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Rova M, Hellberg Lindqvist M, Goetelen T, Blomqvist S, Nilsson T. Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor. Microbiologyopen 2020; 9:e1049. [PMID: 32319739 PMCID: PMC7349173 DOI: 10.1002/mbo3.1049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 01/30/2023] Open
Abstract
Regulation of the expression of the gene for chlorite dismutase (cld), located on the chlorate reduction composite transposon of the chlorate reducer Ideonella dechloratans, was studied. A 200 bp upstream sequence of the cld gene, and mutated and truncated versions thereof, was used in a reporter system in Escherichia coli. It was found that a sequence within this upstream region, which is nearly identical to the canonical FNR-binding sequence of E. coli, is necessary for anaerobic induction of the reporter gene. Anaerobic induction was regained in an FNR-deficient strain of E. coli when supplemented either with the fnr gene from E. coli or with a candidate fnr gene cloned from I. dechloratans. In vivo transcription of the suggested fnr gene of I. dechloratans was demonstrated by qRT-PCR. Based on these results, the cld promoter of I. dechloratans is suggested to be a class II-activated promoter regulated by an FNR-type protein of I. dechloratans. No fnr-type genes have been found on the chlorate reduction composite transposon of I. dechloratans, making anaerobic upregulation of the cld gene after a gene transfer event dependent on the presence of an fnr-type gene in the recipient.
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Affiliation(s)
- Maria Rova
- Department of Engineering and Chemical Sciences, Karlstad University, Karlstad, Sweden
| | | | - Thijs Goetelen
- Department of Engineering and Chemical Sciences, Karlstad University, Karlstad, Sweden
| | - Shady Blomqvist
- Department of Engineering and Chemical Sciences, Karlstad University, Karlstad, Sweden
| | - Thomas Nilsson
- Department of Engineering and Chemical Sciences, Karlstad University, Karlstad, Sweden
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Louie TS, Giovannelli D, Yee N, Narasingarao P, Starovoytov V, Göker M, Klenk HP, Lang E, Kyrpides NC, Woyke T, Bini E, Häggblom MM. High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1 T, a gammaproteobacterium isolated from estuarine sediment. Stand Genomic Sci 2016; 11:66. [PMID: 27721915 PMCID: PMC5052931 DOI: 10.1186/s40793-016-0191-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/31/2016] [Indexed: 11/10/2022] Open
Abstract
Sedimenticola selenatireducens strain AK4OH1T (= DSM 17993T = ATCC BAA-1233T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. The draft genome comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report the main features of the genome of S. selenatireducens strain AK4OH1T.
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Affiliation(s)
- Tiffany S Louie
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
| | - Donato Giovannelli
- Institute of Earth, Ocean, and Atmospheric Science, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ USA ; Institute of Marine Science, ISMAR, National Research Council of Italy, CNR, Ancona, Italy ; Institute for Advanced Studies, Program in Interdisciplinary Studies, Princeton, NJ USA
| | - Nathan Yee
- Department of Environmental Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
| | - Priya Narasingarao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
| | - Valentin Starovoytov
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany ; Newcastle University, School of Biology, Newcastle upon Tyne, UK
| | - Elke Lang
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA
| | - Elisabetta Bini
- Pharmacy Practice and Administration, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ USA ; Present address: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN USA
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
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Abstract
Respiration of perchlorate and chlorate [collectively, (per)chlorate] was only recognized in the last 20 years, yet substantial advances have been made in our understanding of the underlying metabolisms. Although it was once considered solely anthropogenic, pervasive natural sources, both terrestrial and extraterrestrial, indicate an ancient (per)chlorate presence across our solar system. These discoveries stimulated interest in (per)chlorate microbiology, and the application of advanced approaches highlights exciting new facets. Forward and reverse genetics revealed new information regarding underlying molecular biology and associated regulatory mechanisms. Structural and functional analysis characterized core enzymes and identified novel reaction sequences. Comparative genomics elucidated evolutionary aspects, and stress analysis identified novel response mechanisms to reactive chlorine species. Finally, systems biology identified unique metabolic versatility and novel mechanisms of (per)chlorate respiration, including symbiosis and a hybrid enzymatic-abiotic metabolism. While many published studies focus on (per)chlorate and their basic metabolism, this review highlights seminal advances made over the last decade and identifies new directions and potential novel applications.
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Affiliation(s)
- Matthew D Youngblut
- Energy Biosciences Institute, University of California, Berkeley, California 94704;
| | - Ouwei Wang
- Energy Biosciences Institute, University of California, Berkeley, California 94704; .,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Tyler P Barnum
- Energy Biosciences Institute, University of California, Berkeley, California 94704; .,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - John D Coates
- Energy Biosciences Institute, University of California, Berkeley, California 94704; .,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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