51
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Methanotrophy across a natural permafrost thaw environment. ISME JOURNAL 2018; 12:2544-2558. [PMID: 29955139 PMCID: PMC6155033 DOI: 10.1038/s41396-018-0065-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 11/09/2022]
Abstract
The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ13C-CH4 isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.
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52
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Halla N, Fernandes IP, Heleno SA, Costa P, Boucherit-Otmani Z, Boucherit K, Rodrigues AE, Ferreira ICFR, Barreiro MF. Cosmetics Preservation: A Review on Present Strategies. Molecules 2018; 23:E1571. [PMID: 29958439 PMCID: PMC6099538 DOI: 10.3390/molecules23071571] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/24/2018] [Accepted: 06/26/2018] [Indexed: 12/17/2022] Open
Abstract
Cosmetics, like any product containing water and organic/inorganic compounds, require preservation against microbial contamination to guarantee consumer’s safety and to increase their shelf-life. The microbiological safety has as main goal of consumer protection against potentially pathogenic microorganisms, together with the product’s preservation resulting from biological and physicochemical deterioration. This is ensured by chemical, physical, or physicochemical strategies. The most common strategy is based on the application of antimicrobial agents, either by using synthetic or natural compounds, or even multifunctional ingredients. Current validation of a preservation system follow the application of good manufacturing practices (GMPs), the control of the raw material, and the verification of the preservative effect by suitable methodologies, including the challenge test. Among the preservatives described in the positive lists of regulations, there are parabens, isothiasolinone, organic acids, formaldehyde releasers, triclosan, and chlorhexidine. These chemical agents have different mechanisms of antimicrobial action, depending on their chemical structure and functional group’s reactivity. Preservatives act on several cell targets; however, they might present toxic effects to the consumer. Indeed, their use at high concentrations is more effective from the preservation viewpoint being, however, toxic for the consumer, whereas at low concentrations microbial resistance can develop.
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Affiliation(s)
- Noureddine Halla
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LAPSAB), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000 Tlemcen, Algeria.
- Laboratory of Biotoxicology, Pharmacognosy and Biological Recovery of Plants, Department of Biology, Faculty of Sciences, University of Moulay-Tahar, 20000 Saida, Algeria.
| | - Isabel P Fernandes
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), Polytechnic Institute of Bragança, Campus Santa Apolónia, 5301-253 Bragança, Portugal.
| | - Sandrina A Heleno
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), Polytechnic Institute of Bragança, Campus Santa Apolónia, 5301-253 Bragança, Portugal.
| | - Patrícia Costa
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
| | - Zahia Boucherit-Otmani
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LAPSAB), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000 Tlemcen, Algeria.
| | - Kebir Boucherit
- Antibiotics Antifungal Laboratory, Physical Chemistry, Synthesis and Biological Activity (LAPSAB), Department of Biology, Faculty of Sciences, University of Tlemcen, BP 119, 13000 Tlemcen, Algeria.
| | - Alírio E Rodrigues
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
| | - Isabel C F R Ferreira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
| | - Maria Filomena Barreiro
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal.
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), Polytechnic Institute of Bragança, Campus Santa Apolónia, 5301-253 Bragança, Portugal.
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53
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Matsumoto A. [Importance of an Aldehyde Dehydrogenase 2 Polymorphism in Preventive Medicine]. Nihon Eiseigaku Zasshi 2018; 73:9-20. [PMID: 29386454 DOI: 10.1265/jjh.73.9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Unlike genetic alterations in other aldehyde dehydrogenase (ALDH) isozymes, a defective ALDH2 polymorphism (rs671), which is carried by almost half of East Asians, does not show a clear phenotype such as a shortened life span. However, impacts of a defective ALDH2 allele, ALDH2*2, on various disease risks have been reported. As ALDH2 is responsible for the detoxification of endogenous aldehydes, a negative effect of this polymorphism is predicted, but bidirectional effects have been actually observed and the mechanisms underlying such influences are often complex. One reason for this complexity may be the existence of compensatory aldehyde detoxification systems and the secondary effects of these systems. There are many issues to be addressed with regard to the ALDH2 polymorphism in the field of preventive medicine, including the following concerns. First, ALDH2 in the fetal stage plays a role in aldehyde detoxification; therefore, prenatal health effects of environmental aldehyde exposure are of concern for ALDH2*2-carrying fetuses. Second, ALDH2*2 carriers are at high risk of drinking-related cancers. However, their drinking habits result in less worsening of physiological findings, such as energy metabolism index and liver functions, compared with non-ALDH2*2 carriers, and therefore opportunities to detect excessive drinking can be lost. Third, personalized medicine such as personalized prescriptions for ALDH2*2 carriers will be required in the clinical setting, and accumulation of evidence is awaited. Lastly, since the ALDH2 polymorphism is not considered in workers' limits of exposure to aldehydes and their precursors, efforts to lower exposure levels beyond legal standards are required.
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Affiliation(s)
- Akiko Matsumoto
- Department of Social Medicine, Saga University School of Medicine
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54
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Attéré SA, Vincent AT, Paccaud M, Frenette M, Charette SJ. The Role for the Small Cryptic Plasmids As Moldable Vectors for Genetic Innovation in Aeromonas salmonicida subsp. salmonicida. Front Genet 2017; 8:211. [PMID: 29326751 PMCID: PMC5736529 DOI: 10.3389/fgene.2017.00211] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/28/2017] [Indexed: 11/17/2022] Open
Abstract
In Aeromonas salmonicida subsp. salmonicida, a bacterium that causes fish disease, there are two types of small plasmids (<15 kbp): plasmids without known function, called cryptic plasmids, and plasmids that bear beneficial genes for the bacterium. Four among them are frequently detected in strains of A. salmonicida subsp. salmonicida: pAsa1, pAsa2, pAsa3, and pAsal1. The latter harbors a gene which codes for an effector of the type three secretion system, while the three others are cryptic. It is currently unclear why these cryptic plasmids are so highly conserved throughout strains of A. salmonicida subsp. salmonicida. In this study, three small plasmids, named pAsa10, pAsaXI and pAsaXII, are described. Linked to tetracycline resistance, a partial Tn1721 occupies half of pAsa10. A whole Tn1721 is also present in pAsa8, another plasmid previously described in A. salmonicida subsp. salmonicida. The backbone of pAsa10 has no relation with other plasmids described in this bacterium. However, the pAsaXI and pAsaXII plasmids are derivatives of cryptic plasmids pAsa3 and pAsa2, respectively. pAsaXI is identical to pAsa3, but bears a transposon with a gene that encodes for a putative virulence factor. pAsaXII, also found in Aeromonas bivalvium, has a 95% nucleotide identity with the backbone of pAsa2. Like pAsa7, another pAsa2-like plasmid recently described, orf2 and orf3 are missing and are replaced in pAsaXII by genes that encode a formaldehyde detoxification system. These new observations suggest that transposons and particularly Tn1721 are frequent and diversified in A. salmonicida subsp. salmonicida. Moreover, the discovery of pAsaXI and pAsaXII expands the group of small plasmids that are derived from cryptic plasmids and have a function. Although their precise roles remain to be determined, the present study shows that cryptic plasmids could serve as moldable vectors to acquire mobile elements such as transposons. Consequently, they could act as key agents of the diversification of virulence and adaptive traits of Aeromonas salmonicida subsp. salmonicida.
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Affiliation(s)
- Sabrina A Attéré
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Antony T Vincent
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Mégane Paccaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Michel Frenette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada
| | - Steve J Charette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
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55
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Kusstatscher P, Cernava T, Liebminger S, Berg G. Replacing conventional decontamination of hatching eggs with a natural defense strategy based on antimicrobial, volatile pyrazines. Sci Rep 2017; 7:13253. [PMID: 29038499 PMCID: PMC5643471 DOI: 10.1038/s41598-017-13579-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/25/2017] [Indexed: 11/20/2022] Open
Abstract
The treatment of hatching eggs relies on classic yet environmentally harmful decontamination methods such as formaldehyde fumigation. We evaluated bacteria-derived volatiles as a replacement within a fundamentally novel approach based on volatile organic compounds (VOCs), which are naturally involved in microbial communication and antagonism due to their high antimicrobial efficiency. Pyrazine (5-isobutyl-2,3-dimethylpyrazine) was applied passively and actively in prototypes of a pre-industry-scale utilization. Altogether, pyrazine decontamination rates of up to 99.6% were observed, which is comparable to formaldehyde fumigation. While active evaporation was highly efficient in all experiments, passive treatment showed reducing effects in two of four tested groups only. These results were confirmed by visualization using LIVE/DEAD staining microscopy. The natural egg shell microbiome was characterized by an unexpected bacterial diversity of Pseudomonadales, Enterobacteriales, Sphingomonadales, Streptophyta, Burkholderiales, Actinomycetales, Xanthomonadales, Rhizobiales, Bacillales, Clostridiales, Lactobacillales, and Flavobacteriales members. Interestingly, we found that especially low pyrazine concentrations lead to a microbiome shift, which can be explained by varying antimicrobial effects on different microorganisms. Micrococcus spp., which are linked to embryonic death and reduced hatchability, was found to be highly sensitive to pyrazines. Taken together, pyrazine application was shown to be a promising, environmentally friendly alternative for fumigation treatments of hatchery eggs.
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Affiliation(s)
- Peter Kusstatscher
- ACIB GmbH, Petersgasse 14, 8010, Graz, Austria
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Tomislav Cernava
- ACIB GmbH, Petersgasse 14, 8010, Graz, Austria.
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
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56
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Dou K, Chen G, Yu F, Liu Y, Chen L, Cao Z, Chen T, Li Y, You J. Bright and sensitive ratiometric fluorescent probe enabling endogenous FA imaging and mechanistic exploration of indirect oxidative damage due to FA in various living systems. Chem Sci 2017; 8:7851-7861. [PMID: 29163922 PMCID: PMC5674201 DOI: 10.1039/c7sc03719h] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
As a notorious toxin, formaldehyde (FA) poses an immense threat to human health. Aberrantly elevated FA levels lead to serious pathologies, including organ damage, neurodegeneration, and cancer. Unfortunately, current techniques limit FA imaging to general comparative studies, instead of a mechanistic exploration of its biological role, and this is presumably due to the lack of robust molecular tools for reporting FA in living systems. More importantly, despite being reductive, FA, however, can induce oxidative damage to organisms, thus providing a challenge to the mechanistic study of FA using fluorescence imaging. Herein, we presented the design and multi-application of a bright sensitive ratiometric fluorescent probe 1-(4-(1H-phenanthro[9,10-d]imidazol-2-yl)phenyl) but-3-en-1-amine (PIPBA). With a π-extended phenylphenanthroimidazole fluorophore and an allylamine group, PIPBA exhibited high quantum yield (φ = 0.62) in blue fluorescent emission and selective reactivity toward FA. When sensing FA, PIPBA transformed to PIBE, which is a product capable of releasing bright green fluorescence (φ = 0.51) with its enhanced intramolecular charge transfer (ICT). Transformation of PIPBA to PIBE contributed to 80 nm of red shift in emission wavelength and a highly sensitive ratiometric response (92.2-fold), as well as a quite low detection limit (0.84 μM). PIPBA was successfully applied to various living systems, realizing, for the first time, ratiometric quantification (in cells), in vivo imaging (zebrafish), and living tissue imaging (vivisectional mouse under anaesthetic) of endogenous FA that was spontaneously generated by biological systems. Furthermore, with the aid of PIPBA, we obtained visual evidence for the oxidative damage of FA in both HeLa cells and renal tissue of a living mouse. The results demonstrated that FA exerted indirect oxidative damage by interacting with free radicals, thus producing more oxidizing species, which eventually caused aggravated oxidative damage to the organism. The indirect oxidative damage due to FA could be alleviated by an exogenous or endogenous antioxidant. The excellent behaviors of PIPBA demonstrate that a chemical probe can detect endogenous FA in cells/tissue/vivo, promising to be an effective tool for further exploration of the biological mechanism of FA in living systems.
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Affiliation(s)
- Kun Dou
- The Key Laboratory of Life-Organic Analysis , Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine , College of Chemistry and Chemical Engineering , Qufu Normal University , Qufu 273165 , China . ;
| | - Guang Chen
- The Key Laboratory of Life-Organic Analysis , Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine , College of Chemistry and Chemical Engineering , Qufu Normal University , Qufu 273165 , China . ; .,Key Laboratory of Coastal Environmental Processes and Ecological Remediation , Yantai Institute of Coastal Zone Research , Chinese Academy of Sciences , Yantai 264003 , China.,Key Laboratory of Tibetan Medicine Research , Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources , Northwest Institute of Plateau Biology , Chinese Academy of Science , Xining 810001 , Qinghai , PR China
| | - Fabiao Yu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation , Yantai Institute of Coastal Zone Research , Chinese Academy of Sciences , Yantai 264003 , China
| | - Yuxia Liu
- The Key Laboratory of Life-Organic Analysis , Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine , College of Chemistry and Chemical Engineering , Qufu Normal University , Qufu 273165 , China . ;
| | - Lingxin Chen
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation , Yantai Institute of Coastal Zone Research , Chinese Academy of Sciences , Yantai 264003 , China
| | - Ziping Cao
- The Key Laboratory of Life-Organic Analysis , Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine , College of Chemistry and Chemical Engineering , Qufu Normal University , Qufu 273165 , China . ;
| | - Tao Chen
- Key Laboratory of Tibetan Medicine Research , Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources , Northwest Institute of Plateau Biology , Chinese Academy of Science , Xining 810001 , Qinghai , PR China
| | - Yulin Li
- Key Laboratory of Tibetan Medicine Research , Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources , Northwest Institute of Plateau Biology , Chinese Academy of Science , Xining 810001 , Qinghai , PR China
| | - Jinmao You
- The Key Laboratory of Life-Organic Analysis , Key Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine , College of Chemistry and Chemical Engineering , Qufu Normal University , Qufu 273165 , China . ; .,Key Laboratory of Coastal Environmental Processes and Ecological Remediation , Yantai Institute of Coastal Zone Research , Chinese Academy of Sciences , Yantai 264003 , China
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57
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Rohlhill J, Sandoval NR, Papoutsakis ET. Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol. ACS Synth Biol 2017; 6:1584-1595. [PMID: 28463494 PMCID: PMC5569641 DOI: 10.1021/acssynbio.7b00114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Tight and tunable control of gene
expression is a highly desirable
goal in synthetic biology for constructing predictable gene circuits
and achieving preferred phenotypes. Elucidating the sequence–function
relationship of promoters is crucial for manipulating gene expression
at the transcriptional level, particularly for inducible systems dependent
on transcriptional regulators. Sort-seq methods employing fluorescence-activated
cell sorting (FACS) and high-throughput sequencing allow for the quantitative
analysis of sequence–function relationships in a robust and
rapid way. Here we utilized a massively parallel sort-seq approach
to analyze the formaldehyde-inducible Escherichia coli promoter (Pfrm) with single-nucleotide
resolution. A library of mutated formaldehyde-inducible promoters
was cloned upstream of gfp on a plasmid. The library
was partitioned into bins via FACS on the basis of green fluorescent
protein (GFP) expression level, and mutated promoters falling into
each expression bin were identified with high-throughput sequencing.
The resulting analysis identified two 19 base pair repressor binding
sites, one upstream of the −35 RNA polymerase (RNAP) binding
site and one overlapping with the −10 site, and assessed the
relative importance of each position and base therein. Key mutations
were identified for tuning expression levels and were used to engineer
formaldehyde-inducible promoters with predictable activities. Engineered
variants demonstrated up to 14-fold lower basal expression, 13-fold
higher induced expression, and a 3.6-fold stronger response as indicated
by relative dynamic range. Finally, an engineered formaldehyde-inducible
promoter was employed to drive the expression of heterologous methanol
assimilation genes and achieved increased biomass levels on methanol,
a non-native substrate of E. coli.
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Affiliation(s)
- Julia Rohlhill
- Department of Chemical & Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
| | - Nicholas R. Sandoval
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Eleftherios T. Papoutsakis
- Department of Chemical & Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
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58
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Denby KJ, Iwig J, Bisson C, Westwood J, Rolfe MD, Sedelnikova SE, Higgins K, Maroney MJ, Baker PJ, Chivers PT, Green J. The mechanism of a formaldehyde-sensing transcriptional regulator. Sci Rep 2016; 6:38879. [PMID: 27934966 PMCID: PMC5146963 DOI: 10.1038/srep38879] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/15/2016] [Indexed: 01/12/2023] Open
Abstract
Most organisms are exposed to the genotoxic chemical formaldehyde, either from endogenous or environmental sources. Therefore, biology has evolved systems to perceive and detoxify formaldehyde. The frmRA(B) operon that is present in many bacteria represents one such system. The FrmR protein is a transcriptional repressor that is specifically inactivated in the presence of formaldehyde, permitting expression of the formaldehyde detoxification machinery (FrmA and FrmB, when the latter is present). The X-ray structure of the formaldehyde-treated Escherichia coli FrmR (EcFrmR) protein reveals the formation of methylene bridges that link adjacent Pro2 and Cys35 residues in the EcFrmR tetramer. Methylene bridge formation has profound effects on the pattern of surface charge of EcFrmR and combined with biochemical/biophysical data suggests a mechanistic model for formaldehyde-sensing and derepression of frmRA(B) expression in numerous bacterial species.
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Affiliation(s)
- Katie J Denby
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jeffrey Iwig
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Claudine Bisson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jodie Westwood
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Matthew D Rolfe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Svetlana E Sedelnikova
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Khadine Higgins
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003, USA
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003, USA
| | - Patrick J Baker
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Peter T Chivers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.,Departments of Biosciences and Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Jeffrey Green
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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59
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Osman D, Piergentili C, Chen J, Sayer LN, Usón I, Huggins TG, Robinson NJ, Pohl E. The Effectors and Sensory Sites of Formaldehyde-responsive Regulator FrmR and Metal-sensing Variant. J Biol Chem 2016; 291:19502-16. [PMID: 27474740 PMCID: PMC5016687 DOI: 10.1074/jbc.m116.745174] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/21/2016] [Indexed: 11/29/2022] Open
Abstract
The DUF156 family of DNA-binding transcriptional regulators includes metal sensors that respond to cobalt and/or nickel (RcnR, InrS) or copper (CsoR) plus CstR, which responds to persulfide, and formaldehyde-responsive FrmR. Unexpectedly, the allosteric mechanism of FrmR from Salmonella enterica serovar Typhimurium is triggered by metals in vitro, and variant FrmR(E64H) gains responsiveness to Zn(II) and cobalt in vivo Here we establish that the allosteric mechanism of FrmR is triggered directly by formaldehyde in vitro Sensitivity to formaldehyde requires a cysteine (Cys(35) in FrmR) conserved in all DUF156 proteins. A crystal structure of metal- and formaldehyde-sensing FrmR(E64H) reveals that an FrmR-specific amino-terminal Pro(2) is proximal to Cys(35), and these residues form the deduced formaldehyde-sensing site. Evidence is presented that implies that residues spatially close to the conserved cysteine tune the sensitivities of DUF156 proteins above or below critical thresholds for different effectors, generating the semblance of specificity within cells. Relative to FrmR, RcnR is less responsive to formaldehyde in vitro, and RcnR does not sense formaldehyde in vivo, but reciprocal mutations FrmR(P2S) and RcnR(S2P), respectively, impair and enhance formaldehyde reactivity in vitro Formaldehyde detoxification by FrmA requires S-(hydroxymethyl)glutathione, yet glutathione inhibits formaldehyde detection by FrmR in vivo and in vitro Quantifying the number of FrmR molecules per cell and modeling formaldehyde modification as a function of [formaldehyde] demonstrates that FrmR reactivity is optimized such that FrmR is modified and frmRA is derepressed at lower [formaldehyde] than required to generate S-(hydroxymethyl)glutathione. Expression of FrmA is thereby coordinated with the accumulation of its substrate.
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Affiliation(s)
- Deenah Osman
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Cecilia Piergentili
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Junjun Chen
- Procter and Gamble, Mason Business Center, Cincinnati, Ohio 45040
| | | | - Isabel Usón
- the Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, 08028 Barcelona, Spain, and the Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas G Huggins
- Procter and Gamble, Mason Business Center, Cincinnati, Ohio 45040
| | - Nigel J Robinson
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom,
| | - Ehmke Pohl
- From the Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
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60
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Lobato-Márquez D, Díaz-Orejas R, García-Del Portillo F. Toxin-antitoxins and bacterial virulence. FEMS Microbiol Rev 2016; 40:592-609. [PMID: 27476076 DOI: 10.1093/femsre/fuw022] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 12/25/2022] Open
Abstract
Bacterial virulence relies on a delicate balance of signals interchanged between the invading microbe and the host. This communication has been extensively perceived as a battle involving harmful molecules produced by the pathogen and host defenses. In this review, we focus on a largely unexplored element of this dialogue, as are toxin-antitoxin (TA) systems of the pathogen. TA systems are reported to respond to stresses that are also found in the host and, as a consequence, could modulate the physiology of the intruder microbe. This view is consistent with recent studies that demonstrate a contribution of distinct TA systems to virulence since their absence alters the course of the infection. TA loci are stress response modules that, therefore, could readjust pathogen metabolism to favor the generation of slow-growing or quiescent cells 'before' host defenses irreversibly block essential pathogen activities. Some toxins of these TA modules have been proposed as potential weapons used by the pathogen to act on host targets. We discuss all these aspects based on studies that support some TA modules as important regulators in the pathogen-host interface.
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Affiliation(s)
- Damián Lobato-Márquez
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain Centro de Investigaciones Biológicas-CSIC (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ramón Díaz-Orejas
- Centro de Investigaciones Biológicas-CSIC (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Francisco García-Del Portillo
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
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Couñago RM, Chen NH, Chang CW, Djoko KY, McEwan AG, Kobe B. Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region. Nucleic Acids Res 2016; 44:6981-93. [PMID: 27307602 PMCID: PMC5001606 DOI: 10.1093/nar/gkw543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 06/03/2016] [Indexed: 01/04/2023] Open
Abstract
Pathogenic bacteria such as Haemophilus influenzae, a major cause of lower respiratory tract diseases, must cope with a range of electrophiles generated in the host or by endogenous metabolism. Formaldehyde is one such compound that can irreversibly damage proteins and DNA through alkylation and cross-linking and interfere with redox homeostasis. Its detoxification operates under the control of HiNmlR, a protein from the MerR family that lacks a specific sensor region and does not bind metal ions. We demonstrate that HiNmlR is a thiol-dependent transcription factor that modulates H. influenzae response to formaldehyde, with two cysteine residues (Cys54 and Cys71) identified to be important for its response against a formaldehyde challenge. We obtained crystal structures of HiNmlR in both the DNA-free and two DNA-bound forms, which suggest that HiNmlR enhances target gene transcription by twisting of operator DNA sequences in a two-gene operon containing overlapping promoters. Our work provides the first structural insights into the mechanism of action of MerR regulators that lack sensor regions.
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Affiliation(s)
- Rafael M Couñago
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Nathan H Chen
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia
| | - Chiung-Wen Chang
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | - Karrera Y Djoko
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia
| | - Alastair G McEwan
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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