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Todorov SD, Alves VF, Popov I, Weeks R, Pinto UM, Petrov N, Ivanova IV, Chikindas ML. Antimicrobial Compounds in Wine. Probiotics Antimicrob Proteins 2024; 16:763-783. [PMID: 37855943 DOI: 10.1007/s12602-023-10177-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Ipsum vinum est potestas et possession (wine itself is power and possession). Wine is a complex system that triggers multisensory cognitive stimuli. Wine and its consumption are thoroughly intertwined with the development of human society. The beverage was appreciated in many ancient mythologies and plays an essential part in Christianity and rituals to this day. Wine has been said to enlighten and inspire artists and has even been prohibited by law and some religions, but has nevertheless played a role in human civilizations since the beginning. Winemaking is also a prospering and economically important industry and a longtime symbol of status and luxury. In winemaking, the formation of the final product is influenced by several factors that contribute to the chemical and sensory complexity often associated with quality vintages. Factors such as terroir, climatic conditions, variety of the grape, all aspects of the winemaking process to the smallest details, including metabolic processes carried out by yeast and malolactic bacteria, and the conditions for the maturation and storage of the final product, up to, and even beyond the point of deciding to open the bottle and enjoy the wine. In conjunction with the empiric and scientific process of winemaking, different molecules with antibacterial activity can be identified in wine during the production process, and several of them are clearly present in the final product. Some of these antibacterial components are phytochemicals, such as flavonoids and phenolic compounds, that may be delivered to the final product (wine) as a part of the grape, a variety of potential additive compounds, or from the oak barrels or clay amphoras used during the maturation process. Others are produced by yeasts and malolactic bacteria and play a role not only in the moderation of the fermentation process but contributing to the microbiological safety and beneficial properties spectra of the final product. Lactic acid bacteria, responsible for conducting malolactic fermentation, contribute to the final balance of the wine but are also directly involved in the production of different compounds exhibiting antibacterial activity. Some examples of these compounds include bacteriocins (antibacterial peptides), diacetyl, organic acids, reuterin, hydrogen peroxide, and carbon dioxide. Major aspects of these different beneficial metabolites are the subject of discussion in this review with the aim of highlighting their beneficial functions.
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Affiliation(s)
- Svetoslav Dimitrov Todorov
- ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.
- Food Research Center (FoRC), Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.
- CISAS- Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, 4900-347, Viana do Castelo, Portugal.
| | - Virginia Farias Alves
- Faculdade de Farmácia, Universidade Federal de Goiás (UFG), 74605-170, Goiânia, GO, Brazil
| | - Igor Popov
- Center for Agrobiotechnology, Don State Technical University, 344000, Gagarina Sq., 1, Rostov-On-Don, Russia
- Division of Immunobiology and Biomedicine, Center of Genetics and Life Sciences, Sirius University of Science and Technology, Olimpijskij av., 1, 354340, Federal Territory Sirius, Russia
| | - Richard Weeks
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, 08901, New Brunswick, NJ, USA
| | - Uelinton Manoel Pinto
- Food Research Center (FoRC), Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Nikolay Petrov
- Laboratory of Virology, New Bulgarian University, Montevideo str. 21, 1618, Sofia, Bulgaria
| | - Iskra Vitanova Ivanova
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University St. Kliment Ohridski, 8, Bul. Dragan Tzankov, 1164, Sofia, Bulgaria
| | - Michael L Chikindas
- Center for Agrobiotechnology, Don State Technical University, 344000, Gagarina Sq., 1, Rostov-On-Don, Russia
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, 08901, New Brunswick, NJ, USA
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, 119991, Moscow, Russia
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Yadav V, Zohib M, Singh S, Pal RK, Tripathi S, Jain A, Biswal BK, Dasgupta A, Arora A. Structural and biophysical characterization of PadR family protein Rv1176c of Mycobacterium tuberculosis H37Rv. Int J Biol Macromol 2024; 263:130455. [PMID: 38417748 DOI: 10.1016/j.ijbiomac.2024.130455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Rv1176c of Mycobacterium tuberculosis H37Rv belongs to the PadR-s1 subfamily of the PadR family of protein. Rv1176c forms a stable dimer in solution. Its stability is characterized by a thermal melting transition temperature (Tm) of 39.4 °C. The crystal structure of Rv1176c was determined at a resolution of 2.94 Å, with two monomers in the asymmetric unit. Each monomer has a characteristic N-terminal winged-helix-turn-helix DNA-binding domain. Rv1176c C-terminal is a coiled-coil dimerization domain formed of α-helices α5 to α7. In the Rv1176c dimer, there is domain-swapping of the C-terminal domain in comparison to other PadR homologs. In the dimer, there is a long inter-subunit tunnel in which different ligands can bind. Rv1176c was found to bind to the promoter region of its own gene with high specificity. M. smegmatis MC2 155 genome lacks homolog of Rv1176c. Therefore, it was used as a surrogate to characterize the functional role of Rv1176c. Expression of Rv1176c in M. smegmatis MC2 155 cells imparted enhanced tolerance towards oxidative stress. Rv1176c expressing M. smegmatis MC2 155 cells exhibited enhanced intracellular survival in J774A.1 murine macrophage cells. Overall, our studies demonstrate Rv1176c to be a PadR-s1 subfamily transcription factor that can moderate the effect of oxidative stress.
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Affiliation(s)
- Vikash Yadav
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Zohib
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shriya Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ravi Kant Pal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Sarita Tripathi
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Anupam Jain
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Bichitra Kumar Biswal
- X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India
| | - Arunava Dasgupta
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashish Arora
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Muñoz R, Rivas BDL, Rodríguez H, Esteban-Torres M, Reverón I, Santamaría L, Landete JM, Plaza-Vinuesa L, Sánchez-Arroyo A, Jiménez N, Curiel JA. Food phenolics and Lactiplantibacillus plantarum. Int J Food Microbiol 2024; 412:110555. [PMID: 38199014 DOI: 10.1016/j.ijfoodmicro.2023.110555] [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: 11/30/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
Phenolic compounds are important constituents of plant food products. These compounds play a key role in food characteristics such as flavor, astringency and color. Lactic acid bacteria are naturally found in raw vegetables, being Lactiplantibacillus plantarum the most commonly used commercial starter for the fermentation of plant foods. Hence, the metabolism of phenolic compounds of L. plantarum has been a subject of study in recent decades. Such studies confirm that L. plantarum, in addition to presenting catalytic capacity to transform aromatic alcohols and phenolic glycosides, exhibits two main differentiated metabolic routes that allow the biotransformation of dietary hydroxybenzoic and hydroxycinnamic acid-derived compounds. These metabolic pathways lead to the production of new compounds with new biological and organoleptic properties. The described metabolic pathways involve the action of specialized esterases, decarboxylases and reductases that have been identified through genetic analysis and biochemically characterized. The purpose of this review is to provide a comprehensive and up-to-date summary of the current knowledge of the metabolism of food phenolics in L. plantarum.
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Affiliation(s)
- Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain.
| | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Héctor Rodríguez
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - María Esteban-Torres
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - José Maria Landete
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Ana Sánchez-Arroyo
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - Natalia Jiménez
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain
| | - José Antonio Curiel
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, Madrid, Spain.
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Alan Y. Chemical changes of potential probiotic Lactiplantibacillus plantarum and Lactobacillus pentosus starter cultures in natural Gemlik type black olive fermentation. Food Chem 2024; 434:137472. [PMID: 37722330 DOI: 10.1016/j.foodchem.2023.137472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/11/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
The aim of this study was to determine the ability of probiotic Lactiplantibacillus plantarum and Lactobacillus pentosus starter cultures to maintain Olea europaea L. cv. Gemlik fermentation and some chemical changes occurred by HPLC. It was observed that starter cultures decreased the pH by increasing the acidity of the fermentation medium. In addition, it was determined that the number of yeast-mold (Y-M) and aerobic mesophilic bacteria (AMB) were lower than the number of lactic acid bacteria (LAB) in the samples with starter cultures. As the fermentation period progressed, it was observed that the amount and variety of phenolic substances increased, albeit slightly, in the brined olive samples to which the starter culture was added. Alcohols, biogenic amines, sugars and organic acids increased or decreased in all samples. During the fermentation gallic acid, apigenin, kaempferol, curcumin, vanillin, caffeic acid, salicylic acid, putrescine, triamine, spermidine and maleic acid could not be detected.
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Affiliation(s)
- Yusuf Alan
- Department of Medical Services and Techniques, Bitlis Eren University, Bitlis, Turkey.
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Augustiniene E, Kutraite I, Valanciene E, Matulis P, Jonuskiene I, Malys N. Transcription factor-based biosensors for detection of naturally occurring phenolic acids. N Biotechnol 2023; 78:1-12. [PMID: 37714511 DOI: 10.1016/j.nbt.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Phenolic acids including hydroxybenzoic and hydroxycinnamic acids are secondary plant and fungal metabolites involved in many physiological processes offering health and dietary benefits. They are often utilised as precursors for production of value-added compounds. The limited availability of synthetic biology tools, such as whole-cell biosensors suitable for monitoring the dynamics of phenolic acids intracellularly and extracellularly, hinders the capabilities to develop high-throughput screens to study their metabolism and forward engineering. Here, by applying a multi-genome approach, we have identified phenolic acid-inducible gene expression systems composed of transcription factor-inducible promoter pairs responding to eleven different phenolic acids. Subsequently, they were used for the development of whole-cell biosensors based on model bacterial hosts, such as Escherichia coli, Cupriavidus necator and Pseudomonas putida. The dynamics and range of the biosensors were evaluated by establishing their response and sensitivity landscapes. The specificity and previously uncharacterised interactions between transcription factor and its effector(s) were identified by a screen of twenty major phenolic acids. To exemplify applicability, we utilise a protocatechuic acid-biosensor to identify enzymes with enhanced activity for conversion of p-hydroxybenzoate to protocatechuate. Transcription factor-based biosensors developed in this study will advance the analytics of phenolic acids and expedite research into their metabolism.
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Affiliation(s)
- Ernesta Augustiniene
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Ingrida Kutraite
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Egle Valanciene
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Paulius Matulis
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Ilona Jonuskiene
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Naglis Malys
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania; Department of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania.
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A Novel Glycoside Hydrolase DogH Utilizing Soluble Starch to Maltose Improve Osmotic Tolerance in Deinococcus radiodurans. Int J Mol Sci 2023; 24:ijms24043437. [PMID: 36834856 PMCID: PMC9967864 DOI: 10.3390/ijms24043437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Deinococcus radiodurans is a microorganism that can adjust, survive or thrive in hostile conditions and has been described as "the strongest microorganism in the world". The underlying mechanism behind the exceptional resistance of this robust bacterium still remains unclear. Osmotic stress, caused by abiotic stresses such as desiccation, salt stress, high temperatures and freezing, is one of the main stresses suffered by microorganisms, and it is also the basic response pathway by which organisms cope with environmental stress. In this study, a unique trehalose synthesis-related gene, dogH (Deinococcus radiodurans orphan glycosyl hydrolase-like family 10), which encodes a novel glycoside hydrolase, was excavated using a multi-omics combination method. The content accumulation of trehalose and its precursors under hypertonic conditions was quantified by HPLC-MS. Ours results showed that the dogH gene was strongly induced by sorbitol and desiccation stress in D. radiodurans. DogH glycoside hydrolase hydrolyzes α-1,4-glycosidic bonds by releasing maltose from starch in the regulation of soluble sugars, thereby increasing the concentration of TreS (trehalose synthase) pathway precursors and trehalose biomass. The maltose and alginate content in D. radiodurans amounted to 48 μg mg protein-1 and 45 μg mg protein-1, respectively, which were 9 and 28 times higher than those in E. coli, respectively. The accumulation of greater intracellular concentrations of osmoprotectants may be the true reason for the higher osmotic stress tolerance of D. radiodurans.
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Pham VD, Korver DR, Gänzle MG. Conversion of Phenolic Acids in Canola Fermentation: Impact on Antimicrobial Activity against Salmonella enterica and Campylobacter jejuni. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2059-2069. [PMID: 36669157 DOI: 10.1021/acs.jafc.2c08322] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Canola meal (CM) is commonly used in poultry feeds. CM has a high protein content but also contains high levels of antimicrobial phenolic acids. Lactic acid bacteria can alter CM phenolic composition during fermentation and influence its antimicrobial activity against pathogens. Fermented CM was analyzed for phenolic composition using tandem mass spectrometry (LC-MS/MS) and high-performance liquid chromatography (HPLC). Sinapic acid and derivatives were the major phenolic acids in CM. Growth of lactobacilli in CM was attenuated when compared to cereal substrates. Glucosides and esters of sinapic acid were extensively hydrolyzed during fermentation with Lactiplantibacillus plantarum and Furfurilactobacillus milii. Lp. plantarum transformed hydroxycinnamic acids to dihydro, 4-vinyl, and 4-ethyl derivatives, Ff. milii reduced hydroxycinnamic acids to dihydroderivatives, but Limosilactobacillus reuteri did not convert hydroxycinnamic acids. The minimum inhibitory concentration of phenolic extracts was assessed with lactobacilli, Salmonella, and Campylobacter jejuni as indicator strains. Fermentation of CM with Lp. plantarum or Ff. milii increased the antimicrobial activity of phenolic extracts against Salmonella enterica and Campylobacter jejuni. Fermentation with Lm. reuteri TMW1.656 but not fermentation with Lm. reuteri TMW1.656ΔrtcN increased the antimicrobial activity of extracts owing to the production of reutericyclin. This study demonstrates that fermentation of CM with lactobacilli converts hydroxycinammic esters and may increase the antimicrobial activity of phenolic compounds in CM against pathogens.
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Affiliation(s)
- Vi D Pham
- Department. of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Douglas R Korver
- Department. of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Michael G Gänzle
- Department. of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Zhang J, Wu YF, Tang ST, Chen J, Rosen BP, Zhao FJ. A PadR family transcriptional repressor controls transcription of a trivalent metalloid resistance operon of Azospirillum halopraeferens strain Au 4. Environ Microbiol 2022; 24:5139-5150. [PMID: 35880613 DOI: 10.1111/1462-2920.16147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022]
Abstract
Methylarsenite [MAs(III)] is a highly toxic arsenical produced by some microbes as an antibiotic. In this study, we demonstrate that a PadR family transcriptional regulator, PadRars , from Azospirillum halopraeferens strain Au 4 directly binds to the promoter region of the arsenic resistance (ars) operon (consisting of padRars , arsV, and arsW) and represses transcription of arsV and arsW genes involved in MAs(III) resistance. Quantitative reverse transcriptase PCR and transcriptional reporter assays showed that transcription of the ars operon is induced strongly by MAs(III) and less strongly by arsenite and antimonite. Electrophoretic mobility shift assays with recombinant PadRars showed that it represses transcription of the ars operon by binding to two inverted-repeat sequences within the ars promoter. PadRars has two conserved cysteine pairs, Cys56/57 and Cys133/134; mutation of the first pair to serine abolished the transcriptional response of the ars operon to trivalent metalloids, suggesting that Cys56/57 form a binding site for trivalent metalloids. Either C133S or C134S derivative responses to MAs(III) but not As(III) or Sb(III), suggesting that it is a third ligand to trivalent metalloids. PadRars represents a new type of repressor proteins regulating transcription of an ars operon involved in the resistance to trivalent metalloids, especially MAs(III). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jun Zhang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yi-Fei Wu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shi-Tong Tang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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How Microbiome Composition Correlates with Biochemical Changes during Sauerkraut Fermentation: a Focus on Neglected Bacterial Players and Functionalities. Microbiol Spectr 2022; 10:e0016822. [PMID: 35699432 PMCID: PMC9430578 DOI: 10.1128/spectrum.00168-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
This study provided a new perspective on the bacterial community succession during sauerkraut fermentation, and on resulting metabolic functions. While culture-dependent methods confirmed the key role of the well-known core microbiome species, metagenomic approach (shotgun) revealed Secundilactobacillus malefermentans as a species of the core microbiome, especially during the last weeks of fermentation. Although the potentiality of S. malefermentans has not yet fully explored, it held core functional genes usually attributed to others lactic acid bacteria driving sauerkraut fermentation. Based on our results it is arguable that S. malefermentans might have a key a role during sauerkraut fermentation carried out at low temperature. Under our experimental conditions, the profile of phenolic compounds changed throughout sauerkraut fermentation. The amount of free phenolics, including free phenolic acids, increased at the beginning of the fermentation, whereas the conversion of phenolic acids into microbial derivatives was consistent during the last part of the sauerkraut fermentation. We pioneered correlating changes in the phenolics profile to changes in the microbiome, although the framework presented is still fragmentary. Annotated genes linked to the phenolic compounds metabolism (VprA and padA) were found in many core species during the whole process. A high metabolic potential for phenolics bioconversion emerged for lactobacilli and Pediococcus spp. through correlation analysis between microbiome composition and phenolics profile. IMPORTANCE Our study was not limited to describe the succession pattern of the microbial community during sauerkraut fermentation, but also revealed how some neglected bacterial players belong to the core species during sauerkrauts processing, especially at low temperature. Such species might have a role as potential starters to optimize the fermentation processes and to obtain sauerkrauts with improved and standardized nutritional and sensory features. Furthermore, our correlations between microbiome composition and phenolics profile might also represent new references for sauerkraut biotechnology, aiming to identify new metabolic drivers of potential sauerkraut functionalities. Finally, sauerkraut ecosystem is a tractable model, although with high level of complexity, and resultant ecological information might be extended to other plant ecosystems.
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Abstract
More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.
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Affiliation(s)
- Ronald R. Breaker
- Corresponding Author: Ronald R. Breaker - Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, United States; Phone: 203-432-9389; , Twitter: @RonBreaker
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Optimization of Parameters Using Response Surface Methodology to Develop a Novel Kefir-Like Functional Beverage from Cheese Whey Enriched with Myrtle Juice. J CHEM-NY 2021. [DOI: 10.1155/2021/2984470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whey, liquid wastewater from cheese production, is one of the sources of dietary protein and lactose that are still largely unused for human consumption. It is only in recent years that it has aroused the interest of industries and sought as a valuable raw material and thus represents an opportunity for the manufacture of new products. The manufacture of fermented whey drink requires the mixing of whey with fruit juice or an aromatic plant to improve its organoleptic properties and acceptability. Myrtle, an aromatic medicinal plant, known for its health benefits is not well exploited for making dairy products. This is the first report on the development of kefir-myrtle beverage. Three factors were optimized (whey permeates (%), myrtle’s juice (%), and kefir grains as inoculum (%)) using a central composite design with response surface methodology. The analyses showed that the number of lactic acid bacteria (LAB) and yeast cells varied from 5.4 to 9.2 log10 CFU/mL and from 4.3 to 6.2 log10 CFU/mL, respectively. A decrease in pH and an increase in the total polyphenol content and antioxidant activity were observed. The analysis of variance indicated the goodness of fit of the model with R2 from 0.827 to 0.966. The absolute average deviation values of each model were low and ranged from 1.61% to 4.23%. The optimized fermented kefir whey beverage accomplished an overall acceptability of 5.41 (1 to 9 preference scale) and a high number of LAB cells (8.53 log10 CFU/mL). The viability of LAB and yeast cell was maintained at 7.61 and 6.19 log10 CFU/mL, respectively, after 14 days of storage.
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Takenaka S, Kawashima T, Arita M. A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria. FEMS Microbiol Lett 2021; 368:6360976. [PMID: 34468734 PMCID: PMC8440127 DOI: 10.1093/femsle/fnab117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.
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Affiliation(s)
- Shinkuro Takenaka
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kawashima
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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13
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Identification of a PadR-type regulator essential for intracellular pathogenesis of Burkholderia pseudomallei. Sci Rep 2021; 11:10405. [PMID: 34001967 PMCID: PMC8128862 DOI: 10.1038/s41598-021-89852-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/28/2021] [Indexed: 11/14/2022] Open
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis, a disease endemic to the tropics. Melioidosis manifests in various ways ranging from acute skin lesions to pneumonia and, in rare cases, infection of the central nervous system. Bp is a facultative intracellular pathogen and it can infect various cell types. The Bp intracellular lifecycle has been partially elucidated and is highly complex. Herein, we have identified a transcriptional regulator, BP1026B_II1198, that is differentially expressed as Bp transits through host cells. A deletion mutant of BP1026B_II1198 was attenuated in RAW264.7 cell and BALB/c mouse infection. To further characterize the function of this transcriptional regulator, we endeavored to determine the regulon of BP1026B_II1198. RNA-seq analysis showed the global picture of genes regulated while ChIP-seq analysis identified two specific BP1026B_II1198 binding regions on chromosome II. We investigated the transposon mutants of these genes controlled by BP1026B_II1198 and confirmed that these genes contribute to pathogenesis in RAW264.7 murine macrophage cells. Taken together, the data presented here shed light on the regulon of BP1026B_II1198 and its role during intracellular infection and highlights an integral portion of the highly complex regulation network of Bp during host infection.
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14
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Gaba S, Kumari A, Medema M, Kaushik R. Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order. Sci Rep 2020; 10:21205. [PMID: 33273480 PMCID: PMC7713125 DOI: 10.1038/s41598-020-77723-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Halobacteria, a class of Euryarchaeota are extremely halophilic archaea that can adapt to a wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl. It consists of the orders: Halobacteriales, Haloferaciales and Natriabales. Pan-genome analysis of class Halobacteria was done to explore the core (300) and variable components (Softcore: 998, Cloud:36531, Shell:11784). The core component revealed genes of replication, transcription, translation and repair, whereas the variable component had a major portion of environmental information processing. The pan-gene matrix was mapped onto the core-gene tree to find the ancestral (44.8%) and derived genes (55.1%) of the Last Common Ancestor of Halobacteria. A High percentage of derived genes along with presence of transformation and conjugation genes indicate the occurrence of horizontal gene transfer during the evolution of Halobacteria. A Core and pan-gene tree were also constructed to infer a phylogeny which implicated on the new super-order comprising of Natrialbales and Halobacteriales.
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Affiliation(s)
- Sonam Gaba
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.,Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Abha Kumari
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Marnix Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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Effects of Different Stress Parameters on Growth and on Oleuropein-Degrading Abilities of Lactiplantibacillus plantarum Strains Selected as Tailored Starter Cultures for Naturally Table Olives. Microorganisms 2020; 8:microorganisms8101607. [PMID: 33086685 PMCID: PMC7590217 DOI: 10.3390/microorganisms8101607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023] Open
Abstract
The use of β-glucosidase positive strains, as tailored-starter cultures for table olives fermentation, is a useful biotechnological tool applied to accelerate the debittering process. Nowadays, strains belonging to Lactiplantibacillus plantarum species are selected for their high versatility and tolerance to stress conditions. The present study investigated the effect of different stress factors (pH, temperature and NaCl) on growth and on oleuropein-degrading abilities of selected L. plantarum strains. In addition, the presence of the beta-glucosidase gene was investigated by applying a PCR based approach. Results revealed that, overall, the performances of the tested strains appeared to be robust toward the different stressors. However, the temperature of 16 °C significantly affected the growth performance of the strains both singularly and in combination with other stressing factors since it prolongs the latency phase and reduces the maximum growth rate of strains. Similarly, the oleuropein degradation was mainly affected by the low temperature, especially in presence of low salt content. Despite all strains displayed the ability to reduce the oleuropein content, the beta-glucosidase gene was detected in five out of the nine selected strains, demonstrating that the ability to hydrolyze the oleuropein is not closely related to the presence of beta-glucosidase. Data of the present study suggest that is extremely important to test the technological performances of strains at process conditions in order to achieve a good selection of tailored starter cultures for table olives.
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16
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Abstract
AbstractThis paper presents the effect of polyphenols on microorganisms inhabiting the human gastrointestinal tract (mainly bacteria belonging to the Lactobacillus genus) and pathogenic microorganisms classified as the most common food contaminants. Plant secondary metabolites have the ability to modulate the growth of many microorganisms. Due to the metabolic changes induced by their presence in the environment, many pathogenic microorganisms are unable to grow, which in turn cause a significant reduction in their pathogenic potential. These processes include primarily the induction of ruptures in the cell membrane and disturbance of cell respiration. Often, the lack of integrity of cell membranes also leads to the disturbance of intracellular homeostasis and leakage of cellular components, such as proteins, ATP molecules or intracellular ions. Autoxidizing polyphenols also act as pro-oxidative substances. Hydrogen peroxide formed in the process of oxidation of polyphenolic compounds acts as a bactericidal substance (by induction of DNA breaks). With regard to intestinal microbiota, polyphenols are considered prebiotic substances that increase the number of commensal bacteria. They can positively influence the growth of Lactobacillus bacteria, which have the ability to metabolize undigested antioxidants in the digestive tract of humans and animals. Depending on the pH of the environment and the presence of ions, plant polyphenols in the human digestive tract can act as substances with antioxidant potential or become pro-oxidants. Thus, combining functional food with polyphenols and Lactobacillus bacteria not only protects food products against the development of undesirable and pathogenic microbiota, but also has a positive effect on human health. The paper also describes the possibility of changes in the genome of Lactobacillus bacteria (under the influence of polyphenols) and the influence of Lactobacillus spp. bacteria on the antimicrobial properties of polyphenols. The enzymatic abilities of bacteria of the genus Lactobacillus, which influence the transformation of polyphenolic compounds, were also described.
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Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain. Sci Rep 2020; 10:10850. [PMID: 32616741 PMCID: PMC7331579 DOI: 10.1038/s41598-020-67635-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/05/2020] [Indexed: 01/09/2023] Open
Abstract
Isobutanol, in spite of its significant superiority over ethanol as a biofuel, remains commercially non-viable due to the non-availability of a suitable chassis which can handle the solvent toxicity associated with its production. To meet this challenge, we chose Lactococcus lactis which is known for its ability to handle environmental stress and carried out Adaptive laboratory evolution (ALE) in a continuous stirred tank reactor (CSTR) to evolve an isobutanol tolerant strain. The strain was grown for more than 60 days (> 250 generations) while gradually increasing the selection pressure, i.e. isobutanol concentration, in the feed. This led to the evolution of a strain that had an exceptionally high tolerance of up to 40 g/l of isobutanol even though a scanning electron microscope (SEM) study as well as analysis of membrane potential revealed only minor changes in cellular morphology. Whole genome sequencing which was done to confirm the strain integrity also showed comparatively few mutations in the evolved strain. However, the criticality of these mutations was reflected in major changes that occurred in the transcriptome, where gene expression levels from a wide range of categories that involved membrane transport, amino acid metabolism, sugar uptake and cell wall synthesis were significantly altered. Analysing the synergistic effect of these changes that lead to the complex phenotype of isobutanol tolerance can help in the construction of better host platforms for isobutanol production.
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18
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Microbiological, Biochemical, and Functional Aspects of Fermented Vegetable and Fruit Beverages. J CHEM-NY 2020. [DOI: 10.1155/2020/5790432] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In recent years, the request for the functional beverages that promote health and wellness has increased. In fact, fermented juices are an excellent delivering means for bioactive components. Their production is of crucial importance to supply probiotics, in particular, for people with particulars needs like dairy-product allergic consumers and vegetarians. This review focuses on recent findings regarding the microbial composition and the health benefits of fermented fruit and vegetable beverages by lactic acid bacteria, kefir grains, and SCOBY as well as discussing the metabolites resulting from these fermentations process. Moreover, limits that could restrain their production at the industrial level and solutions that have been proposed to overcome these constraints are also reviewed.
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19
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Prathiviraj R, Chellapandi P. Modeling a global regulatory network of Methanothermobacter thermautotrophicus strain ∆H. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s13721-020-0223-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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20
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Scornec H, Palud A, Pédron T, Wheeler R, Petitgonnet C, Boneca IG, Cavin JF, Sansonetti PJ, Licandro H. Study of the cwaRS-ldcA Operon Coding a Two-Component System and a Putative L,D-Carboxypeptidase in Lactobacillus paracasei. Front Microbiol 2020; 11:156. [PMID: 32194510 PMCID: PMC7062640 DOI: 10.3389/fmicb.2020.00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/22/2020] [Indexed: 11/22/2022] Open
Abstract
The cell surface is the primary recognition site between the bacterium and the host. An operon of three genes, LSEI_0219 (cwaR), LSEI_0220 (cwaS), and LSEI_0221 (ldcA), has been previously identified as required for the establishment of Lactobacillus paracasei in the gut. The genes cwaR and cwaS encode a predicted two-component system (TCS) and ldcA a predicted D-alanyl-D-alanine carboxypeptidase which is a peptidoglycan (PG) biosynthesis enzyme. We explored the functionality and the physiological role of these three genes, particularly their impact on the bacterial cell wall architecture and on the bacterial adaptation to environmental perturbations in the gut. The functionality of CwaS/R proteins as a TCS has been demonstrated by biochemical analysis. It is involved in the transcriptional regulation of several genes of the PG biosynthesis. Analysis of the muropeptides of PG in mutants allowed us to re-annotate LSEI_0221 as a putative L,D-carboxypeptidase (LdcA). The absence of this protein coincided with a decrease of two surface antigens: LSEI_0020, corresponding to p40 or msp2 whose implication in the host epithelial homeostasis has been recently studied, and LSEI_2029 which has never been functionally characterized. The inactivation of each of these three genes induces susceptibility to antimicrobial peptides (hBD1, hBD2, and CCL20), which could be the main cause of the gut establishment deficiency. Thus, this operon is necessary for the presence of two surface antigens and for a suitable cell wall architecture.
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Affiliation(s)
- Hélène Scornec
- PAM UMR, AgroSup Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aurore Palud
- PAM UMR, AgroSup Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Thierry Pédron
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
- Unité INSERM, Institut Pasteur, Paris, France
| | - Richard Wheeler
- Unité de Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur, Paris, France
- Avenir Group, INSERM, Paris, France
| | - Clément Petitgonnet
- PAM UMR, AgroSup Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Ivo Gomperts Boneca
- Unité de Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur, Paris, France
- Avenir Group, INSERM, Paris, France
| | - Jean-François Cavin
- PAM UMR, AgroSup Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Philippe J. Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
- Unité INSERM, Institut Pasteur, Paris, France
- Chaire de Microbiologie et Maladies Infectieuses, Collège de France, Paris, France
| | - Hélène Licandro
- PAM UMR, AgroSup Dijon, Université de Bourgogne Franche-Comté, Dijon, France
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21
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Zhang Y, Zhang W, Han L, Li J, Shi X, Hikichi Y, Ohnishi K. Involvement of a PadR regulator PrhP on virulence of Ralstonia solanacearum by controlling detoxification of phenolic acids and type III secretion system. MOLECULAR PLANT PATHOLOGY 2019; 20:1477-1490. [PMID: 31392803 PMCID: PMC6804342 DOI: 10.1111/mpp.12854] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Ralstonia solanacearum can metabolize ferulic acid (FA) and salicylic acid (SA), two representative phenolic acids, to protect it from toxicity of phenolic acids. Here, we genetically demonstrated a novel phenolic acid decarboxylase regulator (PadR)-like regulator PrhP as a positive regulator on detoxification of SA and FA in R. solanacearum. Although the ability to degrade SA and FA enhances the infection process of R. solanacearum toward host plants, PrhP greatly contributes to the infection process besides degradation of SA and FA. Our results from the growth assay, promoter activity assay, RNA-seq and qRT-PCR revealed that PrhP plays multiple roles in the virulence of R. solanacearum: (1) positively regulates expression of genes for degradation of SA and FA; (2) positively regulates expression of genes encoding type III secretion system (T3SS) and type III effectors both in vitro and in planta; (3) positively regulates expression of many virulence-related genes, such as the flagella, type IV pili and cell wall degradation enzymes; and (4) is important for the extensive proliferation in planta. The T3SS is one of the essential pathogenicity determinants in many pathogenic bacteria, and PrhP positively regulates its expression mediated with the key regulator HrpB but through some novel pathway to HrpB in R. solanacearum. This is the first report on PadR regulators to regulate the T3SS and it could improve our understanding of the various biological functions of PadR regulators and the complex regulatory pathway on T3SS in R. solanacearum.
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Affiliation(s)
- Yong Zhang
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
- Key Laboratory of Efficient Utilization of Soil and Fertilizer ResourcesChongqing
| | - Weiqi Zhang
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
| | - Liangliang Han
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
- Research Institute of Molecular Genetics, Kochi UniversityKochiJapan
| | - Jing Li
- The Ninth Peoples Hospital of ChongqingChongqingChina
| | - Xiaojun Shi
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
- Key Laboratory of Efficient Utilization of Soil and Fertilizer ResourcesChongqing
| | - Yasufumi Hikichi
- Laboratory of Plant Pathology and BiotechnologyKochi UniversityKochiJapan
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi UniversityKochiJapan
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22
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Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T. Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 2019; 4:e00288-19. [PMID: 31409660 PMCID: PMC6697440 DOI: 10.1128/msystems.00288-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023] Open
Abstract
Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Hauf S, Möller L, Fuchs S, Halbedel S. PadR-type repressors controlling production of a non-canonical FtsW/RodA homologue and other trans-membrane proteins. Sci Rep 2019; 9:10023. [PMID: 31296881 PMCID: PMC6624303 DOI: 10.1038/s41598-019-46347-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 06/27/2019] [Indexed: 01/02/2023] Open
Abstract
The Gram-positive bacterium Listeria monocytogenes occurs ubiquitously in the environment and infects humans upon ingestion. It encodes four PadR-like repressors, out of which LftR has been characterized previously and was shown to control gene expression in response to the antibiotic aurantimycin produced by other environmental bacteria. To better understand the PadR regulons of L. monocytogenes, we performed RNA-sequencing with mutants of the other three repressors LadR, LstR and Lmo0599. We show that LadR is primarily responsible for the regulation of the mdrL gene, encoding an efflux pump, while LstR and Lmo0599 mainly regulate their own operons. The lstR operon contains the lmo0421 gene, encoding a homolog of the RodA/FtsW protein family. However, this protein does not possess such functionality, as we demonstrate here. The lmo0599 operon contains two additional genes coding for the hypothetical trans-membrane proteins lmo0600 and lmo0601. A striking phenotype of the lmo0599 mutant is its impaired growth at refrigeration temperature. In light of these and other results we suggest that Lmo0599 should be renamed and propose LltR (listerial low temperature regulator) as its new designation. Based on the nature of the PadR target genes we assume that these repressors collectively respond to compounds acting on the cellular envelope.
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Affiliation(s)
- Samuel Hauf
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany
| | - Lars Möller
- ZBS 4 - Advanced Light and Electron Microscopy, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | - Stephan Fuchs
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, 38855, Wernigerode, Germany.
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24
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Antognoni F, Mandrioli R, Potente G, Taneyo Saa DL, Gianotti A. Changes in carotenoids, phenolic acids and antioxidant capacity in bread wheat doughs fermented with different lactic acid bacteria strains. Food Chem 2019; 292:211-216. [PMID: 31054667 DOI: 10.1016/j.foodchem.2019.04.061] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/08/2019] [Accepted: 04/16/2019] [Indexed: 10/27/2022]
Abstract
Amongst the processing technologies able to improve the functional features of cereal-based foods, sourdough fermentation using Lactic Acid Bacteria (LAB) has been recently rediscovered for its beneficial effects. Wheat (Triticum aestivum L.) bread doughs were prepared using LAB strains belonging to different Lactobacillus species and changes in phenolic acid, carotenoid content and antioxidant capacity were evaluated. Two L. plantarum strains out of six were able to significantly increase carotenoid content in the dough, suggesting that a higher mobilization/solubilisation of these antioxidant compounds occurs. Within different fractions (free, soluble-conjugated, insoluble-bound), the relative distribution of ferulic acid and antioxidant activity changes depending on the specific strain. Overall, results indicate that some LAB strains cause in situ changes, significantly increasing the content of functional compounds in doughs during fermentation. This, in turn, could improve the functional features of bakery foods characterised by a high content in carotenoids and other bioactive compounds.
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Affiliation(s)
- Fabiana Antognoni
- Department for Life Quality Studies, University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy.
| | - Roberto Mandrioli
- Department for Life Quality Studies, University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy.
| | - Giulia Potente
- Department for Life Quality Studies, University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Danielle Laure Taneyo Saa
- Department of Agricultural and Food Sciences and Technologies, University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Andrea Gianotti
- Department of Agricultural and Food Sciences and Technologies, University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy.
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25
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Card RM, La T, Burrough ER, Ellis RJ, Nunez-Garcia J, Thomson JR, Mahu M, Phillips ND, Hampson DJ, Rohde J, Tucker AW. Weakly haemolytic variants of Brachyspira hyodysenteriae newly emerged in Europe belong to a distinct subclade with unique genetic properties. Vet Res 2019; 50:21. [PMID: 30845993 PMCID: PMC6407217 DOI: 10.1186/s13567-019-0639-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/26/2019] [Indexed: 11/10/2022] Open
Abstract
Brachyspira (B.) hyodysenteriae is widespread globally, and can cause mucohaemorrhagic colitis (swine dysentery, SD) with severe economic impact in infected herds. Typical strains of B. hyodysenteriae are strongly haemolytic on blood agar, and the haemolytic activity is believed to contribute to virulence in vivo. However, recently there have been reports of atypical weakly haemolytic isolates of B. hyodysenteriae (whBh). In this study, 34 European whBh and 82 strongly haemolytic isolates were subjected to comparative genomic analysis. A phylogenetic tree constructed using core single nucleotide polymorphisms showed that the whBh formed a distinct sub-clade. All eight genes previously associated with haemolysis in B. hyodysenteriae were present in the whBh. No consistent patterns of amino acid substitutions for all whBh were found in these genes. In contrast, a genome region containing six coding sequences (CDSs) had consistent nucleotide sequence differences between strongly and whBh isolates. Two CDSs were predicted to encode ABC transporter proteins, and a TolC family protein, which may have a role in the export of haemolysins from B. hyodysenteriae. Another difference in this region was the presence of three CDSs in whBh that are pseudogenes in strongly haemolytic isolates. One of the intact CDSs from whBh encoded a predicted PadR-like transcriptional repressor that may play a role in repression of haemolysis functions. In summary, a sub-clade of whBh isolates has emerged in Europe, and several genomic differences, that potentially explain the weakly haemolytic phenotype, were identified. These markers may provide targets for discriminatory molecular tests needed in SD surveillance.
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Affiliation(s)
- Roderick M. Card
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, UK
| | - Tom La
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
| | - Eric R. Burrough
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, USA
| | - Richard J. Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, Addlestone, UK
| | - Javier Nunez-Garcia
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, Addlestone, UK
- Present Address: Genomics Medicine Ireland, Dublin, Ireland
| | | | - Maxime Mahu
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Nyree D. Phillips
- School of Veterinary and Life Sciences, Murdoch University, Perth, Australia
| | - David J. Hampson
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Judith Rohde
- Institute for Microbiology, University of Veterinary Medicine, Hannover, Germany
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Structural and functional characterization of the transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv. Biochem J 2018; 475:3393-3416. [DOI: 10.1042/bcj20180356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022]
Abstract
Rv3488 of Mycobacterium tuberculosis H37Rv has been assigned to the phenolic acid decarboxylase repressor (PadR) family of transcriptional regulators that play key roles in multidrug resistance and virulence of prokaryotes. The binding of cadmium, zinc, and several other metals to Rv3488 was discovered and characterized by isothermal titration calorimetery to be an exothermic process. Crystal structures of apo-Rv3488 and Rv3488 in complex with cadmium or zinc ions were determined by X-ray crystallography. The structure of Rv3488 revealed a dimeric protein with N-terminal winged-helix-turn-helix DNA-binding domains composed of helices α1, α2, α3, and strands β1 and β2, with the dimerization interface being formed of helices α4 and α1. The overall fold of Rv3488 was similar to PadR-s2 and metal sensor transcriptional regulators. In the crystal structure of Rv3488–Cd complex, two octahedrally coordinated Cd2+ ions were present, one for each subunit. The same sites were occupied by zinc ions in the structure of Rv3488–Zn, with two additional zinc ions complexed in one monomer. EMSA studies showed specific binding of Rv3488 with its own 30-bp promoter DNA. The functional role of Rv3488 was characterized by expressing the rv3488 gene under the control of hsp60 promoter in Mycobacterium smegmatis. Expression of Rv3488 increased the intracellular survival of recombinant M. smegmatis in murine macrophage cell line J774A.1 and also augmented its tolerance to Cd2+ ions. Overall, the studies show that Rv3488 may have transcription regulation and metal-detoxifying functions and its expression in M. smegmatis increases intracellular survival, perhaps by counteracting toxic metal stress.
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Pham N, Dao N, Saviola B. Over expression of the constitutive expression refractory Mycobacterium tuberculosis Rv3488 protein with an acid-inducible expression system. J Microbiol Methods 2018; 154:112-117. [PMID: 30287353 DOI: 10.1016/j.mimet.2018.09.021] [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: 04/11/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
As inducible protein expression plasmids available for mycobacterial species are limited, here we demonstrate the utility of an acid-inducible promoter driving gene and subsequent protein expression of a difficult to express protein. We wanted to assess the use of an acid inducible promoter expression system to produce proteins in a mycobacterial system, specifically proteins that when overexpressed interfere with mycobacterial cell growth. Overexpression of those types of proteins would require a tightly regulated promoter system. We employed the Mycobacterium tuberculosis lipF minimal acid-inducible promoter (mpr) which had previously been shown to be upregulated by acidic stress >100 X and to have a low basal level of expression in the absence of acidic stress. It is active from pH 4.3 up to pH 6.4 making this an acid range that is compatible with mycobacterial growth or survival and active at acidic ranges encountered in vivo within acidified phagosomes of macrophages. We therefore cloned the M. tuberculosis gene Rv3488, whose product had been unable to be expressed constitutively, into a plasmid downstream of the lipF mpr promoter and overexpressed this gene in the presence of acidic pH in Mycobacterium smegmatis. Sustained overexpression of the gene leads to inhibition of replication of mycobacterial cells as well as inhibition of carotenoid pigment synthesis, while short-term overexpression leads to appropriate protein expression.
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Affiliation(s)
- Nam Pham
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, 309 E. Second St. Pomona, CA 91766, United States
| | - Nelson Dao
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, 309 E. Second St. Pomona, CA 91766, United States
| | - Beatrice Saviola
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, 309 E. Second St. Pomona, CA 91766, United States.
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Kwak YM, Park SC, Na H, Kang SG, Lee G, Ko H, Kim P, Oh B, Yoon S. Crystal structure of the VanR transcription factor and the role of its unique α‐helix in effector recognition. FEBS J 2018; 285:3786-3800. [DOI: 10.1111/febs.14629] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/03/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Yun Mi Kwak
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Sun Cheol Park
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Hye‐won Na
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Seung Goo Kang
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
| | - Geun‐Shik Lee
- College of Veterinary Medicine Kangwon National University Chuncheon Korea
| | - Hyun‐Jeong Ko
- Laboratory of Microbiology and Immunology College of Pharmacy Kangwon National University Chuncheon Korea
| | - Pyeung‐Hyeun Kim
- Department of Molecular Bioscience School of Biomedical Science Kangwon National University Chuncheon Korea
| | - Byung‐Chul Oh
- Lee Gil Ya Cancer and Diabetes Institute College of Medicine Gachon University Incheon Korea
| | - Sung‐il Yoon
- Division of Biomedical Convergence College of Biomedical Science Kangwon National University Chuncheon Korea
- Institute of Bioscience and Biotechnology Kangwon National University Chuncheon Korea
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Maeda M, Tokashiki M, Tokashiki M, Uechi K, Ito S, Taira T. Characterization and induction of phenolic acid decarboxylase from Aspergillus luchuensis. J Biosci Bioeng 2018. [DOI: 10.1016/j.jbiosc.2018.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Carrasco JA, Lucena-Padrós H, Brenes M, Ruiz-Barba JL. Expression of genes involved in metabolism of phenolic compounds by Lactobacillus pentosus and its relevance for table-olive fermentations. Food Microbiol 2018; 76:382-389. [PMID: 30166164 DOI: 10.1016/j.fm.2018.06.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/07/2018] [Accepted: 06/30/2018] [Indexed: 11/20/2022]
Abstract
Genes with the potential to code for enzymes involved in phenolic compound metabolism were detected in the genome of Lactobacillus pentosus IG1, isolated from a green olive fermentation. Based on homology, these genes could code for a 6-P-β Glucosidase, two different Tannases, a Gallate decarboxylase and a p-Coumaric decarboxylase. Expression of up to seven of these genes was studied in L. pentosus IG1 (olive fermentation) and CECT4023T (corn silage), including responses upon exposure to relevant phenolic compounds and different olive extracts. Genes potentially coding Tannase, Gallate decarboxylase and p-Coumaric acid decarboxylase significatively increased their expression upon exposure to such compounds and extracts, although it was strain dependent. In general, both the genetic organization and the characteristics of gene expression resembled very much those described for Lactobacillus plantarum. In accordance to the observed induced gene expression, metabolism of specific phenolic compounds was achieved by L. pentosus. Thus, methyl gallate, gallic acid and the hydroxycinamic acids p-coumaric, caffeic and ferulic were metabolized. In addition, the amount of phenolics such as tyrosol, oleuropein, rutin and verbascoside included in a minimal culture medium was noticeably reduced, again dependent on the strain considered.
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Affiliation(s)
- José Antonio Carrasco
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario, Edificio 46, Carretera de Utrera, Km 1, 41013 Sevilla, Spain.
| | - Helena Lucena-Padrós
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario, Edificio 46, Carretera de Utrera, Km 1, 41013 Sevilla, Spain.
| | - Manuel Brenes
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario, Edificio 46, Carretera de Utrera, Km 1, 41013 Sevilla, Spain.
| | - José Luis Ruiz-Barba
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario, Edificio 46, Carretera de Utrera, Km 1, 41013 Sevilla, Spain.
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da Costa WLO, Araújo CLDA, Dias LM, Pereira LCDS, Alves JTC, Araújo FA, Folador EL, Henriques I, Silva A, Folador ARC. Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PLoS One 2018; 13:e0198965. [PMID: 29940001 PMCID: PMC6016940 DOI: 10.1371/journal.pone.0198965] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023] Open
Abstract
Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of this bacterium, and the use of bioinformatics tools can assist in the biological understanding of this organism through functional annotation analysis. Thus, our study aimed to assign functions to proteins previously described as HPs, present in the genome of E. antarcticum B7. We used an extensive in silico workflow combining several bioinformatics tools for function annotation, sub-cellular localization and physicochemical characterization, three-dimensional structure determination, and protein-protein interactions. This genome contains 2772 genes, of which 765 CDS were annotated as HPs. The amino acid sequences of all HPs were submitted to our workflow and we successfully attributed function to 132 HPs. We identified 11 proteins that play important roles in the mechanisms of adaptation to adverse environments, such as flagellar biosynthesis, biofilm formation, carotenoids biosynthesis, and others. In addition, three predicted HPs are possibly related to arsenic tolerance. Through an in vitro assay, we verified that E. antarcticum B7 can grow at high concentrations of this metal. The approach used was important to precisely assign function to proteins from diverse classes and to infer relationships with proteins with functions already described in the literature. This approach aims to produce a better understanding of the mechanism by which this bacterium adapts to extreme environments and to the finding of targets with biotechnological interest.
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Affiliation(s)
- Wana Lailan Oliveira da Costa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Carlos Leonardo de Aragão Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Larissa Maranhão Dias
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Lino César de Sousa Pereira
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Jorianne Thyeska Castro Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Fabrício Almeida Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraiba, João Pessoa, Paraíba, Brazil
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
- * E-mail: ,
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Blahut M, Dzul S, Wang S, Kandegedara A, Grossoehme NE, Stemmler T, Outten FW. Conserved cysteine residues are necessary for nickel-induced allosteric regulation of the metalloregulatory protein YqjI (NfeR) in E. coli. J Inorg Biochem 2018; 184:123-133. [PMID: 29723740 DOI: 10.1016/j.jinorgbio.2018.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 04/19/2018] [Accepted: 04/22/2018] [Indexed: 11/28/2022]
Abstract
Transition metal homeostasis is necessary to sustain life. First row transition metals act as cofactors within the cell, performing vital functions ranging from DNA repair to respiration. However, intracellular metal concentrations exceeding physiological requirements may be toxic. In E. coli, the YqjH flavoprotein is thought to play a role in iron homeostasis. YqjH is transcriptionally regulated by the ferric uptake regulator and a newly discovered regulator encoded by yqjI. The apo-form of YqjI is a transcriptional repressor of both the yqjH and yqjI genes. YqjI repressor function is disrupted upon binding of nickel. The YqjI N-terminus is homologous to nickel-binding proteins, implicating this region as a nickel-binding domain. Based on function, yqjI and yqjH should be renamed Ni-responsive Fe-uptake regulator (nfeR) and Ni-responsive Fe-uptake flavoprotein (nfeF), respectively. X-ray Absorption Spectroscopy was employed to characterize the nickel binding site(s) within YqjI. Putative nickel binding ligands were targeted by site-directed mutagenesis and resulting variants were analyzed in vivo for repressor function. Isothermal titration calorimetry and competitive binding assays were used to further quantify nickel interactions with wild-type YqjI and its mutant derivatives. Results indicate plasticity in the nickel binding domain of YqjI. Residues C42 and C43 were found to be required for in vivo response of YqjI to nickel stress, though these residues are not required for in vitro nickel binding. We propose that YqjI may contain a vicinal disulfide bond between C42 and C43 that is important for nickel-responsive allosteric interactions between YqjI domains.
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Affiliation(s)
- Matthew Blahut
- University of South Carolina, Department of Chemistry and Biochemistry, Columbia, SC 29208, USA
| | - Stephen Dzul
- Wayne State University, Department of Pharmaceutical Sciences, Detroit, MI 48201, USA
| | - Suning Wang
- University of South Carolina, Department of Chemistry and Biochemistry, Columbia, SC 29208, USA
| | - Ashoka Kandegedara
- Wayne State University, Department of Pharmaceutical Sciences, Detroit, MI 48201, USA
| | - Nicholas E Grossoehme
- Winthrop University, Department of Chemistry, Physics, and Geology, Rock Hill, SC 29733, USA
| | - Timothy Stemmler
- Wayne State University, Department of Pharmaceutical Sciences, Detroit, MI 48201, USA
| | - F Wayne Outten
- University of South Carolina, Department of Chemistry and Biochemistry, Columbia, SC 29208, USA.
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Park SC, Kwak YM, Song WS, Hong M, Yoon SI. Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR. Nucleic Acids Res 2018; 45:13080-13093. [PMID: 29136175 PMCID: PMC5728393 DOI: 10.1093/nar/gkx1055] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/19/2017] [Indexed: 12/24/2022] Open
Abstract
The PadR family is a large group of transcriptional regulators that function as environmental sensors. PadR negatively controls the expression of phenolic acid decarboxylase, which detoxifies harmful phenolic acids. To identify the mechanism by which PadR regulates phenolic acid-mediated gene expression, we performed structural and mutational studies of effector and operator recognition by Bacillus subtilis PadR. PadR contains an N-terminal winged helix-turn-helix (wHTH) domain (NTD) and a C-terminal homodimerization domain (CTD) and dimerizes into a dolmen shape. The PadR dimer interacts with the palindromic sequence of the operator DNA using the NTD. Two tyrosine residues and a positively charged residue in the NTD provide major DNA-binding energy and are highly conserved in the PadR family, suggesting that these three residues represent the canonical DNA-binding motif of the PadR family. PadR directly binds a phenolic acid effector molecule using a unique interdomain pocket created between the NTD and the CTD. Although the effector-binding site of PadR is positionally segregated from the DNA-binding site, effector binding to the interdomain pocket causes PadR to be rearranged into a DNA binding-incompatible conformer through an allosteric interdomain-reorganization mechanism.
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Affiliation(s)
- Sun Cheol Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yun Mi Kwak
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wan Seok Song
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.,Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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Valdetara F, Fracassetti D, Campanello A, Costa C, Foschino R, Compagno C, Vigentini I. A Response Surface Methodology Approach to Investigate the Effect of Sulfur Dioxide, pH, and Ethanol on DbCD and DbVPR Gene Expression and on the Volatile Phenol Production in Dekkera/Brettanomyces bruxellensis CBS2499. Front Microbiol 2017; 8:1727. [PMID: 28955312 PMCID: PMC5601905 DOI: 10.3389/fmicb.2017.01727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 08/24/2017] [Indexed: 11/21/2022] Open
Abstract
Dekkera/Brettanomyces bruxellensis, the main spoilage yeast in barrel-aged wine, metabolize hydroxycinnamic acids into off-flavors, namely ethylphenols. Recently, both the enzymes involved in this transformation, the cinnamate decarboxylase (DbCD) and the vinylphenol reductase (DbVPR), have been identified. To counteract microbial proliferation in wine, sulfur dioxide (SO2) is used commonly to stabilize the final product, but limiting its use is advised to preserve human health and boost sustainability in winemaking. In the present study, the influence of SO2 was investigated in relation with pH and ethanol factors on the expression of DbCD and DbVPR genes and volatile phenol production in D. bruxellensis CBS2499 strain under different model wines throughout a response surface methodology (RSM). In order to ensure an exact quantification of DbCD and DbVPR expression, an appropriate housekeeping gene was sought among DbPDC, DbALD, DbEF, DbACT, and DbTUB genes by GeNorm and Normfinder algorithms. The latter gene showed the highest expression stability and it was chosen as the reference housekeeping gene in qPCR assays. Even though SO2 could not be commented as main factor because of its statistical irrelevance on the response of DbCD gene, linear interactions with pH and ethanol concurred to define a significant effect (p < 0.05) on its expression. The DbCD gene was generally downregulated respect to a permissive growth condition (0 mg/L mol. SO2, pH 4.5 and 5% v/v ethanol); the combination of the factor levels that maximizes its expression (0.83-fold change) was calculated at 0.25 mg/L mol. SO2, pH 4.5 and 12.5% (v/v) ethanol. On the contrary, DbVPR expression was not influenced by main factors or by their interactions; however, its expression is maximized (1.80-fold change) at the same conditions calculated for DbCD gene. While no linear interaction between factors influenced the off-flavor synthesis, ethanol and pH produced a significant effect as individual factors. The obtained results can be useful to improve the SO2 management at the grape harvesting and during winemaking in order to minimize the D./B. bruxellensis spoilage.
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Affiliation(s)
- Federica Valdetara
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di MilanoMilan, Italy
| | - Daniela Fracassetti
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di MilanoMilan, Italy
| | - Alessia Campanello
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di MilanoMilan, Italy
| | | | - Roberto Foschino
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di MilanoMilan, Italy
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di MilanoMilan, Italy
| | - Ileana Vigentini
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di MilanoMilan, Italy
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Transcriptional Repressor PtvR Regulates Phenotypic Tolerance to Vancomycin in Streptococcus pneumoniae. J Bacteriol 2017; 199:JB.00054-17. [PMID: 28484041 DOI: 10.1128/jb.00054-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/26/2017] [Indexed: 02/05/2023] Open
Abstract
Reversible or phenotypic tolerance to antibiotics within microbial populations has been implicated in treatment failure of chronic infections and development of persister cells. However, the molecular mechanisms regulating phenotypic drug tolerance are largely unknown. In this study, we identified a four-gene operon in Streptococcus pneumoniae that contributes to phenotypic tolerance to vancomycin (ptv). RNA sequencing, quantiative reverse transcriptase PCR, and transcriptional luciferase reporter experiments revealed that transcription of the ptv operon (consisting of ptvR, ptvA, ptvB, and ptvC) is induced by exposure to vancomycin. Further investigation showed that transcription of the ptv operon is repressed by PtvR, a PadR family repressor. Transcriptional induction of the ptv operon by vancomycin was achieved by transcriptional derepression of this locus, which was mediated by PtvR. Importantly, fully derepressing ptvABC by deleting ptvR or overexpressing the ptv operon with an exogenous promoter significantly enhanced vancomycin tolerance. Gene deletion analysis revealed that PtvA, PtvB, and PtvC are all required for the PtvR-regulated phenotypic tolerance to vancomycin. Finally, the results of an electrophoretic mobility shift assay with recombinant PtvR showed that PtvR represses the transcription of the ptv operon by binding to two palindromic sequences within the ptv promoter. Together, the ptv locus represents an inducible system in S. pneumoniae in response to stressful conditions, including those caused by antibiotics.IMPORTANCE Reversible or phenotypic tolerance to antibiotics within microbial populations is associated with treatment failure of bacterial diseases, but the underlying mechanisms regulating phenotypic drug tolerance remain obscure. This study reports our finding of a multigene locus that contributes to inducible tolerance to vancomycin in Streptococcus pneumoniae, an important opportunistic human pathogen. The vancomycin tolerance phenotype depends on the PtvR transcriptional repressor and three predicted membrane-associated proteins encoded by the ptv locus. This represents the first example of a gene locus in S. pneumoniae that is responsible for antibiotic tolerance and has important implications for further understanding bacterial responses and phenotypic tolerance to antibiotic treatment in this and other pathogens.
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Mo X, Shi C, Gui C, Zhang Y, Ju J, Wang Q. Identification of nocamycin biosynthetic gene cluster from Saccharothrix syringae NRRL B-16468 and generation of new nocamycin derivatives by manipulating gene cluster. Microb Cell Fact 2017; 16:100. [PMID: 28599654 PMCID: PMC5466765 DOI: 10.1186/s12934-017-0718-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/05/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Nocamycins I and II, produced by the rare actinomycete Saccharothrix syringae, belong to the tetramic acid family natural products. Nocamycins show potent antimicrobial activity and they hold great potential for antibacterial agent design. However, up to now, little is known about the exact biosynthetic mechanism of nocamycin. RESULTS In this report, we identified the gene cluster responsible for nocamycin biosynthesis from S. syringae and generated new nocamycin derivatives by manipulating its gene cluster. The biosynthetic gene cluster for nocamycin contains a 61 kb DNA locus, consisting of 21 open reading frames (ORFs). Five type I polyketide synthases (NcmAI, NcmAII, NcmAIII, NcmAIV, NcmAV) and a non-ribosomal peptide synthetase (NcmB) are proposed to be involved in synthesis of the backbone structure, a Dieckmann cyclase NcmC catalyze the releasing of linear chain and the formation of tetramic acid moiety, five enzymes (NcmEDGOP) are related to post-tailoring steps, and five enzymes (NcmNJKIM) function as regulators. Targeted inactivation of ncmB led to nocamycin production being completely abolished, which demonstrates that this gene cluster is involved in nocamycin biosynthesis. To generate new nocamycin derivatives, the gene ncmG, encoding for a cytochrome P450 oxidase, was inactivated. Two new nocamycin derivatives nocamycin III and nocamycin IV were isolated from the ncmG deletion mutant strain and their structures were elucidated by spectroscopic data analyses. Based on bioinformatics analysis and new derivatives isolated from gene inactivation mutant strains, a biosynthetic pathway of nocamycins was proposed. CONCLUSION These findings provide the basis for further understanding of nocamycin biosynthetic mechanism, and set the stage to rationally engineer new nocamycin derivatives via combinatorial biosynthesis strategy.
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Affiliation(s)
- Xuhua Mo
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
| | - Chunrong Shi
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
| | - Chun Gui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Rd., Guangzhou, 510301 China
| | - Yanjiao Zhang
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Rd., Guangzhou, 510301 China
| | - Qingji Wang
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
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Takeuchi K, Imai M, Shimada I. Dynamic equilibrium on DNA defines transcriptional regulation of a multidrug binding transcriptional repressor, LmrR. Sci Rep 2017; 7:267. [PMID: 28325892 PMCID: PMC5428041 DOI: 10.1038/s41598-017-00257-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/14/2017] [Indexed: 11/09/2022] Open
Abstract
LmrR is a multidrug binding transcriptional repressor that controls the expression of a major multidrug transporter, LmrCD, in Lactococcus lactis. Promiscuous compound ligations reduce the affinity of LmrR for the lmrCD operator by several fold to release the transcriptional repression; however, the affinity reduction is orders of magnitude smaller than that of typical transcriptional repressors. Here, we found that the transcriptional regulation of LmrR is achieved through an equilibrium between the operator-bound and non-specific DNA-adsorption states in vivo. The effective dissociation constant of LmrR for the lmrCD operator under the equilibrium is close to the endogenous concentration of LmrR, which allows a substantial reduction of LmrR occupancy upon compound ligations. Therefore, LmrR represents a dynamic type of transcriptional regulation of prokaryotic multidrug resistance systems, where the small affinity reduction induced by compounds is coupled to the functional relocalization of the repressor on the genomic DNA via nonspecific DNA adsorption.
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Affiliation(s)
- Koh Takeuchi
- Biomedicinal Information Research Center & Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan.,PRESTO, JST, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan
| | - Misaki Imai
- Research and Development Department, Japan Biological Informatics Consortium, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan
| | - Ichio Shimada
- Biomedicinal Information Research Center & Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Aomi 2-3-26, Koto-ku, Tokyo, 135-0064, Japan. .,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Rozhon W. The replication protein of pHW126 auto-controls its expression. Plasmid 2017; 90:38-43. [PMID: 28300545 DOI: 10.1016/j.plasmid.2017.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
Abstract
pHW126 belongs to a small group of rolling circle plasmids. So far, the region mediating autonomous replication has been identified and it was shown that the rep gene is required for replication. However, the regulation of rep expression remained elusive. Here evidence is presented that expression of the replication gene rep is auto-regulated. Sequence analysis revealed a conserved stretch in the rep promoter consisting of three imperfect direct repeats (DR2.1, DR2.2 and DR2.3). Assays for promoter activity showed that these direct repeats act as an enhancer of transcriptional activity. Interestingly, the activating effect was reduced in the presence of Rep protein. Electrophoretic mobility shift assays demonstrated that the Rep protein can directly bind to direct repeats DR2.1 and DR2.3 while DR2.2 is not bound but places DR2.1 and DR2.3 in an appropriate distance. These results show that the synthesis of Rep protein is auto-regulated. In the absence of Rep protein the promoter is, due to the presence of the direct repeats acting as a transcriptional enhancer, highly active. Binding of Rep to the direct repeats reduces the transcription rate significantly. Since this regulation mechanism is independent of a specialised regulator protein it is presumably a very economic strategy.
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Affiliation(s)
- Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School for Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Straße 1, 85354 Freising-Weihenstephan, Germany.
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Baiano A, Scrocco C, Sepielli G, Del Nobile MA. Wine Processing: A Critical Review of Physical, Chemical, and Sensory Implications of Innovative Vinification Procedures. Crit Rev Food Sci Nutr 2017; 56:2391-407. [PMID: 25629416 DOI: 10.1080/10408398.2013.842886] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Wine is one of the most popular alcoholic beverages in the world, although it is mainly consumed in European and South American countries. Several thousand years have passed since the product of grape fermentation was accidentally discovered. Over the last 100-150 years, winemaking has been completely revolutionized in terms of procedures and equipment. This work is aimed to give a comprehensive overview of the consolidated use of winemaking innovations that are still in the development stage or already applied to commercial products. Their effects on physical, chemical, and sensory characteristics of wines will also be discussed in comparison with the consolidated vinification procedures.
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Affiliation(s)
- Antonietta Baiano
- a Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente , University of Foggia , Foggia , Italy
| | - Carmela Scrocco
- a Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente , University of Foggia , Foggia , Italy
| | - Grazia Sepielli
- a Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente , University of Foggia , Foggia , Italy
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Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis. Biochem Biophys Res Commun 2016; 483:264-270. [PMID: 28027933 DOI: 10.1016/j.bbrc.2016.12.155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 11/21/2022]
Abstract
A phenolic acid decarboxylase (padC) regulator, PadR and its homologs proteins belong to the PadR family. Despite the growing numbers of the PadR family members and their various roles in bacteria, such as detoxifications, drug transports and circadian rhythms, biochemical and biophysical studies of the PadR family are very limited. Thus, a ligand-induced regulatory mechanism of the PadR family transcription factors remains to be elucidated. Here, we report a crystal structure of a Bacteroides fragilis PadR-like protein, BF2549 and revealed its interaction with putative operator DNA and ligand molecules. Comparative structural and primary sequence analyses provide a PadR-specific motif that is conserved in the PadR family but deviated from the MarR family. Furthermore, putative ligand binding sites are observed in the BF2549 structure. Finally, a homology-based structure model of BF2549 and 29-mer dsDNA propose regulatory mechanisms of the PadR family in transcriptional derepression.
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Isom CE, Menon SK, Thomas LM, West AH, Richter-Addo GB, Karr EA. Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291. BMC Microbiol 2016; 16:231. [PMID: 27716049 PMCID: PMC5050560 DOI: 10.1186/s12866-016-0850-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/24/2016] [Indexed: 01/05/2023] Open
Abstract
Background Clostridium difficile is a spore-forming obligate anaerobe that can remain viable for extended periods, even in the presence of antibiotics, which contributes to the persistence of this bacterium as a human pathogen during host-to-host transmission and in hospital environments. We examined the structure and function of a gene product with the locus tag CDR20291_0991 (cdPadR1) as part of our broader goal aimed at elucidating transcription regulatory mechanisms involved in virulence and antibiotic resistance of the recently emergent hypervirulent C. difficile strain R20291. cdPadR1 is genomically positioned near genes that are involved in stress response and virulence. In addition, it was previously reported that cdPadR1 and a homologue from the historical C. difficile strain 630 (CD630_1154) were differentially expressed when exposed to stressors, including antibiotics. Results The crystal structure of cdPadR1 was determined to 1.9 Å resolution, which revealed that it belongs to the PadR-s2 subfamily of PadR transcriptional regulators. cdPadR1 binds its own promoter and other promoter regions from within the C. difficile R20291 genome. DNA binding experiments demonstrated that cdPadR1 binds a region comprised of inverted repeats and an AT-rich core with the predicted specific binding motif, GTACTAT(N2)ATTATA(N)AGTA, within its own promoter that is also present in 200 other regions in the C. difficile R20291 genome. Mutation of the highly conserved W in α4 of the effector binding/oligomerization domain, which is predicted to be involved in multi-drug recognition and dimerization in other PadR-s2 proteins, resulted in alterations of cdPadR1 binding to the predicted binding motif, potentially due to loss of higher order oligomerization. Conclusions Our results indicate that cdPadR1 binds a region within its own promoter consisting of the binding motif GTACTAT(N2)ATTATA(N)AGTA and seems to associate non-specifically with longer DNA fragments in vitro, which may facilitate promoter and motif searching. This suggests that cdPadR1 acts as a transcriptional auto-regulator, binding specific sites within its own promoter, and is part of a broad gene regulatory network involved, in part, with environmental stress response, antibiotic resistance and virulence. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0850-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catherine E Isom
- Price Family Foundation Institute of Structural Biology and Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA.,Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Smita K Menon
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Leonard M Thomas
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Ann H West
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - George B Richter-Addo
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Elizabeth A Karr
- Price Family Foundation Institute of Structural Biology and Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA.
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Zaccaria E, Wells JM, van Baarlen P. Metabolic Context of the Competence-Induced Checkpoint for Cell Replication in Streptococcus suis. PLoS One 2016; 11:e0153571. [PMID: 27149631 PMCID: PMC4858297 DOI: 10.1371/journal.pone.0153571] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/31/2016] [Indexed: 11/19/2022] Open
Abstract
Natural genetic transformation is a transient, rapidly progressing energy-consuming process characterized by expression of the transformasome and competence-associated regulatory genes. This transient state is tightly controlled to avoid potentially adverse effects of genetic recombination on genome integrity during cell division. We investigated the global response of Streptococcus suis to exposure to the SigX competence-inducing peptide (XIP), and thus to the activation of the competence machinery, using time series analysis together with PCA analysis, gene clustering followed by heatmap visualisation, and GO enrichment analysis. We explored the possible regulatory link between metabolism and competence, and predicted the physiological adaptation of S. suis during competence induction, progression and exit using transcriptome analysis. We showed that competence development is associated with a suppression of basal metabolism, which may have consequences for the microbe's resilience to fluctuations in the environment, as competence is costly in terms of use of energy and protein translation. Furthermore our data suggest that several basal metabolic pathways are incompatible with activation of competence in S. suis. This study also showed that targeting specific pathways during the development of competence, might render S. suis more vulnerable toward novel antibiotic therapies.
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Affiliation(s)
- Edoardo Zaccaria
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Jerry M. Wells
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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Li S, Hwang XY, Stav S, Breaker RR. The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA (NEW YORK, N.Y.) 2016; 22:530-41. [PMID: 26843526 PMCID: PMC4793209 DOI: 10.1261/rna.054890.115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/10/2015] [Indexed: 05/21/2023]
Abstract
The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or "azaaromatics," trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics.
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Affiliation(s)
- Sanshu Li
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Xue Ying Hwang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Shira Stav
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
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An R, Grewal PS. Comparative Analysis of Xenorhabdus koppenhoeferi Gene Expression during Symbiotic Persistence in the Host Nematode. PLoS One 2016; 11:e0145739. [PMID: 26745883 PMCID: PMC4706420 DOI: 10.1371/journal.pone.0145739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/08/2015] [Indexed: 01/24/2023] Open
Abstract
Species of Xenorhabdus and Photorhabdus bacteria form mutualistic associations with Steinernema and Heterorhabditis nematodes, respectively and serve as model systems for studying microbe-animal symbioses. Here, we profiled gene expression of Xenorhabdus koppenhoeferi during their symbiotic persistence in the newly formed infective juveniles of the host nematode Steinernema scarabaei through the selective capture of transcribed sequences (SCOTS). The obtained gene expression profile was then compared with other nematode-bacteria partnerships represented by Steinernema carpocapsae-Xenorhabdus nematophila and Heterorhabditis bacteriophora-Photorhabdus temperata. A total of 29 distinct genes were identified to be up-regulated and 53 were down-regulated in X. koppenhoeferi while in S. scarabaei infective juveniles. Of the identified genes, 8 of the up-regulated and 14 of the down-regulated genes were similarly expressed in X. nematophila during persistence in its host nematode S. carpocapsae. However, only one from each of these up- and down-regulated genes was common to the mutualistic partnership between the bacterium P. temperata and the nematode H. bacteriophora. Interactive network analysis of the shared genes between X. koppenhoeferi and X. nematophila demonstrated that the up-regulated genes were mainly involved in bacterial survival and the down-regulated genes were more related to bacterial virulence and active growth. Disruption of two selected genes pta (coding phosphotransacetylase) and acnB (coding aconitate hydratase) in X. nematophila with shared expression signature with X. koppenhoeferi confirmed that these genes are important for bacterial persistence in the nematode host. The results of our comparative analyses show that the two Xenorhabdus species share a little more than a quarter of the transcriptional mechanisms during persistence in their nematode hosts but these features are quite different from those used by P. temperata bacteria in their nematode host H. bacteriophora.
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Affiliation(s)
- Ruisheng An
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E. J. Chapman Drive, Knoxville, TN, 37996, United States of America
| | - Parwinder S. Grewal
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E. J. Chapman Drive, Knoxville, TN, 37996, United States of America
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Flórez AB, Álvarez S, Zabala D, Braña AF, Salas JA, Méndez C. Transcriptional regulation of mithramycin biosynthesis in Streptomyces argillaceus: dual role as activator and repressor of the PadR-like regulator MtrY. MICROBIOLOGY-SGM 2015; 161:272-284. [PMID: 25416691 DOI: 10.1099/mic.0.080895-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The mithramycin biosynthesis gene cluster of Streptomyces argillaceus ATCC 12956 contains 34 ORFs and includes two putative regulatory genes (mtmR and mtrY), which encode proteins of the SARP (Streptomyces antibiotic regulatory protein) and PadR transcriptional regulator families, respectively. MtmR was proposed to behave as a positive regulator of mithramycin biosynthesis. Inactivation and overexpression of mtrY indicated that it is also a positive regulator of mithramycin biosynthesis, being non-essential but required to maintain high levels of mithramycin production in the producer strain. Transcriptional analyses by reverse transcription PCR and quantitative real-time PCR of mithramycin genes, and promoter-probe assays in S. argillaceus polyketide synthase and regulatory mutants and the WT strain, and in the heterologous host Streptomyces albus, were carried out to analyse the role of MtmR and MtrY in the regulation of the mithramycin gene cluster. These experiments revealed that MtmR had a positive role, activating expression of at least six polycistronic units (mtmR-mtmE, mtmQ-mtmTII, mtmX-mtmY, mtmV-mtmTIII, mtmW-mtmMI and mtmGI-mtrB) and one monocistronic unit (mtmGII) in the mithramycin gene cluster. However, MtrY played a dual role in the mithramycin gene cluster: (i) repressing the expression of resistance genes and its coding gene itself by controlling the activity of the mtrYp promoter that directs expression of the regulator mtrY and resistance genes, with this repression being released in the presence of mithramycin; and (ii) enhancing the expression of mithramycin biosynthesis genes when mithramycin is present, by interacting with the mtmRp promoter that controls expression of the mtmR regulator, amongst others.
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Affiliation(s)
- Ana B Flórez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Susana Álvarez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Daniel Zabala
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
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Chen P, Dong J, Yin H, Bao X, Chen L, He Y, Wan X, Chen R, Zhao Y, Hou X. Single nucleotide polymorphisms and transcription analysis of genes involved in ferulic acid decarboxylation among different beer yeasts. JOURNAL OF THE INSTITUTE OF BREWING 2015. [DOI: 10.1002/jib.249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Peng Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Jianjun Dong
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Hua Yin
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 People's Republic of China
| | - Lu Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Yang He
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Xiujuan Wan
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Rong Chen
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Yuxiang Zhao
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
| | - Xiaoping Hou
- State Key Laboratory of Biological Fermentation Engineering of Beer; Tsingtao Brewery Co. Ltd; Qingdao 266061 People's Republic of China
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van der Berg JP, Madoori PK, Komarudin AG, Thunnissen AM, Driessen AJM. Binding of the Lactococcal Drug Dependent Transcriptional Regulator LmrR to Its Ligands and Responsive Promoter Regions. PLoS One 2015; 10:e0135467. [PMID: 26267906 PMCID: PMC4534193 DOI: 10.1371/journal.pone.0135467] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/22/2015] [Indexed: 11/18/2022] Open
Abstract
The heterodimeric ABC transporter LmrCD from Lactococcus lactis is able to extrude several different toxic compounds from the cell, fulfilling a role in the intrinsic and induced drug resistance. The expression of the lmrCD genes is regulated by the multi-drug binding repressor LmrR, which also binds to its own promoter to autoregulate its own expression. Previously, we reported the crystal structure of LmrR in the presence and absence of the drugs Hoechst 33342 and daunomycin. Analysis of the mechanism how drugs control the repressor activity of LmrR is impeded by the fact that these drugs also bind to DNA. Here we identified, using X-ray crystallography and fluorescence, that riboflavin binds into the drug binding cavity of LmrR, adopting a similar binding mode as Hoechst 33342 and daunomycin. Microscale thermophoresis was employed to quantify the binding affinity of LmrR to its responsive promoter regions and to evaluate the cognate site of LmrR in the lmrCD promoter region. Riboflavin reduces the binding affinity of LmrR for the promoter regions. Our results support a model wherein drug binding to LmrR relieves the LmrR dependent repression of the lmrCD genes.
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Affiliation(s)
- Jan Pieter van der Berg
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Pramod Kumar Madoori
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Amalina Ghaisani Komarudin
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Andy-Mark Thunnissen
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- * E-mail:
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Payero TD, Vicente CM, Rumbero Á, Barreales EG, Santos-Aberturas J, de Pedro A, Aparicio JF. Functional analysis of filipin tailoring genes from Streptomyces filipinensis reveals alternative routes in filipin III biosynthesis and yields bioactive derivatives. Microb Cell Fact 2015; 14:114. [PMID: 26246267 PMCID: PMC4527110 DOI: 10.1186/s12934-015-0307-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/28/2015] [Indexed: 12/11/2022] Open
Abstract
Background Streptomyces filipinensis is the industrial producer of filipin, a pentaene macrolide, archetype of non-glycosylated polyenes, and widely used for the detection and the quantitation of cholesterol in biological membranes and as a tool for the diagnosis of Niemann–Pick type C disease. Genetic manipulations of polyene biosynthetic pathways have proven useful for the discovery of products with improved properties. Here, we describe the late biosynthetic steps for filipin III biosynthesis and strategies for the generation of bioactive filipin III derivatives at high yield. Results A region of 13,778 base pairs of DNA from the S. filipinensis genome was isolated, sequenced, and characterized. Nine complete genes and two truncated ORFs were located. Disruption of genes proved that this genomic region is part of the biosynthetic cluster for the 28-membered ring of the polyene macrolide filipin. This set of genes includes two cytochrome P450 monooxygenase encoding genes, filC and filD, which are proposed to catalyse specific hydroxylations of the macrolide ring at C26 and C1′ respectively. Gene deletion and complementation experiments provided evidence for their role during filipin III biosynthesis. Filipin III derivatives were accumulated by the recombinant mutants at high yield. These have been characterized by mass spectrometry and nuclear magnetic resonance following high-performance liquid chromatography purification thus revealing the post-polyketide steps during polyene biosynthesis. Two alternative routes lead to the formation of filipin III from the initial product of polyketide synthase chain assembly and cyclization filipin I, one trough filipin II, and the other one trough 1′-hydroxyfilipin I, all filipin III intermediates being biologically active. Moreover, minimal inhibitory concentration values against Candida utilis and Saccharomyces cerevisiae were obtained for all filipin derivatives, finding that 1′-hydroxyfilipin and especially filipin II show remarkably enhanced antifungal bioactivity. Complete nuclear magnetic resonance assignments have been obtained for the first time for 1′-hydroxyfilipin I. Conclusions This report reveals the existence of two alternative routes for filipin III formation and opens new possibilities for the generation of biologically active filipin derivatives at high yield and with improved properties. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0307-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamara D Payero
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain. .,Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain.
| | - Cláudia M Vicente
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain. .,Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain.
| | - Ángel Rumbero
- Department of Organic Chemistry, Faculty of Sciences, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Eva G Barreales
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
| | - Javier Santos-Aberturas
- Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain. .,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Antonio de Pedro
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
| | - Jesús F Aparicio
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
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Kaval KG, Hahn B, Tusamda N, Albrecht D, Halbedel S. The PadR-like transcriptional regulator LftR ensures efficient invasion of Listeria monocytogenes into human host cells. Front Microbiol 2015; 6:772. [PMID: 26284051 PMCID: PMC4517056 DOI: 10.3389/fmicb.2015.00772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/14/2015] [Indexed: 12/11/2022] Open
Abstract
Invasion of the bacterial pathogen Listeria monocytogenes into human host cells requires specialized surface molecules for attachment and induction of phagocytosis. However, efficient invasion is also dependent on factors with house-keeping functions, such as SecA2-dependent secretion of autolysins for post-divisional segregation of daughter cells. Mutations in this pathway prevent degradation of peptidoglycan cross-walls, so that long cell chains are formed that cannot be phagocytosed. The extreme chaining of such mutants manifests as rough colony phenotype. One rough clone was isolated from a transposon library with a transposon insertion in the uncharacterized lmo0720 gene (lftS) together with a spontaneous point mutation in the secA2 gene. We separated both mutations and demonstrated that this point mutation in the intramolecular regulator 2 domain of SecA2 was sufficient to inactivate the protein. In contrast, lftS deletion did not cause a ΔsecA2-like phenotype. lftS is located in an operon with lftR (lmo0719), encoding a PadR-like transcriptional regulator, and lftR deletion affected growth, invasion and day-light dependent coordination of swarming. Inactivation of lftS partially suppressed these phenotypes, suggesting a functional relationship between LftR and LftS. However, the invasion defect of the ΔlftR mutant was only marginally suppressed by lftS removal. LftR regulates expression of the lmo0979–0980 (lieAB) operon, encoding a putative multidrug resistance transporter and lieAB transcription was strongly upregulated in the absence of LftR. Deletion of lieAB in the ΔlftR background restores wild type-like invasion levels. Hence, we conclude that tight transcriptional repression of the lieAB operon is essential for efficient listerial host cell invasion.
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Affiliation(s)
- Karan G Kaval
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute Wernigerode, Germany
| | - Birgitt Hahn
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute Wernigerode, Germany
| | - Nayana Tusamda
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute Wernigerode, Germany
| | - Dirk Albrecht
- Institute of Microbiology, University of Greifswald Greifswald, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute Wernigerode, Germany
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Perera VR, Newton GL, Pogliano K. Bacillithiol: a key protective thiol in Staphylococcus aureus. Expert Rev Anti Infect Ther 2015; 13:1089-107. [PMID: 26184907 DOI: 10.1586/14787210.2015.1064309] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillithiol is a low-molecular-weight thiol analogous to glutathione and is found in several Firmicutes, including Staphylococcus aureus. Since its discovery in 2009, bacillithiol has been a topic of interest because it has been found to contribute to resistance during oxidative stress and detoxification of electrophiles, such as the antibiotic fosfomycin, in S. aureus. The rapid increase in resistance of methicillin-resistant Staphylococcus aureus (MRSA) to available therapeutic agents is a great health concern, and many research efforts are focused on identifying new drugs and targets to combat this organism. This review describes the discovery of bacillithiol, studies that have elucidated the physiological roles of this molecule in S. aureus and other Bacilli, and the contribution of bacillithiol to S. aureus fitness during pathogenesis. Additionally, the bacillithiol biosynthesis pathway is evaluated as a novel drug target that can be utilized in combination with existing therapies to treat S. aureus infections.
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Affiliation(s)
- Varahenage R Perera
- Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, Natural Sciences Building 4113, La Jolla, CA 92093-0377, USA
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