradation by the uropathogen Escherichia coli 536. Growth studies indicated E. coli 536 degrades choline primarily by fermentation. Electron microscopy indicated that a bacterial microcompartment was used for this process. Bioinformatic analyses suggested that the choline utilization (cut) gene cluster of E. coli 536 includes two operons, one containing three genes and a main operon of 13 genes. Regulatory studies indicate that the cutX gene encodes a positive transcriptional regulator required for induction of the main cut operon in response to choline supplementation. Each of the 16 genes in the cut cluster was individually deleted, and phenotypes were examined. The cutX, cutY, cutF, cutO, cutC, cutD, cutU, and cutV genes were required for choline degradation, but the remaining genes of the cut cluster were not essential under the conditions used. The reasons for these varied phenotypes are discussed.IMPORTANCE Here, we investigate choline degradation in E. coli 536. These studies provide a basis for understanding a new type of bacterial microcompartment and may provide deeper insight into the link between choline degradation in the human gut and cancer and heart disease. These are also the first studies of choline degradation in E. coli 536, an organism for which sophisticated genetic analysis methods are available. In addition, the cut gene cluster of E. coli 536 is located in pathogenicity island II (PAI-II536) and hence might contribute to pathogenesis.
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Nawrocki KL, Wetzel D, Jones JB, Woods EC, McBride SM. Ethanolamine is a valuable nutrient source that impacts Clostridium difficile pathogenesis. Environ Microbiol 2018; 20:1419-1435. [PMID: 29349925 PMCID: PMC5903940 DOI: 10.1111/1462-2920.14048] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 01/03/2018] [Accepted: 01/14/2018] [Indexed: 12/12/2022]
Abstract
Clostridium (Clostridioides) difficile is a gastrointestinal pathogen that colonizes the intestinal tract of mammals and can cause severe diarrheal disease. Although C. difficile growth is confined to the intestinal tract, our understanding of the specific metabolites and host factors that are important for the growth of the bacterium is limited. In other enteric pathogens, the membrane-derived metabolite, ethanolamine (EA), is utilized as a nutrient source and can function as a signal to initiate the production of virulence factors. In this study, we investigated the effects of ethanolamine and the role of the predicted ethanolamine gene cluster (CD1907-CD1925) on C. difficile growth. Using targeted mutagenesis, we disrupted genes within the eut cluster and assessed their roles in ethanolamine utilization, and the impact of eut disruption on the outcome of infection in a hamster model of disease. Our results indicate that the eut gene cluster is required for the growth of C. difficile on ethanolamine as a primary nutrient source. Further, the inability to utilize ethanolamine resulted in greater virulence and a shorter time to morbidity in the animal model. Overall, these data suggest that ethanolamine is an important nutrient source within the host and that, in contrast to other intestinal pathogens, the metabolism of ethanolamine by C. difficile can delay the onset of disease.
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Affiliation(s)
- Kathryn L. Nawrocki
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniela Wetzel
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua B. Jones
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Emily C. Woods
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
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Abstract
Ethanolamine (EA) is a valuable source of carbon and/or nitrogen for bacteria capable of its catabolism. Because it is derived from the membrane phospholipid phosphatidylethanolamine, it is particularly prevalent in the gastrointestinal tract, which is membrane rich due to turnover of the intestinal epithelium and the resident microbiota. Intriguingly, many gut pathogens carry the eut (ethanolamine utilization) genes. EA utilization has been studied for about 50 years, with most of the early work occurring in just a couple of species of Enterobacteriaceae. Once the metabolic pathways and enzymes were characterized by biochemical approaches, genetic screens were used to map the various activities to the eut genes. With the rise of genomics, the diversity of bacteria containing the eut genes and surprising differences in eut gene content were recognized. Some species contain nearly 20 genes and encode many accessory proteins, while others contain only the core catabolic enzyme. Moreover, the eut genes are regulated by very different mechanisms, depending on the organism and the eut regulator encoded. In the last several years, exciting progress has been made in elucidating the complex regulatory mechanisms that govern eut gene expression. Furthermore, a new appreciation for how EA contributes to infection and colonization in the host is emerging. In addition to providing an overview of EA-related biology, this minireview will give special attention to these recent advances.
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Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Büttner L, de Lima Romão E, Behrendt CL, Lopez CA, Sifuentes-Dominguez L, Huff-Hardy K, Wilson RP, Gillis CC, Tükel Ç, Koh AY, Burstein E, Hooper LV, Bäumler AJ, Winter SE. Precision editing of the gut microbiota ameliorates colitis. Nature 2018; 553:208-211. [PMID: 29323293 DOI: 10.1038/nature25172] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/24/2017] [Indexed: 12/30/2022]
Abstract
Inflammatory diseases of the gastrointestinal tract are frequently associated with dysbiosis, characterized by changes in gut microbial communities that include an expansion of facultative anaerobic bacteria of the Enterobacteriaceae family (phylum Proteobacteria). Here we show that a dysbiotic expansion of Enterobacteriaceae during gut inflammation could be prevented by tungstate treatment, which selectively inhibited molybdenum-cofactor-dependent microbial respiratory pathways that are operational only during episodes of inflammation. By contrast, we found that tungstate treatment caused minimal changes in the microbiota composition under homeostatic conditions. Notably, tungstate-mediated microbiota editing reduced the severity of intestinal inflammation in mouse models of colitis. We conclude that precision editing of the microbiota composition by tungstate treatment ameliorates the adverse effects of dysbiosis in the inflamed gut.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Breck A Duerkop
- Department of Immunology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Lisa Büttner
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Everton de Lima Romão
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Cassie L Behrendt
- Department of Immunology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Luis Sifuentes-Dominguez
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Kayci Huff-Hardy
- Department of Internal Medicine, Division of Digestive & Liver Diseases, University of Texas Southwestern Medical Center 75390, 5323 Harry Hines Boulevard, Dallas, Texas, USA
| | - R Paul Wilson
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, 1801 North Broad Street, Philadelphia, Pennsylvania 19122, USA
| | - Caroline C Gillis
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Çagla Tükel
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, 1801 North Broad Street, Philadelphia, Pennsylvania 19122, USA
| | - Andrew Y Koh
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Ezra Burstein
- Department of Internal Medicine, Division of Digestive & Liver Diseases, University of Texas Southwestern Medical Center 75390, 5323 Harry Hines Boulevard, Dallas, Texas, USA
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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Salmonella FraE, an Asparaginase Homolog, Contributes to Fructose-Asparagine but Not Asparagine Utilization. J Bacteriol 2017; 199:JB.00330-17. [PMID: 28847920 DOI: 10.1128/jb.00330-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/18/2017] [Indexed: 12/15/2022] Open
Abstract
Salmonella enterica can utilize fructose-asparagine (F-Asn) as a source of carbon and nitrogen. This capability has been attributed to five genes in the fra locus. Previously, we determined that mutations in fraB (deglycase), fraD (kinase), or fraA (transporter) eliminated the ability of Salmonella to grow on F-Asn, while a mutation in fraE allowed partial growth. We hypothesized that FraE, a putative periplasmic fructose-asparaginase, converts F-Asn to NH4 + and fructose-aspartate (F-Asp). FraA could then transport F-Asp into the cytoplasm for subsequent catabolism. Here, we report that growth of the fraE mutant on F-Asn is caused by a partially redundant activity provided by AnsB, a periplasmic asparaginase. Indeed, a fraE ansB double mutant is unable to grow on F-Asn. Moreover, biochemical assays using periplasmic extracts of mutants that express only FraE or AnsB confirmed that each of these enzymes converts F-Asn to F-Asp and NH4 + However, FraE does not contribute to growth on asparagine. We tested and confirmed the hypothesis that a fraE ansB mutant can grow on F-Asp, while mutants lacking fraA, fraD, or fraB cannot. This finding provides strong evidence that FraA transports F-Asp but not F-Asn from the periplasm to the cytoplasm. Previously, we determined that F-Asn is toxic to a fraB mutant due to the accumulation of the FraB substrate, 6-phosphofructose-aspartate (6-P-F-Asp). Here, we found that, as expected, a fraB mutant is also inhibited by F-Asp. Collectively, these findings contribute to a better understanding of F-Asn utilization by Salmonella IMPORTANCE Salmonella is able to utilize fructose-asparagine (F-Asn) as a nutrient. We recently reported that the disruption of a deglycase enzyme in the F-Asn utilization pathway inhibits the growth of Salmonella in mice and recognized this pathway as a novel and specific drug target. Here, we characterize the first step in the pathway wherein FraE hydrolyzes F-Asn to release NH4 + and F-Asp in the periplasm of the cell. A fraE mutant continues to grow slowly on F-Asn due to asparaginase activity encoded by ansB.
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Anderson CJ, Kendall MM. Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation. Front Microbiol 2017; 8:1983. [PMID: 29075247 PMCID: PMC5643478 DOI: 10.3389/fmicb.2017.01983] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial pathogens must sense and respond to newly encountered host environments to regulate the expression of critical virulence factors that allow for niche adaptation and successful colonization. Among bacterial pathogens, non-typhoidal serovars of Salmonella enterica, such as serovar Typhimurium (S. Tm), are a primary cause of foodborne illnesses that lead to hospitalizations and deaths worldwide. S. Tm causes acute inflammatory diarrhea that can progress to invasive systemic disease in susceptible patients. The gastrointestinal tract and intramacrophage environments are two critically important niches during S. Tm infection, and each presents unique challenges to limit S. Tm growth. The intestinal tract is home to billions of commensal microbes, termed the microbiota, which limits the amount of available nutrients for invading pathogens such as S. Tm. Therefore, S. Tm encodes strategies to manipulate the commensal population and side-step this nutritional competition. During subsequent stages of disease, S. Tm resists host immune cell mechanisms of killing. Host cells use antimicrobial peptides, acidification of vacuoles, and nutrient limitation to kill phagocytosed microbes, and yet S. Tm is able to subvert these defense systems. In this review, we discuss recently described molecular mechanisms that S. Tm uses to outcompete the resident microbiota within the gastrointestinal tract. S. Tm directly eliminates close competitors via bacterial cell-to-cell contact as well as by stimulating a host immune response to eliminate specific members of the microbiota. Additionally, S. Tm tightly regulates the expression of key virulence factors that enable S. Tm to withstand host immune defenses within macrophages. Additionally, we highlight the chemical and physical signals that S. Tm senses as cues to adapt to each of these environments. These strategies ultimately allow S. Tm to successfully adapt to these two disparate host environments. It is critical to better understand bacterial adaptation strategies because disruption of these pathways and mechanisms, especially those shared by multiple pathogens, may provide novel therapeutic intervention strategies.
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Affiliation(s)
- Christopher J Anderson
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
| | - Melissa M Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
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