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Research Progress on the Construction of Artificial Pathways for the Biosynthesis of Adipic Acid by Engineered Microbes. FERMENTATION 2022. [DOI: 10.3390/fermentation8080393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Adipic acid is an important bulk chemical used in the nylon industry, as well as in food, plasticizers and pharmaceutical fields. It is thus considered one of the most important 12 platform chemicals. The current production of adipic acid relies on non-renewable petrochemical resources and emits large amounts of greenhouse gases. The bio-production of adipic acid from renewable resources via engineered microorganisms is regarded as a green and potential method to replace chemical conversion, and has attracted attention all over the world. Herein we review the current status of research on several artificial pathways for the biosynthesis of adipic acid, especially the reverse degradation pathway, which is a full biosynthetic method and has achieved the highest titer of adipic acid so far. Other artificial pathways including the fatty acid degradation pathway, the muconic acid conversion pathway, the polyketide pathway, the α-ketopimelate pathway and the lysine degradation pathway are also discussed. In addition, the challenges in the bio-production of adipic acid via these artificial pathways are analyzed and the prospects are presented with the intention of providing some significant points for the promotion of adipic acid biosynthesis.
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2
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Zhou S, Alper HS, Zhou J, Deng Y. Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level. Crit Rev Biotechnol 2022; 43:646-663. [PMID: 35450502 DOI: 10.1080/07388551.2022.2040415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of intracellular, biosensor-based dynamic regulation strategies to regulate and improve the production of useful compounds have progressed significantly over previous decades. By employing such an approach, it is possible to simultaneously realize high productivity and optimum growth states. However, industrial fermentation conditions contain a mixture of high- and low-performance non-genetic variants, as well as young and aged cells at all growth phases. Such significant individual variations would hinder the precise controlling of metabolic flux at the single-cell level to achieve high productivity at the macroscopic population level. Intracellular biosensors, as the regulatory centers of metabolic networks, can real-time sense intra- and extracellular conditions and, thus, could be synthetically adapted to balance the biomass formation and overproduction of compounds by individual cells. Herein, we highlight advances in the designing and engineering approaches to intracellular biosensors. Then, the spatiotemporal properties of biosensors associated with the distribution of inducers are compared. Also discussed is the use of such biosensors to dynamically control the cellular metabolic flux. Such biosensors could achieve single-cell regulation or collective regulation goals, depending on whether or not the inducer distribution is only intracellular.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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3
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Ren T, Chi Y, Wang Y, Shi X, Jin X, Jin P. Diversified metabolism makes novel Thauera strain highly competitive in low carbon wastewater treatment. WATER RESEARCH 2021; 206:117742. [PMID: 34653797 DOI: 10.1016/j.watres.2021.117742] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/01/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Thauera, as one of the core members of wastewater biological treatment systems, plays an important role in the process of nitrogen and phosphorus removal from low-carbon source sewage. However, there is a lack of systematic understanding of Thauera's metabolic pathway and genomics. Here we report on the newly isolated Thauera sp. RT1901, which is capable of denitrification using variety carbon sources including aromatic compounds. By comparing the denitrification processes under the conditions of insufficient, adequate and surplus carbon sources, it was found that strain RT1901 could simultaneously use soluble microbial products (SMP) and extracellular polymeric substances (EPS) as electron donors for denitrification. Strain RT1901 was also found to be a denitrifying phosphate accumulating bacterium, able to use nitrate, nitrite, or oxygen as electron acceptors during poly-β-hydroxybutyrate (PHB) catabolism. The annotated genome was used to reconstruct the complete nitrogen and phosphorus metabolism pathways of RT1901. In the process of denitrifying phosphorus accumulation, glycolysis was the only pathway for glycogen metabolism, and the glyoxylic acid cycle replaced the tricarboxylic acid cycle (TCA) to supplement the reduced energy. In addition, the abundance of conventional phosphorus accumulating bacteria decreased significantly and the removal rates of total nitrogen (TN) and chemical oxygen demand (COD) increased after the addition of RT1901 in the low carbon/nitrogen (C/N) ratio of anaerobic aerobic anoxic-sequencing batch reactor (AOA-SBR). This research indicated that the diverse metabolic capabilities of Thauera made it more competitive than other bacteria in the wastewater treatment system.
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Affiliation(s)
- Tong Ren
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Yulei Chi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Yu Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Xuan Shi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Xin Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Pengkang Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China; School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, China.
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4
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Hao T, Li G, Zhou S, Deng Y. Engineering the Reductive TCA Pathway to Dynamically Regulate the Biosynthesis of Adipic Acid in Escherichia coli. ACS Synth Biol 2021; 10:632-639. [PMID: 33687200 DOI: 10.1021/acssynbio.0c00648] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adipic acid is a versatile aliphatic dicarboxylic acid. It is applied mainly in the polymerization of nylon-6,6, which accounts for 50.8% of the global consumption market of adipic acid. The microbial production of adipic acid avoids the usage of petroleum resources and the emission of harmful nitrogen oxides that are generated by traditional chemical synthetic approaches. However, in the fermentation process, the low theoretical yield and the usage of expensive inducers hinders the large-scale industrial production of adipic acid. To overcome these challenges, we established an oxygen-dependent dynamic regulation (ODDR) system to control the expression of key genes (sucD, pyc, mdh, and frdABCD) that could be induced to enhance the metabolic flux of the reductive TCA pathway under anaerobic conditions. Coupling of the constitutively expressed adipic acid synthetic pathway not only avoids the use of inducers but also increases the theoretical yield by nearly 50%. After the gene combination and operon structure were optimized, the reaction catalyzed by frdABCD was found to be the rate-limiting step. Further optimizing the relative expression levels of sucD, pyc, and frdABCD improved the titer of adipic acid 41.62-fold compared to the control strain Mad1415, demonstrating the superior performance of our ODDR system.
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Affiliation(s)
- Tingting Hao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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5
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Osorio H, Mettert E, Kiley P, Dopson M, Jedlicki E, Holmes DS. Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:1642. [PMID: 31379789 PMCID: PMC6659574 DOI: 10.3389/fmicb.2019.01642] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/28/2022] Open
Abstract
The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S]2+ iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S]2+ center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.
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Affiliation(s)
- Héctor Osorio
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - Erin Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Patricia Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile.,Universidad San Sebastian, Santiago, Chile.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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6
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Sevilla E, Bes MT, González A, Peleato ML, Fillat MF. Redox-Based Transcriptional Regulation in Prokaryotes: Revisiting Model Mechanisms. Antioxid Redox Signal 2019; 30:1651-1696. [PMID: 30073850 DOI: 10.1089/ars.2017.7442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SIGNIFICANCE The successful adaptation of microorganisms to ever-changing environments depends, to a great extent, on their ability to maintain redox homeostasis. To effectively maintain the redox balance, cells have developed a variety of strategies mainly coordinated by a battery of transcriptional regulators through diverse mechanisms. Recent Advances: This comprehensive review focuses on the main mechanisms used by major redox-responsive regulators in prokaryotes and their relationship with the different redox signals received by the cell. An overview of the corresponding regulons is also provided. CRITICAL ISSUES Some regulators are difficult to classify since they may contain several sensing domains and respond to more than one signal. We propose a classification of redox-sensing regulators into three major groups. The first group contains one-component or direct regulators, whose sensing and regulatory domains are in the same protein. The second group comprises the classical two-component systems involving a sensor kinase that transduces the redox signal to its DNA-binding partner. The third group encompasses a heterogeneous group of flavin-based photosensors whose mechanisms are not always fully understood and are often involved in more complex regulatory networks. FUTURE DIRECTIONS Redox-responsive transcriptional regulation is an intricate process as identical signals may be sensed and transduced by different transcription factors, which often interplay with other DNA-binding proteins with or without regulatory activity. Although there is much information about some key regulators, many others remain to be fully characterized due to the instability of their clusters under oxygen. Understanding the mechanisms and the regulatory networks operated by these regulators is essential for the development of future applications in biotechnology and medicine.
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Affiliation(s)
- Emma Sevilla
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María Teresa Bes
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Andrés González
- 2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain.,4 Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain
| | - María Luisa Peleato
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - María F Fillat
- 1 Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.,2 Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain.,3 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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7
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Abstract
SIGNIFICANCE Iron-sulfur cluster proteins carry out multiple functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters with small/redox-active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial reprogramming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances: Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review. CRITICAL ISSUES Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family. FUTURE DIRECTIONS Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high-resolution structural data. Although this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
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8
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Mettert EL, Kiley PJ. Reassessing the Structure and Function Relationship of the O 2 Sensing Transcription Factor FNR. Antioxid Redox Signal 2018; 29:1830-1840. [PMID: 28990402 PMCID: PMC6217745 DOI: 10.1089/ars.2017.7365] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE The Escherichia coli regulatory protein fumarate nitrate reduction (FNR) mediates a global transcriptional response upon O2 deprivation. Spanning nearly 40 years of research investigations, our understanding of how FNR senses and responds to O2 has considerably progressed despite a lack of structural information for most of that period. This knowledge has established the paradigm for how facultative anaerobic bacteria sense changes in O2 tension. Recent Advances: Recently, the X-ray crystal structure of Aliivibrio fischeri FNR with its [4Fe-4S] cluster cofactor was solved and has provided valuable new insight into FNR structure and function. These findings have alluded to the conformational changes that may occur to alter FNR activity in response to O2. CRITICAL ISSUES Here, we review the major features of this structure in context of previously acquired data. In doing so, we discuss additional mechanistic aspects of FNR function that warrant further investigation. FUTURE DIRECTIONS To complement the [4Fe-4S]-FNR structure, the structures of apo-FNR and FNR bound to DNA or RNA polymerase are needed. Together, these structures would elevate our understanding of how ligation of its [4Fe-4S] cluster allows FNR to regulate transcription according to the level of environmental O2.
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Affiliation(s)
- Erin L Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison , Madison, Wisconsin
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison , Madison, Wisconsin
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9
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Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
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Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
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10
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Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. mBio 2016; 7:mBio.01173-16. [PMID: 27486197 PMCID: PMC4981724 DOI: 10.1128/mbio.01173-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neisseria meningitidis is a leading cause of bacterial meningitis and septicemia, affecting infants and adults worldwide. N. meningitidis is also a common inhabitant of the human nasopharynx and, as such, is highly adapted to its niche. During bacteremia, N. meningitidis gains access to the blood compartment, where it adheres to endothelial cells of blood vessels and causes dramatic vascular damage. Colonization of the nasopharyngeal niche and communication with the different human cell types is a major issue of the N. meningitidis life cycle that is poorly understood. Here, highly saturated random transposon insertion libraries of N. meningitidis were engineered, and the fitness of mutations during routine growth and that of colonization of endothelial and epithelial cells in a flow device were assessed in a transposon insertion site sequencing (Tn-seq) analysis. This allowed the identification of genes essential for bacterial growth and genes specifically required for host cell colonization. In addition, after having identified the small noncoding RNAs (sRNAs) located in intergenic regions, the phenotypes associated with mutations in those sRNAs were defined. A total of 383 genes and 8 intergenic regions containing sRNA candidates were identified to be essential for growth, while 288 genes and 33 intergenic regions containing sRNA candidates were found to be specifically required for host cell colonization. Meningococcal meningitis is a common cause of meningitis in infants and adults. Neisseria meningitidis (meningococcus) is also a commensal bacterium of the nasopharynx and is carried by 3 to 30% of healthy humans. Under some unknown circumstances, N. meningitidis is able to invade the bloodstream and cause either meningitis or a fatal septicemia known as purpura fulminans. The onset of symptoms is sudden, and death can follow within hours. Although many meningococcal virulence factors have been identified, the mechanisms that allow the bacterium to switch from the commensal to pathogen state remain unknown. Therefore, we used a Tn-seq strategy coupled to high-throughput DNA sequencing technologies to find genes for proteins used by N. meningitidis to specifically colonize epithelial cells and primary brain endothelial cells. We identified 383 genes and 8 intergenic regions containing sRNAs essential for growth and 288 genes and 33 intergenic regions containing sRNAs required specifically for host cell colonization.
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11
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Crack JC, Hutchings MI, Thomson AJ, Le Brun NE. Biochemical properties of Paracoccus denitrificans FnrP: reactions with molecular oxygen and nitric oxide. J Biol Inorg Chem 2016; 21:71-82. [PMID: 26790880 PMCID: PMC4771820 DOI: 10.1007/s00775-015-1326-7] [Citation(s) in RCA: 15] [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: 10/21/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
In Paracoccus denitrificans, three CRP/FNR family regulatory proteins, NarR, NnrR and FnrP, control the switch between aerobic and anaerobic (denitrification) respiration. FnrP is a [4Fe–4S] cluster-containing homologue of the archetypal O2 sensor FNR from E. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to O2, and also NO, availability. Here we show that FnrP undergoes O2-driven [4Fe–4S] to [2Fe–2S] cluster conversion that involves up to 2 O2 per cluster, with significant oxidation of released cluster sulfide to sulfane observed at higher O2 concentrations. The rate of the cluster reaction was found to be ~sixfold lower than that of E. coli FNR, suggesting that FnrP can remain transcriptionally active under microaerobic conditions. This is consistent with a role for FnrP in activating expression of the high O2 affinity cytochrome c oxidase under microaerobic conditions. Cluster conversion resulted in dissociation of the transcriptionally active FnrP dimer into monomers. Therefore, along with E. coli FNR, FnrP belongs to the subset of FNR proteins in which cluster type is correlated with association state. Interestingly, two key charged residues, Arg140 and Asp154, that have been shown to play key roles in the monomer–dimer equilibrium in E. coli FNR are not conserved in FnrP, indicating that different protomer interactions are important for this equilibrium. Finally, the FnrP [4Fe–4S] cluster is shown to undergo reaction with multiple NO molecules, resulting in iron nitrosyl species and dissociation into monomers.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew J Thomson
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK.
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12
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Abstract
The exclusive reservoir of the genus Neisseria is the human. Of the broad range of species that comprise the Neisseria, only two are frequently pathogenic, and only one of those is a resident of the nasopharynx. Although Neisseria meningitidis can cause severe disease if it invades the bloodstream, the vast majority of interactions between humans and Neisseria are benign, with the bacteria inhabiting its mucosal niche as a non-invasive commensal. Understandably, with the exception of Neisseria gonorrhoeae, which preferentially colonises the urogenital tract, the neisseriae are extremely well adapted to survival in the human nasopharynx, their sole biological niche. The purpose of this review is to provide an overview of the molecular mechanisms evolved by Neisseria to facilitate colonisation and survival within the nasopharynx, focussing on N. meningitidis. The organism has adapted to survive in aerosolised transmission and to attach to mucosal surfaces. It then has to replicate in a nutrition-poor environment and resist immune and competitive pressure within a polymicrobial complex. Temperature and relative gas concentrations (nitric oxide and oxygen) are likely to be potent initial signals of arrival within the nasopharyngeal environment, and this review will focus on how N. meningitidis responds to these to increase the likelihood of its survival.
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13
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Influence of association state and DNA binding on the O₂-reactivity of [4Fe-4S] fumarate and nitrate reduction (FNR) regulator. Biochem J 2014; 463:83-92. [PMID: 25019503 PMCID: PMC4214427 DOI: 10.1042/bj20140169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The fumarate and nitrate reduction (FNR) regulator is the master switch for the transition between anaerobic and aerobic respiration in Escherichia coli. Reaction of dimeric [4Fe-4S] FNR with O2 results in conversion of the cluster into a [2Fe-2S] form, via a [3Fe-4S] intermediate, leading to the loss of DNA binding through dissociation of the dimer into monomers. In the present paper, we report studies of two previously identified variants of FNR, D154A and I151A, in which the form of the cluster is decoupled from the association state. In vivo studies of permanently dimeric D154A FNR show that DNA binding does not affect the rate of cluster incorporation into the apoprotein or the rate of O2-mediated cluster loss. In vitro studies show that O2-mediated cluster conversion for D154A and the permanent monomer I151A FNR is the same as in wild-type FNR, but with altered kinetics. Decoupling leads to an increase in the rate of the [3Fe-4S]1+ into [2Fe-2S]2+ conversion step, consistent with the suggestion that this step drives association state changes in the wild-type protein. We have also shown that DNA-bound FNR reacts more rapidly with O2 than FNR free in solution, implying that transcriptionally active FNR is the preferred target for reaction with O2.
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Catenazzi MCE, Jones H, Wallace I, Clifton J, Chong JPJ, Jackson MA, Macdonald S, Edwards J, Moir JWB. A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx. Mol Microbiol 2014; 93:346-55. [PMID: 24910087 PMCID: PMC4441257 DOI: 10.1111/mmi.12664] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2014] [Indexed: 01/01/2023]
Abstract
Neisseria meningitidis is an important human pathogen that is capable of killing within hours of infection. Its normal habitat is the nasopharynx of adult humans. Here we identify a genomic island (the prp gene cluster) in N. meningitidis that enables this species to utilize propionic acid as a supplementary carbon source during growth, particularly under nutrient poor growth conditions. The prp gene cluster encodes enzymes for a methylcitrate cycle. Novel aspects of the methylcitrate cycle in N. meningitidis include a propionate kinase which was purified and characterized, and a putative propionate transporter. This genomic island is absent from the close relative of N. meningitidis, the commensal Neisseria lactamica, which chiefly colonizes infants not adults. We reason that the possession of the prp genes provides a metabolic advantage to N. meningitidis in the adult oral cavity, which is rich in propionic acid-generating bacteria. Data from classical microbiological and sequence-based microbiome studies provide several lines of supporting evidence that N. meningitidis colonization is correlated with propionic acid generating bacteria, with a strong correlation between prp-containing Neisseria and propionic acid generating bacteria from the genus Porphyromonas, and that this may explain adolescent/adult colonization by N. meningitidis.
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Dash SK, Sharma M, Khare S, Kumar A. rmpM Genosensor for Detection of Human Brain Bacterial Meningitis in Cerebrospinal Fluid. Appl Biochem Biotechnol 2013; 171:198-208. [DOI: 10.1007/s12010-013-0339-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 06/17/2013] [Indexed: 11/29/2022]
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Spiro S. Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors. Philos Trans R Soc Lond B Biol Sci 2012; 367:1213-25. [PMID: 22451107 DOI: 10.1098/rstb.2011.0309] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several biochemical mechanisms contribute to the biological generation of nitrous oxide (N(2)O). N(2)O generating enzymes include the respiratory nitric oxide (NO) reductase, an enzyme from the flavo-diiron family, and flavohaemoglobin. On the other hand, there is only one enzyme that is known to use N(2)O as a substrate, which is the respiratory N(2)O reductase typically found in bacteria capable of denitrification (the respiratory reduction of nitrate and nitrite to dinitrogen). This article will briefly review the properties of the enzymes that make and consume N(2)O, together with the accessory proteins that have roles in the assembly and maturation of those enzymes. The expression of the genes encoding the enzymes that produce and consume N(2)O is regulated by environmental signals (typically oxygen and NO) acting through regulatory proteins, which, either directly or indirectly, control the frequency of transcription initiation. The roles and mechanisms of these proteins, and the structures of the regulatory networks in which they participate will also be reviewed.
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Affiliation(s)
- Stephen Spiro
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080, USA.
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17
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Neisseria meningitidis and Neisseria gonorrhoeae are differently adapted in the regulation of denitrification: single nucleotide polymorphisms that enable species-specific tuning of the aerobic–anaerobic switch. Biochem J 2012; 445:69-79. [DOI: 10.1042/bj20111984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The closely related pathogenic Neisseria species N. meningitidis and N. gonorrhoeae are able to respire in the absence of oxygen, using nitrite as an alternative electron acceptor. aniA (copper-containing nitrite reductase) is tightly regulated by four transcriptional regulators: FNR (fumarate and nitrate reductase), NarP, FUR (Ferric uptake regulator) and NsrR. The four regulators control expression of aniA in N. meningitidis by binding to specific and distinct regions of the promoter. We show in the present study that FUR and NarP are both required for the induction of expression of aniA in N. meningitidis, and that they bind adjacent to one another in a non-co-operative manner. Activation via FUR/NarP is dependent on their topological arrangement relative to the RNA polymerase-binding site. Analysis of the sequence of the aniA promoters from multiple N. meningitidis and N. gonorrhoeae strains indicates that there are species-specific single nucleotide polymorphisms, in regions predicted to be important for regulator binding. These sequence differences alter both the in vitro DNA binding and the promoter activation in intact cells by key activators FNR (oxygen sensor) and NarP (which is activated by nitrite in N. meningitidis). The weak relative binding of FNR to the N. gonorrhoeae aniA promoter (compared to N. meningitidis) is compensated for by a higher affinity of the gonococcal aniA promoter for NarP. Despite containing nearly identical genes for catalysing and regulating denitrification, variations in the promoter for the aniA gene appear to have been selected to enable the two pathogens to tune differentially their responses to environmental variables during the aerobic–anaerobic switch.
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Sanders H, Brehony C, Maiden MCJ, Vipond C, Feavers IM. The effect of iron availability on transcription of the Neisseria meningitidis fHbp gene varies among clonal complexes. MICROBIOLOGY-SGM 2012; 158:869-876. [PMID: 22241045 PMCID: PMC3949423 DOI: 10.1099/mic.0.054957-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Factor H binding protein (fHbp) is a major antigenic component of novel vaccines
designed to protect against meningococcal disease. Prediction of the potential coverage of these
vaccines is difficult, as fHbp is antigenically variable and levels of expression differ among
isolates. Transcriptional regulation of the fHbp gene is poorly understood,
although evidence suggests that oxygen availability is involved. In this study iron accessibility
was found to affect fHbp transcription. However, regulation differed among
meningococcal clonal complexes (ccs). For the majority of isolates, increased iron
concentrations upregulated transcription. This effect was enhanced by the presence of a 181 bp
insertion element upstream of fHbp, associated with isolates belonging to cc4 and
cc5. Conversely, meningococci belonging to cc32 showed iron-repressed control of
fHbp, as regulation was dominated by cotranscription with the iron-repressed
upstream gene cbbA. These results highlight the complexity of fHbp
regulation and demonstrate that control of transcription can vary among genetic lineages.
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Affiliation(s)
- Holly Sanders
- National Institute for Biological Standards and Control, Blanche Lane, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Carina Brehony
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Caroline Vipond
- National Institute for Biological Standards and Control, Blanche Lane, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Ian M Feavers
- National Institute for Biological Standards and Control, Blanche Lane, Potters Bar, Hertfordshire EN6 3QG, UK
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Fleischhacker AS, Kiley PJ. Iron-containing transcription factors and their roles as sensors. Curr Opin Chem Biol 2011; 15:335-41. [PMID: 21292540 DOI: 10.1016/j.cbpa.2011.01.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 12/23/2022]
Abstract
Iron-binding transcription factors are widespread throughout the bacterial world and to date are known to bind several types of cofactors, such as Fe2+, heme, or iron-sulfur clusters. The known chemistry of these cofactors is exploited by transcription factors, including Fur, FNR, and NsrR, to sense molecules such as Fe2+, gases (e.g. oxygen and nitric oxide), or reactive oxygen species. New structural data and information generated by genome-wide analysis studies have provided additional details about the mechanism and function of iron-binding transcription factors that act as sensors.
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Affiliation(s)
- Angela S Fleischhacker
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, United States
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20
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Kommineni S, Yukl E, Hayashi T, Delepine J, Geng H, Moënne-Loccoz P, Nakano MM. Nitric oxide-sensitive and -insensitive interaction of Bacillus subtilis NsrR with a ResDE-controlled promoter. Mol Microbiol 2010; 78:1280-93. [PMID: 21091510 DOI: 10.1111/j.1365-2958.2010.07407.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NsrR is a nitric oxide (NO)-sensitive transcription repressor that controls NO metabolism in a wide range of bacteria. In Bacillus subtilis, NsrR represses transcription of the nitrite reductase (nasDEF) genes that are under positive control of the ResD-ResE two-component signal transduction system. Derepression is achieved by reaction of NO with NsrR. Unlike some NsrR orthologues that were shown to contain a NO-sensitive [2Fe-2S] cluster, B. subtilis NsrR, when purified anaerobically either from aerobic or from anaerobic Escherichia coli and B. subtilis cultures, contains a [4Fe-4S] cluster. [4Fe-4S]-NsrR binds around the -35 element of the nasD promoter with much higher affinity than apo-NsrR and binding of [4Fe-4S]-NsrR, but not apo-protein, is sensitive to NO. RNA polymerase and phosphorylated ResD make a ternary complex at the nasD promoter and NsrR dissociates the preformed ternary complex. In addition to the -35 region, NsrR binds to two distinct sites of the upstream regulatory region where ResD also binds. These interactions, unlike the high-affinity site binding, do not depend on the NsrR [4Fe-4S] cluster and binding is not sensitive to NO, suggesting a role for apo-NsrR in transcriptional regulation.
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Affiliation(s)
- Sushma Kommineni
- Department of Science & Engineering, School of Medicine, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, OR 97006, USA
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Schielke S, Frosch M, Kurzai O. Virulence determinants involved in differential host niche adaptation of Neisseria meningitidis and Neisseria gonorrhoeae. Med Microbiol Immunol 2010; 199:185-96. [PMID: 20379743 DOI: 10.1007/s00430-010-0150-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Indexed: 11/28/2022]
Abstract
Neisseria meningitidis and Neisseria gonorrhoeae are the only pathogenic species of the genus Neisseria. Although these two species are closely related, they specialized on survival in completely different environments within the human host-the nasopharynx in the case of N. meningitidis versus the urogenital tract in the case of N. gonorrhoeae. The genetic background of these differences has not yet been determined. Here, we present a comparison of all characterized transcriptional regulators in these species, delineating analogous functions and disclosing differential functional developments of these DNA-binding proteins with a special focus on the recently characterized regulator FarR and its contribution to divergent host niche adaptation in the two Neisseria spp. Furthermore, we summarize the present knowledge on two-partner secretion systems in meningococci, highlighting their overall expression among meningococcal strains in contrast to the complete absence in gonococci. Concluding, the decisive role of these two entirely different factors in host niche adaptation of the two human pathogenic Neisseria species is depicted, illuminating another piece of the puzzle to locate the molecular basis of their differences in preferred colonization sites and pathogenicity.
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Affiliation(s)
- Stephanie Schielke
- Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
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