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Sudo M, Osvatic J, Taylor JD, Dufour SC, Prathep A, Wilkins LGE, Rattei T, Yuen B, Petersen JM. SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers. mSystems 2024; 9:e0113523. [PMID: 38747602 PMCID: PMC11237559 DOI: 10.1128/msystems.01135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/13/2024] [Indexed: 06/19/2024] Open
Abstract
Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.
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Affiliation(s)
- Marta Sudo
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jay Osvatic
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - John D. Taylor
- Life Sciences, The Natural History Museum, London, United Kingdom
| | - Suzanne C. Dufour
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Anchana Prathep
- Department of Biology, Faculty of Science, Prince of Songkla University, HatYai, Thailand
| | - Laetitia G. E. Wilkins
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Rattei
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Benedict Yuen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jillian M. Petersen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
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Cuthbert BJ, Mendoza J, de Miranda R, Papavinasasundaram K, Sassetti CM, Goulding CW. The structure of Mycobacterium thermoresistibile MmpS5 reveals a conserved disulfide bond across mycobacteria. Metallomics 2024; 16:mfae011. [PMID: 38425033 PMCID: PMC10929441 DOI: 10.1093/mtomcs/mfae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Abstract
The tuberculosis (TB) emergency has been a pressing health threat for decades. With the emergence of drug-resistant TB and complications from the COVID-19 pandemic, the TB health crisis is more serious than ever. Mycobacterium tuberculosis (Mtb), the causative agent of TB, requires iron for its survival. Thus, Mtb has evolved several mechanisms to acquire iron from the host. Mtb produces two siderophores, mycobactin and carboxymycobactin, which scavenge for host iron. Mtb siderophore-dependent iron acquisition requires the export of apo-siderophores from the cytosol to the host environment and import of iron-bound siderophores. The export of Mtb apo-siderophores across the inner membrane is facilitated by two mycobacterial inner membrane proteins with their cognate periplasmic accessory proteins, designated MmpL4/MmpS4 and MmpL5/MmpS5. Notably, the Mtb MmpL4/MmpS4 and MmpL5/MmpS5 complexes have also been implicated in the efflux of anti-TB drugs. Herein, we solved the crystal structure of M. thermoresistibile MmpS5. The MmpS5 structure reveals a previously uncharacterized, biologically relevant disulfide bond that appears to be conserved across the Mycobacterium MmpS4/S5 homologs, and comparison with structural homologs suggests that MmpS5 may be dimeric.
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Affiliation(s)
- Bonnie J Cuthbert
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Jessica Mendoza
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Rodger de Miranda
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Celia W Goulding
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
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Naruki M, Watanabe A, Warashina T, Morita T, Arakawa K. Complete genome sequence of Limnobacter thiooxidans CS-K2 T, isolated from freshwater lake sediments in Bavaria, Germany. Microbiol Resour Announc 2024; 13:e0099223. [PMID: 38047682 DOI: 10.1128/mra.00992-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/11/2023] [Indexed: 12/05/2023] Open
Abstract
Limnobacter thiooxidans CS-K2T is a Gram-negative bacterium first isolated from the sediment of the littoral zone of a freshwater lake in Germany. We here present the complete annotated genome sequence of this thiosulfate-oxidizing bacterium, spanning 3.54 Mb and encoding 3,192 protein-coding sequences.
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Affiliation(s)
- Miu Naruki
- Institute for Advanced Biosciences, Keio University , Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa, Kanagawa, Japan
| | - Aoi Watanabe
- Institute for Advanced Biosciences, Keio University , Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa, Kanagawa, Japan
| | - Tomoro Warashina
- Institute for Advanced Biosciences, Keio University , Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa, Kanagawa, Japan
| | - Teppei Morita
- Institute for Advanced Biosciences, Keio University , Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa, Kanagawa, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University , Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa, Kanagawa, Japan
- Faculty of Environment and Information Studies, Keio University , Fujisawa, Kanagawa, Japan
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Xi Z, Dou L, Zhang M, Pan L. Desulfurization properties, pathways, and potential applications of two novel and efficient chemolithotrophic sulfur-oxidizing strains of Pseudomonas sp. GHWS3 and Sphingobacterium sp. GHWS5. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:3495-3511. [PMID: 38085488 DOI: 10.1007/s11356-023-31404-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/03/2023] [Indexed: 01/19/2024]
Abstract
With the accelerated modernization of agriculture and industry, sulfides have been released into the environment as a by-products of various production processes. Elevated levels of sulfide pose a threat to organisms' health and disrupt ecosystem equilibrium. This study successfully isolated two highly efficient sulfur-oxidizing strains, namely Pseudomonas aeruginosa GHWS3 and Sphingobacterium sp. GHWS5. Neither strain exhibited hemolytic activity or pathogenicity. Additionally, GHWS3 inhibited the common aquaculture pathogen Vibrio anguillarum, while GHWS5 exhibited inhibitory effects against Vibrio harveyi. GHWS3 and GHWS5 demonstrated effective removal of sulfide under the following conditions: temperature range of 20-40 °C, pH level of 4.5-8.5, salinity range of 0-50‰, C/N ratio of 5-15, and sulfide concentration of 20-200 mg/L. By amplifying the key functional genes of the sulfur-oxidizing Sox and rDsr systems in both GHWS3 and GHWS5 strains, potential desulfurization pathways were analyzed. Furthermore, both strains displayed high efficiency in removing sulfides from actual aquaculture pond substrate mixtures. The findings of this study provide two promising candidate strains for sulfides removal from farm tailwater, industrial wastewater, and domestic wastewater.
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Affiliation(s)
- Zeyan Xi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Le Dou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Mengyu Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Luqing Pan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, China.
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Nosalova L, Piknova M, Kolesarova M, Pristas P. Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria. Microorganisms 2023; 11:1436. [PMID: 37374938 DOI: 10.3390/microorganisms11061436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.
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Affiliation(s)
- Lea Nosalova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Maria Piknova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Mariana Kolesarova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Peter Pristas
- Centre of Biosciences, Institute of Animal Physiology, Slovak Academy of Sciences, 040 01 Kosice, Slovakia
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Zhan J, Xia D. Bcs1, a novel target for fungicide. Front Chem 2023; 11:1146753. [PMID: 36993815 PMCID: PMC10040684 DOI: 10.3389/fchem.2023.1146753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
The mitochondrial respiratory chain has long been a primary target for the development of fungicides for its indispensable role in various cellular functions including energy metabolism. Over the years, a wide range of natural and synthetic fungicides and pesticides targeting the respiratory chain complexes have been discovered or developed and used in agriculture and in medicine, which brought considerable economic gains but was also accompanied by the emergence of resistance to these compounds. To delay and overcome the onset of resistance, novel targets for fungicides development are actively being pursued. Mitochondrial AAA protein Bcs1 is necessary for the biogenesis of respiratory chain Complex III, also known as cyt bc1 complex, by delivering the last essential iron-sulfur protein subunit in its folded form to the cyt bc1 precomplex. Although no report on the phenotypes of knock-out Bcs1 has been reported in animals, pathogenic Bcs1 mutations cause Complex III deficiency and respiratory growth defects, which makes it a promising new target for the development of fungicides. Recent Cryo-EM and X-ray structures of mouse and yeast Bcs1 revealed the basic oligomeric states of Bcs1, shed light on the translocation mechanism of its substrate ISP, and provided the basis for structure-based drug design. This review summarizes the recent progress made on understanding the structure and function of Bcs1, proposes the use of Bcs1 as an antifungal target, and provides novel prospects for fungicides design by targeting Bcs1.
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Xin Y, Wang Y, Zhang H, Wu Y, Xia Y, Li H, Qu X. Cupriavidus pinatubonensis JMP134 Alleviates Sulfane Sulfur Toxicity after the Loss of Sulfane Dehydrogenase through Oxidation by Persulfide Dioxygenase and Hydrogen Sulfide Release. Metabolites 2023; 13:metabo13020218. [PMID: 36837837 PMCID: PMC9959259 DOI: 10.3390/metabo13020218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
An incomplete Sox system lacking sulfane dehydrogenase SoxCD may produce and accumulate sulfane sulfur when oxidizing thiosulfate. However, how bacteria alleviate the pressure of sulfane sulfur accumulation remains largely unclear. In this study, we focused on the bacterium Cupriavidus pinatubonensis JMP134, which contains a complete Sox system. When soxCD was deleted, this bacterium temporarily produced sulfane sulfur when oxidizing thiosulfate. Persulfide dioxygenase (PDO) in concert with glutathione oxidizes sulfane sulfur to sulfite. Sulfite can spontaneously react with extra persulfide glutathione (GSSH) to produce thiosulfate, which can feed into the incomplete Sox system again and be oxidized to sulfate. Furthermore, the deletion strain lacking PDO and SoxCD produced volatile H2S gas when oxidizing thiosulfate. By comparing the oxidized glutathione (GSSG) between the wild-type and deletion strains, we speculated that H2S is generated during the interaction between sulfane sulfur and the glutathione/oxidized glutathione (GSH/GSSG) redox couple, which may reduce the oxidative stress caused by the accumulation of sulfane sulfur in bacteria. Thus, PDO and H2S release play a critical role in alleviating sulfane sulfur toxicity after the loss of soxCD in C. pinatubonensis JMP134.
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Affiliation(s)
- Yufeng Xin
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence: (Y.X.); (X.Q.); Tel.: +86-15562345068 (Y.X.)
| | - Yaxin Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honglin Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yu Wu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Huanjie Li
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Xiaohua Qu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence: (Y.X.); (X.Q.); Tel.: +86-15562345068 (Y.X.)
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Díaz-Torres O, Lugo-Melchor OY, de Anda J, Orozco-Nunnelly DA, Gradilla-Hernández MS, Senés-Guerrero C. Characterizing a subtropical hypereutrophic lake: From physicochemical variables to shotgun metagenomic data. Front Microbiol 2022; 13:1037626. [DOI: 10.3389/fmicb.2022.1037626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
Lake Cajititlán is a subtropical and endorheic lake, which is heavily impacted by nutrient pollution. Agricultural runoff and poorly treated wastewater have entered this reservoir at alarming rates during past rainy seasons, causing the cultural eutrophication of this body of water and resulting in several massive fish kill events. In this study, shotgun metagenomic sequencing was used to examine the taxonomic and functional structure of microbial communities in Lake Cajititlán during the rainy season. Several water quality features and their interactions with microbial communities were also assessed to identify the major factors affecting the water quality and biota, specifically fish species. According to current water quality regulations, most of the physicochemical variables analyzed (dissolved oxygen, pH, Secchi disk, NH4+, NO3−, blue-green algae, total phosphorus, and chlorophyll-a) were outside of the permissible limits. Planktothrix agardhii and Microcystis aeruginosa were the most abundant phytoplankton species, and the dominant bacterial genera were Pseudomonas, Streptomyces, and Flavobacterium, with Pseudomonas fluorescens, Stenotrophomonas maltophilia, and Aeromonas veronii representing the most abundant bacterial species. All of these microorganisms have been reported to be potentially harmful to fish, and the latter three (P. fluorescens, S. maltophilia, A. veronii) also contain genes associated with pathogenicity in fish mortality (fur, luxS, aer, act, aha, exu, lip, ser). Genetic evidence from the microbial communities analyzed herein reveals that anthropogenic sources of nutrients in the lake altered genes involved in nitrogen, phosphorus, sulfur, and carbon metabolism, mainly at the beginning of the rainy season. These findings suggest that abiotic factors influence the structure of the microbial communities, along with the major biogeochemical cycles of Lake Cajititlán, resulting in temporal variations and an excess of microorganisms that can thrive in high-nutrient and low-oxygen environments. After reviewing the literature, this appears to be the first study that focuses on characterizing the water quality of a subtropical hypereutrophic lake through associations between physicochemical variables and shotgun metagenomic data. In addition, there are few studies that have coupled the metabolism of aquatic ecosystems with nutrient cycles.
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Leberecht KM, Ritter SM, Lapp CJ, Klose L, Eschenröder J, Scholz C, Kühnel S, Stinnesbeck W, Kletzin A, Isenbeck-Schröter M, Gescher J. Microbially promoted calcite precipitation in the pelagic redoxcline: Elucidating the formation of the turbid layer. GEOBIOLOGY 2022; 20:498-517. [PMID: 35514106 DOI: 10.1111/gbi.12492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Large bell-shaped calcite formations called "Hells Bells" were discovered underwater in the stratified cenote El Zapote on the Yucatán Peninsula, Mexico. Together with these extraordinary speleothems, divers found a white, cloudy turbid layer into which some Hells Bells partially extend. Here, we address the central question if the formation of the turbid layer could be based on microbial activity, more specifically, on microbially induced calcite precipitation. Metagenomic and metatranscriptomic profiling of the microbial community in the turbid layer, which overlaps with the pelagic redoxcline in the cenote, revealed chemolithoautotrophic Hydrogenophilales and unclassified β-Proteobacteria as the metabolic key players. Bioinformatic and hydrogeochemical data suggest chemolithoautotrophic oxidation of sulfide to zero-valent sulfur catalyzed by denitrifying organisms due to oxygen deficiency. Incomplete sulfide oxidation via nitrate reduction and chemolithoautotrophy are both proton-consuming processes, which increase the pH in the redoxcline favoring authigenic calcite precipitation and may contribute to Hells Bells growth. The observed mechanism of microbially induced calcite precipitation is potentially applicable to many other stagnant sulfate-rich water bodies.
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Affiliation(s)
- Kerstin M Leberecht
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Simon M Ritter
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Christian J Lapp
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
| | - Lukas Klose
- Department of Physics & Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | | | - Christian Scholz
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Kühnel
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Stinnesbeck
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, Heidelberg, Germany
| | - Arnulf Kletzin
- Department of Biology, Microbiology; Sulfur Biochemistry and Microbial Bioenergetics, Technical University of Darmstadt, Darmstadt, Germany
| | - Margot Isenbeck-Schröter
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, Heidelberg, Germany
| | - Johannes Gescher
- Institute of Technical Microbiology, Hamburg University of Technology, Hamburg, Germany
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Ferreira P, Fernandes P, Ramos M. The archaeal non-heme iron-containing Sulfur Oxygenase Reductase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Zvi-Kedem T, Shemesh E, Tchernov D, Rubin-Blum M. The worm affair: fidelity and environmental adaptation in symbiont species that co-occur in vestimentiferan tubeworms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:744-752. [PMID: 34374209 DOI: 10.1111/1758-2229.12994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/20/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The symbioses between the vestimentiferan tubeworms and their chemosynthetic partners (Gammaproteobacteria, Chromatiales and Sedimenticolaceae) hallmark the success of these organisms in hydrothermal vent and hydrocarbon seep deep-sea habitats. The fidelity of these associations varies, as both the hosts and the symbionts can be loose in partner choice. Some tubeworms may host distinct symbiont phylotypes, which often co-occur in a single host individual. To better understand the genetic basis for the promiscuity of tubeworm symbioses, we assembled and investigated metagenome-assembled genomes of two symbiont phylotypes (species, based on the average nucleotide identity < 95%) in Lamellibrachia anaximandri, a vestimentiferan endemic to the Mediterranean Sea, in individuals collected from Palinuro hydrothermal vents (Italy) and hydrocarbon seeps (Eratosthenes seamount and Palmahim disturbance). Using comparative genomics, we show that mainly mobilome and genes involved in defence mechanisms distinguish the symbiont genotypes. While many central metabolic functions are conserved in the tubeworm symbionts, nitrate respiration (Nar, Nap and Nas proteins) is modular, yet this modularity is not linked to phylotype, but rather to geographic location, potentially implying adaptation to the local environment. Our results hint that variation in a single moonlighting protein may be responsible for the fidelity of these symbioses.
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Affiliation(s)
- Tal Zvi-Kedem
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Eli Shemesh
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, Haifa, 3108000, Israel
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A Complex of LaoA and LaoB Acts as a Tat-Dependent Dehydrogenase for Long-Chain Alcohols in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:e0076221. [PMID: 34085859 DOI: 10.1128/aem.00762-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa can utilize unusual carbon sources, like sodium dodecyl sulfate (SDS) and alkanes. Whereas the initiating enzymatic steps of the corresponding degradation pathways have been characterized in detail, the oxidation of the emerging long-chain alcohols has received little attention. Recently, the genes for the Lao (long-chain-alcohol/aldehyde oxidation) system were discovered to be involved in the oxidation of long-chain alcohols derived from SDS and alkane degradation. In the Lao system, LaoA is predicted to be an alcohol dehydrogenase/oxidase; however, according to genetic studies, efficient long-chain-alcohol oxidation additionally required the Tat-dependent protein LaoB. In the present study, the Lao system was further characterized. In vivo analysis revealed that the Lao system complements the substrate spectrum of the well-described Exa system, which is required for growth with ethanol and other short-chain alcohols. Mutational analysis revealed that the Tat site of LaoB was required for long-chain-alcohol oxidation activity, strongly suggesting a periplasmic localization of the complex. Purified LaoA was fully active only when copurified with LaoB. Interestingly, in vitro activity of the purified LaoAB complex also depended on the presence of the Tat site. The copurified LaoAB complex contained a flavin cofactor and preferentially oxidized a range of saturated, unbranched primary alcohols. Furthermore, the LaoAB complex could reduce cytochrome c550-type redox carriers like ExaB, a subunit of the Exa alcohol dehydrogenase system. LaoAB complex activity was stimulated by rhamnolipids in vitro. In summary, LaoAB constitutes an unprecedented protein complex with specific properties apparently required for oxidizing long-chain alcohols. IMPORTANCE Pseudomonas aeruginosa is a major threat to public health. Its ability to thrive in clinical settings, water distribution systems, or even jet fuel tanks is linked to detoxification and degradation of diverse hydrophobic substrates that are metabolized via alcohol intermediates. Our study illustrates a novel flavoprotein long-chain-alcohol dehydrogenase consisting of a facultative two-subunit complex, which is unique among related enzymes, while the homologs of the corresponding genes are found in numerous bacterial genomes. Understanding the catalytic and compartmentalization processes involved is of great interest for biotechnological and hygiene research, as it may be a potential starting point for rationally designing novel antibacterial substances with high specificity against this opportunistic pathogen.
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Alam M, Fernandes S, Mandal S, Rameez MJ, Bhattacharya S, Peketi A, Mazumdar A, Ghosh W. 34S enrichment as a signature of thiosulfate oxidation in the "Proteobacteria". FEMS Microbiol Lett 2021; 368:6307019. [PMID: 34151347 DOI: 10.1093/femsle/fnab073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/17/2021] [Indexed: 12/17/2022] Open
Abstract
Kinetics of thiosulfate oxidation, product and intermediate formation, and 34S fractionation, were studied for the members of Alphaproteobacteria Paracoccus sp. SMMA5 and Mesorhizobium thiogangeticum SJTT, the Betaproteobacteria member Pusillimonas ginsengisoli SBO3, and the Acidithiobacillia member Thermithiobacillus sp. SMMA2, during chemolithoautotrophic growth in minimal salts media supplemented with 20 mM thiosulfate. The two Alphaproteobacteria oxidized thiosulfate directly to sulfate, progressively enriching the end-product with 34S; Δ34Sthiosulfate-sulfate values recorded at the end of the two processes (when no thiosulfate was oxidized any further) were -2.9‰ and -3.5‰, respectively. Pusillimonas ginsengisoli SBO3 and Thermithiobacillus sp. SMMA2, on the other hand, oxidized thiosulfate to sulfate via tetrathionate intermediate formation, with progressive 34S enrichment in the end-product sulfate throughout the incubation period; Δ34Sthiosulfate-sulfate, at the end of the two processes (when no further oxidation took place), reached -3.5‰ and -3.8‰, respectively. Based on similar 34S fractionation patterns recorded previously during thiosulfate oxidation by strains of Paracoccus pantotrophus, Advenella kashmirensis and Hydrogenovibrio crunogenus, it was concluded that progressive reverse fractionation, enriching the end-product sulfate with 34S, could be a characteristic signature of bacterial thiosulfate oxidation.
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Affiliation(s)
- Masrure Alam
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Svetlana Fernandes
- Gas Hydrate Research Group, Geological Oceanography, CSIR-National Institute of Oceanography, Dona Paula, Goa-403004, India
| | - Subhrangshu Mandal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Maida Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Sabyasachi Bhattacharya
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Aditya Peketi
- Gas Hydrate Research Group, Geological Oceanography, CSIR-National Institute of Oceanography, Dona Paula, Goa-403004, India
| | - Aninda Mazumdar
- Gas Hydrate Research Group, Geological Oceanography, CSIR-National Institute of Oceanography, Dona Paula, Goa-403004, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, West Bengal, India
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14
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Lian FB, Chen XY, Jiang S, Li GY, Du ZJ. Marinobacter orientalis sp. nov., a thiosulfate-oxidizing bacterium isolated from a marine solar saltern. Antonie Van Leeuwenhoek 2021; 114:765-775. [PMID: 33751321 DOI: 10.1007/s10482-021-01556-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/06/2021] [Indexed: 11/25/2022]
Abstract
A facultatively anaerobic bacterium, strain W62T, was isolated from the marine solar saltern in Weihai, China. Cells of the novel strain were Gram-stain negative, non-flagellated, non-gliding, rod-shaped and around 0.3-0.5 × 2.5-3.9 µm in size. Optimum growth occurred at 33-37 °C, with 3-5% (w/v) NaCl and at pH 7.0-7.5. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, strain W62T had close relationship with Marinobacter vulgaris F01T (98.6%), Marinobacter confluentis KCTC 42705T (98.4%) and Marinobacter halotolerans NBRC 110910T (97.7%). Genome sequencing revealed a genome size of 4,050,555 bp, a G+C content of 57.3% and a complete sox system related to thiosulfate oxidization. Strain W62T had ubiquinone-9 as the sole respiratory quinone and possessed Summed Features 3 (C16:1 ω7c/C16:1 ω6c), C16:0 and C18:1 ω9c as the major fatty acids. The major polar lipids of strain W62T were identified as aminophospholipid, phosphatidylglycerol and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain W62T should represent a novel specie of the genus Marinobacter, for which the name Marinobacter orientalis sp. nov. is proposed. The type strain is W62T (= MCCC 1H00317T = KCTC 62593T).
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Affiliation(s)
- Feng-Bai Lian
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Xu-Yang Chen
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Shan Jiang
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Guang-Yu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, Fujian, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
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15
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Lian FB, Li YQ, Zhang J, Jiang S, Du ZJ. Sulfitobacter maritimus sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 33502295 DOI: 10.1099/ijsem.0.004659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic bacterium, strain S0837T, was isolated from the marine sediment of Jingzi Wharf, Weihai, China. Cells of the novel strain were Gram-stain-negative, non-flagellated, non-gliding, non-pigmented and rod-shaped. Cells were around 0.3-0.5×1.0-1.4 µm in size and often appeared singly. Optimum growth occurred at 33 °C, with 2 % (w/v) NaCl and at pH 7.0-7.5. On the basis of the results of 16S rRNA gene sequences, stain S0837T had the closest relative with Sulfitobacter delicatus KCTC 32183T (98.0 %). Genome sequencing revealed a genome size of 3 785 026 bp, a G+C content of 59.8 mol% and several genes related with sulphur oxidation. The strain shared 98.0 % 16S rRNA sequence similarities with closely related type species and shared ANI value below 95-96 %, dDDH value of showed relatedness of 27.4, 25.2 and 25.2 % respectively with the closely related type species. Strain S0837T had ubiquinone-10 as the sole respiratory quinone, and possessed summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as the major fatty acid. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain S0837T should represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter maritimus sp. nov. is proposed. The type strain is S0837T (=MCCC 1K04635T=KCTC 72860T).
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Affiliation(s)
- Feng-Bai Lian
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Yong-Qin Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang 524048, Guangdong, PR China
| | - Jing Zhang
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Shan Jiang
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, Shandong, PR China
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16
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Likhitrattanapisal S, Siriarchawatana P, Seesang M, Chunhametha S, Boonsin W, Phithakrotchanakoon C, Kitikhun S, Eurwilaichitr L, Ingsriswang S. Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries. Sci Rep 2021; 11:582. [PMID: 33436774 PMCID: PMC7804445 DOI: 10.1038/s41598-020-79786-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.
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Affiliation(s)
- Somsak Likhitrattanapisal
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Paopit Siriarchawatana
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Mintra Seesang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Suwanee Chunhametha
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Worawongsin Boonsin
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Chitwadee Phithakrotchanakoon
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Supattra Kitikhun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Lily Eurwilaichitr
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
| | - Supawadee Ingsriswang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
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17
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Camacho D, Frazao R, Fouillen A, Nanci A, Lang BF, Apte SC, Baron C, Warren LA. New Insights Into Acidithiobacillus thiooxidans Sulfur Metabolism Through Coupled Gene Expression, Solution Chemistry, Microscopy, and Spectroscopy Analyses. Front Microbiol 2020; 11:411. [PMID: 32231653 PMCID: PMC7082400 DOI: 10.3389/fmicb.2020.00411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/27/2020] [Indexed: 01/23/2023] Open
Abstract
Here, we experimentally expand understanding of the reactions and enzymes involved in Acidithiobacillus thiooxidans ATCC 19377 S0 andS 2 O 3 2 - metabolism by developing models that integrate gene expression analyzed by RNA-Seq, solution sulfur speciation, electron microscopy and spectroscopy. The A. thiooxidansS 2 O 3 2 - metabolism model involves the conversion ofS 2 O 3 2 - to SO 4 2 - , S0 andS 4 O 6 2 - , mediated by the sulfur oxidase complex (Sox), tetrathionate hydrolase (TetH), sulfide quinone reductase (Sqr), and heterodisulfate reductase (Hdr) proteins. These same proteins, with the addition of rhodanese (Rhd), were identified to convert S0 to SO 3 2 - ,S 2 O 3 2 - and polythionates in the A. thiooxidans S0 metabolism model. Our combined results shed light onto the important role specifically of TetH inS 2 O 3 2 - metabolism. Also, we show that activity of Hdr proteins rather than Sdo are likely associated with S0 oxidation. Finally, our data suggest that formation of intracellularS 2 O 3 2 - is a critical step in S0 metabolism, and that recycling of internally generated SO 3 2 - occurs, through comproportionating reactions that result inS 2 O 3 2 - . Electron microscopy and spectroscopy confirmed intracellular production and storage of S0 during growth on both S0 andS 2 O 3 2 - substrates.
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Affiliation(s)
- David Camacho
- School of Geography and Earth Science, Faculty of Science, McMaster University, Hamilton, ON, Canada
| | - Rodolfo Frazao
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Aurélien Fouillen
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Laboratory for the Study of Calcified Tissues and Biomaterials, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada
| | - Antonio Nanci
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Laboratory for the Study of Calcified Tissues and Biomaterials, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada
| | - B. Franz Lang
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Simon C. Apte
- CSIRO, Land and Water, Lucas Heights, NSW, Australia
| | - Christian Baron
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Lesley A. Warren
- School of Geography and Earth Science, Faculty of Science, McMaster University, Hamilton, ON, Canada
- Department of Civil and Mineral Engineering, Faculty of Applied Science and Engineering, University of Toronto, Toronto, ON, Canada
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18
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Mandal S, Rameez MJ, Chatterjee S, Sarkar J, Pyne P, Bhattacharya S, Shaw R, Ghosh W. Molecular mechanism of sulfur chemolithotrophy in the betaproteobacterium Pusillimonas ginsengisoli SBSA. MICROBIOLOGY-SGM 2020; 166:386-397. [PMID: 31999239 DOI: 10.1099/mic.0.000890] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Chemolithotrophic sulfur oxidation represents a significant part of the biogeochemical cycling of this element. Due to its long evolutionary history, this ancient metabolism is well known for its extensive mechanistic and phylogenetic diversification across a diverse taxonomic spectrum. Here we carried out whole-genome sequencing and analysis of a new betaproteobacterial isolate, Pusillimonas ginsengisoli SBSA, which is found to oxidize thiosulfate via the formation of tetrathionate as an intermediate. The 4.7 Mb SBSA genome was found to encompass a soxCDYZAXOB operon, plus single thiosulfate dehydrogenase (tsdA) and sulfite : acceptor oxidoreductase (sorAB) genes. Recombination-based knockout of tsdA revealed that the entire thiosulfate is first converted to tetrathionate by the activity of thiosulfate dehydrogenase (TsdA) and the Sox pathway is not functional in this bacterium despite the presence of all necessary sox genes. The ∆soxYZ and ∆soxXA knockout mutants exhibited a wild-type-like phenotype for thiosulfate/tetrathionate oxidation, whereas ∆soxB, ∆soxCD and soxO::KanR mutants only oxidized thiosulfate up to tetrathionate intermediate and had complete impairment in tetrathionate oxidation. The substrate-dependent O2 consumption rate of whole cells and the sulfur-oxidizing enzyme activities of cell-free extracts, measured in the presence/absence of thiol inhibitors/glutathione, indicated that glutathione plays a key role in SBSA tetrathionate oxidation. The present findings collectively indicate that the potential glutathione : tetrathionate coupling in P. ginsengisoli involves a novel enzymatic component, which is different from the dual-functional thiol dehydrotransferase (ThdT), while subsequent oxidation of the sulfur intermediates produced (e.g. glutathione : sulfodisulfane molecules) may proceed via the iterative action of soxBCD .
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Affiliation(s)
- Subhrangshu Mandal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Moidu Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Sumit Chatterjee
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Jagannath Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Prosenjit Pyne
- Present address: National Institute of Cholera and Enteric Diseases (NICED), P- C.I.T. Scheme XM, Beleghata, 33, CIT Rd, Beleghata, Kolkata - 700054, India.,Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | | | - Rahul Shaw
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata-700054, India
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19
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Bacterial Intracellular Sulphur Globules. BACTERIAL ORGANELLES AND ORGANELLE-LIKE INCLUSIONS 2020. [DOI: 10.1007/978-3-030-60173-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Cui YX, Biswal BK, van Loosdrecht MCM, Chen GH, Wu D. Long term performance and dynamics of microbial biofilm communities performing sulfur-oxidizing autotrophic denitrification in a moving-bed biofilm reactor. WATER RESEARCH 2019; 166:115038. [PMID: 31505308 DOI: 10.1016/j.watres.2019.115038] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
Sulfide-oxidizing autotrophic denitrification (SOAD) implemented in a moving-bed biofilm reactor (MBBR) is a promising alternative to conventional heterotrophic denitrification in mainstream biological nitrogen removal. The sulfide-oxidation intermediate - elemental sulfur - is crucial for the kinetic and microbial properties of the sulfur-oxidizing bacterial communities, but its role is yet to be studied in depth. Hence, to investigate the performance and microbial communities of the aforementioned new biosystem, we operated for a long term a laboratory-scale (700 d) SOAD MBBR to treat synthetic saline domestic sewage, with an increase of the surface loading rate from 8 to 50 mg N/(m2·h) achieved by shortening the hydraulic retention time from 12 h to 2 h. The specific reaction rates of the reactor were eventually increased up to 0.37 kg N/(m3·d) and 0.73 kg S/(m3·d) for nitrate reduction and sulfide oxidation with no significant sulfur elemental accumulation. Two sulfur-oxidizing bacterial (SOB) clades, Sox-independent SOB (SOBI) and Sox-dependent SOB (SOBII), were responsible for indirect two-step sulfur oxidation (S2-→S0→SO42-) and direct one-step sulfur oxidation (S2-→SO42-), respectively. The SOBII biomass-specific electron transfer capacity could be around 2.5 times greater than that of SOBI (38 mmol e-/(gSOBII·d) versus 15 mmol e-/(gSOBI·d)), possibly resulting in the selection of SOBII over SOBI under stress conditions (such as a shorter HRT). Further studies on the methods and mechanism of selecting of SOBII over SOBI in biofilm reactors are recommended. Overall, the findings shed light on the design and operation of MBBR-based SOAD processes for mainstream biological denitrification.
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Affiliation(s)
- Yan-Xiang Cui
- Department of Civil and Environmental Engineering, Water Technology Center, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch), The Hong Kong University of Science and Technology, Hong Kong China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Basanta Kumar Biswal
- Department of Civil and Environmental Engineering, Water Technology Center, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch), The Hong Kong University of Science and Technology, Hong Kong China
| | | | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, Water Technology Center, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch), The Hong Kong University of Science and Technology, Hong Kong China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China
| | - Di Wu
- Department of Civil and Environmental Engineering, Water Technology Center, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch), The Hong Kong University of Science and Technology, Hong Kong China; Shenzhen Research Institute, Fok Ying Tung Graduate School, The Hong Kong University of Science and Technology, Guangdong, China.
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21
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Rameez MJ, Pyne P, Mandal S, Chatterjee S, Alam M, Bhattacharya S, Mondal N, Sarkar J, Ghosh W. Two pathways for thiosulfate oxidation in the alphaproteobacterial chemolithotroph Paracoccus thiocyanatus SST. Microbiol Res 2019; 230:126345. [PMID: 31585234 DOI: 10.1016/j.micres.2019.126345] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/08/2019] [Accepted: 09/21/2019] [Indexed: 02/02/2023]
Abstract
Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy involves direct oxidation of thiosulfate (S2O32-) to sulfate (SO42-) without any free intermediate. This pathway mediated by SoxXAYZBCD is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate(S4O62-)-oxidizing alphaproteobacterium Paracoccus thiocyanatus SST, and compare them with the prototypical Sox process of Paracoccus pantotrophus. Our results reveal a unique case where an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation converting ∼10% of the thiosulfate supplied, whilst ∼90% of the substrate is oxidized via a pathway that produces tetrathionate as an intermediate. Sulfur oxidation kinetics of a deletion mutant showed that thiosulfate-to-tetrathionate conversion, in SST, is catalyzed by a thiosulfate dehydrogenase (TsdA) homolog that has far-higher substrate-affinity than the Sox system of this bacterium, which in turn is also less efficient than the P. pantotrophus Sox. Deletion of soxB abolished sulfate-formation from thiosulfate/tetrathionate, while thiosulfate-to-tetrathionate conversion remained unperturbed. Physiological studies revealed the involvement of glutathione in SST tetrathionate oxidation. However, zero impact of the insertional mutation of a thiol dehydrotransferase (thdT) homolog, together with the absence of sulfite as an intermediate, indicated that SST tetrathionate oxidation is mechanistically novel, and distinct from its betaproteobacterial counterpart mediated by glutathione, ThdT, SoxBCD and sulfite:acceptor oxidoreductase. The present findings highlight extensive functional diversification of sulfur-oxidizing enzymes across phylogenetically close, as well as distant, bacteria.
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Affiliation(s)
- Moidu Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Prosenjit Pyne
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Subhrangshu Mandal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Sumit Chatterjee
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Masrure Alam
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | | | - Nibendu Mondal
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Jagannath Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
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22
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Houghton JL, Foustoukos DI, Fike DA. The effect of O 2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila. GEOBIOLOGY 2019; 17:564-576. [PMID: 31180189 DOI: 10.1111/gbi.12352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur-oxidizing micro-organisms in particular. In this study, the thiosulfate-oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04-1.9 mM) and high pressure (5-10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed-system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O2 was 0.25 hr-1 . This is comparable to the μmax (0.28 hr-1 ) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half-saturation constant for O2 ( KO2 ) estimated from this study was 0.2 mM (at a cell density of 105 cells/ml) and was robust at all pressures tested (0.4-10 MPa), consistent with piezotolerant behavior of this strain. The cell-specific KO2 was determined to be 1.5 pmol O2 /cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell-specific KO2 and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).
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Affiliation(s)
- Jennifer L Houghton
- Department of Earth and Planetary Sciences, Washington University, St. Louis, Missouri
| | - Dionysis I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, District of Columbia
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University, St. Louis, Missouri
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23
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Cui YX, Biswal BK, Guo G, Deng YF, Huang H, Chen GH, Wu D. Biological nitrogen removal from wastewater using sulphur-driven autotrophic denitrification. Appl Microbiol Biotechnol 2019; 103:6023-6039. [DOI: 10.1007/s00253-019-09935-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/06/2023]
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Watanabe T, Kojima H, Umezawa K, Hori C, Takasuka TE, Kato Y, Fukui M. Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera. Front Microbiol 2019; 10:316. [PMID: 30858836 PMCID: PMC6397845 DOI: 10.3389/fmicb.2019.00316] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/06/2019] [Indexed: 01/08/2023] Open
Abstract
Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘Sulfuricellaceae’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.
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Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Umezawa
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Chiaki Hori
- Research Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yukako Kato
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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25
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Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Yang CL, Gao XY, Lin CM, Li YQ, Li Y, Lin JQ, Chen LX. Sulfur Oxidation in the Acidophilic Autotrophic Acidithiobacillus spp. Front Microbiol 2019; 9:3290. [PMID: 30687275 PMCID: PMC6335251 DOI: 10.3389/fmicb.2018.03290] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Sulfur oxidation is an essential component of the earth's sulfur cycle. Acidithiobacillus spp. can oxidize various reduced inorganic sulfur compounds (RISCs) with high efficiency to obtain electrons for their autotrophic growth. Strains in this genus have been widely applied in bioleaching and biological desulfurization. Diverse sulfur-metabolic pathways and corresponding regulatory systems have been discovered in these acidophilic sulfur-oxidizing bacteria. The sulfur-metabolic enzymes in Acidithiobacillus spp. can be categorized as elemental sulfur oxidation enzymes (sulfur dioxygenase, sulfur oxygenase reductase, and Hdr-like complex), enzymes in thiosulfate oxidation pathways (tetrathionate intermediate thiosulfate oxidation (S4I) pathway, the sulfur oxidizing enzyme (Sox) system and thiosulfate dehydrogenase), sulfide oxidation enzymes (sulfide:quinone oxidoreductase) and sulfite oxidation pathways/enzymes. The two-component systems (TCSs) are the typical regulation elements for periplasmic thiosulfate metabolism in these autotrophic sulfur-oxidizing bacteria. Examples are RsrS/RsrR responsible for S4I pathway regulation and TspS/TspR for Sox system regulation. The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in Acidithiobacillus spp. The future research directions and existing barriers in the bacterial sulfur metabolism are also emphasized here and the breakthroughs in these areas will accelerate the research on the sulfur oxidation in Acidithiobacillus spp. and other sulfur oxidizers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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26
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Götz F, Pjevac P, Markert S, McNichol J, Becher D, Schweder T, Mussmann M, Sievert SM. Transcriptomic and proteomic insight into the mechanism of cyclooctasulfur‐ versus thiosulfate‐oxidation by the chemolithoautotroph
Sulfurimonas denitrificans. Environ Microbiol 2018; 21:244-258. [DOI: 10.1111/1462-2920.14452] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 10/16/2018] [Accepted: 10/16/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Florian Götz
- Biology Department Woods Hole Oceanographic Institution Woods Hole MA, 02543 USA
- Department of Pharmaceutical Biotechnology Institute of Pharmacy, University of Greifswald D‐17487, Greifswald Germany
| | - Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science Research Network ‘Chemistry Meets Microbiology’, University of Vienna Althanstr‐14, 1090, Vienna Austria
| | - Stephanie Markert
- Department of Pharmaceutical Biotechnology Institute of Pharmacy, University of Greifswald D‐17487, Greifswald Germany
- Institute of Marine Biotechnology Walther‐Rathenau‐Strasse 49, D‐17489, Greifswald Germany
| | - Jesse McNichol
- Biology Department Woods Hole Oceanographic Institution Woods Hole MA, 02543 USA
| | - Dörte Becher
- Institute of Microbiology University of Greifswald D‐17487, Greifswald Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology Institute of Pharmacy, University of Greifswald D‐17487, Greifswald Germany
- Institute of Marine Biotechnology Walther‐Rathenau‐Strasse 49, D‐17489, Greifswald Germany
| | - Marc Mussmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science Research Network ‘Chemistry Meets Microbiology’, University of Vienna Althanstr‐14, 1090, Vienna Austria
- Department of Molecular Ecology Max Planck Institute for Marine Microbiology Celsiusstr. 1, 28359, Bremen Germany
| | - Stefan M. Sievert
- Biology Department Woods Hole Oceanographic Institution Woods Hole MA, 02543 USA
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27
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Cao X, Koch T, Steffens L, Finkensieper J, Zigann R, Cronan JE, Dahl C. Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor. eLife 2018; 7:e37439. [PMID: 30004385 PMCID: PMC6067878 DOI: 10.7554/elife.37439] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/12/2018] [Indexed: 01/02/2023] Open
Abstract
Many Bacteria and Archaea employ the heterodisulfide reductase (Hdr)-like sulfur oxidation pathway. The relevant genes are inevitably associated with genes encoding lipoate-binding proteins (LbpA). Here, deletion of the gene identified LbpA as an essential component of the Hdr-like sulfur-oxidizing system in the Alphaproteobacterium Hyphomicrobium denitrificans. Thus, a biological function was established for the universally conserved cofactor lipoate that is markedly different from its canonical roles in central metabolism. LbpAs likely function as sulfur-binding entities presenting substrate to different catalytic sites of the Hdr-like complex, similar to the substrate-channeling function of lipoate in carbon-metabolizing multienzyme complexes, for example pyruvate dehydrogenase. LbpAs serve a specific function in sulfur oxidation, cannot functionally replace the related GcvH protein in Bacillus subtilis and are not modified by the canonical E. coli and B. subtilis lipoyl attachment machineries. Instead, LplA-like lipoate-protein ligases encoded in or in immediate vicinity of hdr-lpbA gene clusters act specifically on these proteins.
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Affiliation(s)
- Xinyun Cao
- Department of BiochemistryUniversity of IllinoisUrbanaUnited States
| | - Tobias Koch
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Lydia Steffens
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Julia Finkensieper
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Renate Zigann
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - John E Cronan
- Department of BiochemistryUniversity of IllinoisUrbanaUnited States
- Department of MicrobiologyUniversity of IllinoisUrbanaUnited States
| | - Christiane Dahl
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
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28
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LaoABCR, a Novel System for Oxidation of Long-Chain Alcohols Derived from SDS and Alkane Degradation in Pseudomonas aeruginosa. Appl Environ Microbiol 2018; 84:AEM.00626-18. [PMID: 29678916 DOI: 10.1128/aem.00626-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/15/2018] [Indexed: 12/20/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa strain PAO1 is able to use a variety of organic pollutants as growth substrates, including the anionic detergent sodium dodecyl sulfate (SDS) and long-chain alkanes. While the enzymes initiating SDS and alkane degradation are well known, the subsequent enzymatic steps for degradation of the derived primary long-chain alcohols have not yet been identified. By evaluating genes specifically induced during growth with SDS, a gene cluster encoding a putative alcohol dehydrogenase (PA0364/LaoA), a probable inner membrane protein (PA0365/LaoB), and a presumable aldehyde dehydrogenase (PA0366/LaoC) was identified and designated the Lao (long-chain-alcohol/aldehyde-oxidation) system. Growth experiments with deletion mutants with SDS, 1-dodecanol, and alkanes revealed that LaoA and LaoB are involved in the degradation of primary long-chain alcohols. Moreover, detection of 1-dodecanol oxidation in cell extracts by activity staining revealed an interdependency of LaoA and LaoB for efficient 1-dodecanol oxidation. An in silico analysis yielded no well-characterized homologue proteins for LaoA and LaoB. Furthermore, a gene adjacent to the lao gene cluster encodes a putative transcriptional regulator (PA0367/LaoR). A laoR deletion mutant exhibited constitutive expression of LaoA and LaoB, indicating that LaoR is a repressor for the expression of laoABC Taken together, these results showed that the proteins LaoA and LaoB constitute a novel oxidation system for long-chain alcohols derived from pollutants.IMPORTANCE The versatile and highly adaptive bacterium Pseudomonas aeruginosa is able to colonize a variety of habitats, including anthropogenic environments, where it is often challenged with toxic compounds. Its ability to degrade such compounds and to use them as growth substrates can significantly enhance spreading of this opportunistic pathogen in hygienic settings, such as clinics or water distribution systems. Thus, knowledge about the metabolism of P. aeruginosa can contribute to novel approaches for preventing its growth and reducing nosocomial infections. As the Lao system is important for the degradation of two different classes of pollutants, the identification of these novel enzymes can be a useful contribution for developing effective antibacterial strategies.
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29
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Pyne P, Alam M, Rameez MJ, Mandal S, Sar A, Mondal N, Debnath U, Mathew B, Misra AK, Mandal AK, Ghosh W. Homologs from sulfur oxidation (Sox) and methanol dehydrogenation (Xox) enzyme systems collaborate to give rise to a novel pathway of chemolithotrophic tetrathionate oxidation. Mol Microbiol 2018; 109:169-191. [DOI: 10.1111/mmi.13972] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Prosenjit Pyne
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Masrure Alam
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Moidu Jameela Rameez
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Subhrangshu Mandal
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Abhijit Sar
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Nibendu Mondal
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Utsab Debnath
- Division of Molecular Medicine; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Boby Mathew
- Clinical Proteomics Unit, Division of Molecular Medicine; St. John's Research Institute St. John's National Academy of Health Sciences, 100ft Road; Koramangala 560034 Bangalore India
| | - Anup Kumar Misra
- Division of Molecular Medicine; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
| | - Amit Kumar Mandal
- Clinical Proteomics Unit, Division of Molecular Medicine; St. John's Research Institute St. John's National Academy of Health Sciences, 100ft Road; Koramangala 560034 Bangalore India
| | - Wriddhiman Ghosh
- Department of Microbiology; Bose Institute, P-1/12 CIT Scheme VIIM; Kolkata 700054 India
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30
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A novel soxO gene, encoding a glutathione disulfide reductase, is essential for tetrathionate oxidation in Advenella kashmirensis. Microbiol Res 2017; 205:1-7. [DOI: 10.1016/j.micres.2017.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/19/2017] [Accepted: 08/05/2017] [Indexed: 11/30/2022]
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31
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Functional Analysis of the Minimal Twin-Arginine Translocation System Components from Streptococcus thermophilus CGMCC 7.179 in Escherichia coli DE3. Curr Microbiol 2017; 74:678-684. [DOI: 10.1007/s00284-017-1234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/14/2017] [Indexed: 11/26/2022]
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32
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Meier DV, Pjevac P, Bach W, Hourdez S, Girguis PR, Vidoudez C, Amann R, Meyerdierks A. Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. ISME JOURNAL 2017; 11:1545-1558. [PMID: 28375213 DOI: 10.1038/ismej.2017.37] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/30/2017] [Accepted: 02/02/2017] [Indexed: 11/09/2022]
Abstract
At deep-sea hydrothermal vents, primary production is carried out by chemolithoautotrophic microorganisms, with the oxidation of reduced sulfur compounds being a major driver for microbial carbon fixation. Dense and highly diverse assemblies of sulfur-oxidizing bacteria (SOB) are observed, yet the principles of niche differentiation between the different SOB across geochemical gradients remain poorly understood. In this study niche differentiation of the key SOB was addressed by extensive sampling of active sulfidic vents at six different hydrothermal venting sites in the Manus Basin, off Papua New Guinea. We subjected 33 diffuse fluid and water column samples and 23 samples from surfaces of chimneys, rocks and fauna to a combined analysis of 16S rRNA gene sequences, metagenomes and real-time in situ measured geochemical parameters. We found Sulfurovum Epsilonproteobacteria mainly attached to surfaces exposed to diffuse venting, while the SUP05-clade dominated the bacterioplankton in highly diluted mixtures of vent fluids and seawater. We propose that the high diversity within Sulfurimonas- and Sulfurovum-related Epsilonproteobacteria observed in this study derives from the high variation of environmental parameters such as oxygen and sulfide concentrations across small spatial and temporal scales.
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Affiliation(s)
- Dimitri V Meier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Petra Pjevac
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Wolfgang Bach
- Department of Geosciences and MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Stephane Hourdez
- CNRS, Genetics of Adaptation to Extreme Environments Group, Roscoff, France.,Université Pierre et Marie Curie, Genetics of Adaptation to Extreme Environments Group, Roscoff, France
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Charles Vidoudez
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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33
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Grabarczyk DB, Berks BC. Intermediates in the Sox sulfur oxidation pathway are bound to a sulfane conjugate of the carrier protein SoxYZ. PLoS One 2017; 12:e0173395. [PMID: 28257465 PMCID: PMC5336275 DOI: 10.1371/journal.pone.0173395] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/20/2017] [Indexed: 01/04/2023] Open
Abstract
The Sox pathway found in many sulfur bacteria oxidizes thiosulfate to sulfate. Pathway intermediates are covalently bound to a cysteine residue in the carrier protein SoxYZ. We have used biochemical complementation by SoxYZ-conjugates to probe the identity of the intermediates in the Sox pathway. We find that unconjugated SoxYZ and SoxYZ-S-sulfonate are unlikely to be intermediates during normal turnover in disagreement with current models. By contrast, conjugates with multiple sulfane atoms are readily metabolised by the Sox pathway. The most parsimonious interpretation of these data is that the true carrier species in the Sox pathway is a SoxYZ-S-sulfane adduct.
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Affiliation(s)
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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34
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Lau NS, Sam KK, Amirul AAA. Genome features of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3. Stand Genomic Sci 2017; 12:12. [PMID: 28138356 PMCID: PMC5259889 DOI: 10.1186/s40793-017-0232-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/08/2017] [Indexed: 11/16/2022] Open
Abstract
Yangia sp. CCB-MM3 was one of several halophilic bacteria isolated from soil sediment in the estuarine Matang Mangrove, Malaysia. So far, no member from the genus Yangia, a member of the Rhodobacteraceae family, has been reported sequenced. In the current study, we present the first complete genome sequence of Yangia sp. strain CCB-MM3. The genome includes two chromosomes and five plasmids with a total length of 5,522,061 bp and an average GC content of 65%. Since a different strain of Yangia sp. (ND199) was reported to produce a polyhydroxyalkanoate copolymer, the ability for this production was tested in vitro and confirmed for strain CCB-MM3. Analysis of its genome sequence confirmed presence of a pathway for production of propionyl-CoA and gene cluster for PHA production in the sequenced strain. The genome sequence described will be a useful resource for understanding the physiology and metabolic potential of Yangia as well as for comparative genomic analysis with other Rhodobacteraceae.
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Affiliation(s)
- Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, 11900 Penang Malaysia
| | - Ka-Kei Sam
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, 11900 Penang Malaysia
| | - Abdullah Al-Ashraf Amirul
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, 11900 Penang Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, Minden, 11800 Penang Malaysia
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35
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Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). Stand Genomic Sci 2016; 11:38. [PMID: 27274784 PMCID: PMC4891895 DOI: 10.1186/s40793-016-0162-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 05/24/2016] [Indexed: 02/01/2023] Open
Abstract
Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1T is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1T is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
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36
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Houghton JL, Foustoukos DI, Flynn TM, Vetriani C, Bradley AS, Fike DA. Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry. Environ Microbiol 2016; 18:3057-72. [PMID: 26914243 DOI: 10.1111/1462-2920.13232] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 01/17/2016] [Indexed: 11/29/2022]
Abstract
Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here the reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise, is presented. At pH 8.0, thiosulfate was stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation were extracellular elemental sulfur and sulfate. We were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reports of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway (soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observed in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling.
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Affiliation(s)
- J L Houghton
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA.
| | - D I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, 20015, USA
| | - T M Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA.,Computation Institution, The University of Chicago, Chicago, IL, 60637, USA
| | - C Vetriani
- Department of Biochemistry and Microbiology and Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA
| | - D A Fike
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA
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37
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Neveu M, Poret-Peterson AT, Anbar AD, Elser JJ. Ordinary stoichiometry of extraordinary microorganisms. GEOBIOLOGY 2016; 14:33-53. [PMID: 26311124 DOI: 10.1111/gbi.12153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 07/18/2015] [Indexed: 06/04/2023]
Abstract
All life on Earth seems to be made of the same chemical elements in relatively conserved proportions (stoichiometry). Whether this stoichiometry is conserved in settings that differ radically in physicochemical conditions (extreme environments) from those commonly encountered elsewhere on the planet provides insight into possible stoichiometries for putative life beyond Earth. Here, we report measurements of elemental stoichiometry for extremophile microbes from hot springs of Yellowstone National Park (YNP). Phototrophic and chemotrophic microbes were collected in locations spanning large ranges of temperature (24 °C to boiling), pH (1.6-9.6), redox (0.1-7.2 mg L(-1) dissolved oxygen), and nutrient concentrations (0.01-0.25 mg L(-1) NO2-, 0.7-12.9 mg L(-1) NO3-, 0.01-42 mg L(-1) NH4 (+), 0.003-1.1 mg L(-1) P mostly as phosphate). Despite these extreme conditions, the microbial cells sampled had a major and trace element stoichiometry within the ranges commonly encountered for microbes living in the more moderate environments of lakes and surface oceans. The cells did have somewhat high C:P and N:P ratios that are consistent with phosphorus (P) limitation. Furthermore, chemotrophs and phototrophs had similar compositions with the exception of Mo content, which was enriched in cells derived from chemotrophic sites. Thus, despite the extraordinary physicochemical and biological diversity of YNP environments, life in these settings, in a stoichiometric sense, remains much the same as we know it elsewhere.
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Affiliation(s)
- M Neveu
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - A T Poret-Peterson
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - A D Anbar
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, USA
| | - J J Elser
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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38
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Structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle. Proc Natl Acad Sci U S A 2015; 112:E7166-75. [PMID: 26655737 DOI: 10.1073/pnas.1506386112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The bacterial Sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. Intermediates in the Sox pathway are covalently attached to the heterodimeric carrier protein SoxYZ through conjugation to a cysteine on a protein swinging arm. We have investigated how the carrier protein shuttles intermediates between the enzymes of the Sox pathway using the interaction between SoxYZ and the enzyme SoxB as our model. The carrier protein and enzyme interact only weakly, but we have trapped their complex by using a "suicide enzyme" strategy in which an engineered cysteine in the SoxB active site forms a disulfide bond with the incoming carrier arm cysteine. The structure of this trapped complex, together with calorimetric data, identifies sites of protein-protein interaction both at the entrance to the enzyme active site tunnel and at a second, distal, site. We find that the enzyme distinguishes between the substrate and product forms of the carrier protein through differences in their interaction kinetics and deduce that this behavior arises from substrate-specific stabilization of a conformational change in the enzyme active site. Our analysis also suggests how the carrier arm-bound substrate group is able to outcompete the adjacent C-terminal carboxylate of the carrier arm for binding to the active site metal ions. We infer that similar principles underlie carrier protein interactions with other enzymes of the Sox pathway.
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Meyer DD, Andrino FG, Possedente de Lira S, Fornaro A, Corção G, Brandelli A. Sulphate production by Paracoccus pantotrophus ATCC 35512 from different sulphur substrates: sodium thiosulphate, sulphite and sulphide. ENVIRONMENTAL TECHNOLOGY 2015; 37:768-773. [PMID: 26269005 DOI: 10.1080/09593330.2015.1081411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
One of the problems in waste water treatment plants (WWTPs) is the increase in emissions of hydrogen sulphide (H2S), which can cause damage to the health of human populations and ecosystems. To control emissions of this gas, sulphur-oxidizing bacteria can be used to convert H2S to sulphate. In this work, sulphate detection was performed by spectrophotometry, ion chromatography and atomic absorption spectrometry, using Paracoccus pantotrophus ATCC 35512 as a reference strain growing in an inorganic broth supplemented with sodium thiosulphate (Na2S2O3·5H2O), sodium sulphide (Na2S) or sodium sulphite (Na2SO3), separately. The strain was metabolically competent in sulphate production. However, it was only possible to observe significant differences in sulphate production compared to abiotic control when the inorganic medium was supplemented with sodium thiosulphate. The three methods for sulphate detection showed similar patterns, although the chromatographic method was the most sensitive for this study. This strain can be used as a reference for sulphate production in studies with sulphur-oxidizing bacteria originating from environmental samples of WWTPs.
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Affiliation(s)
- Daniel Derrossi Meyer
- a Departamento de Microbiologia , Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul , Rua Sarmento Leite 500, 90050-170 Porto Alegre , Brazil
| | - Felipe Gabriel Andrino
- b Escola Superior de Agricultura Luiz de Queiroz (ESALQ) , Universidade de São Paulo , Av. Pádua Dias 11, 13418-900 Piracicaba , Brazil
| | - Simone Possedente de Lira
- b Escola Superior de Agricultura Luiz de Queiroz (ESALQ) , Universidade de São Paulo , Av. Pádua Dias 11, 13418-900 Piracicaba , Brazil
| | - Adalgiza Fornaro
- c Departamento de Ciências Atmosféricas , Instituto de Astronomia, Geofísica e Ciências Atmosféricas, Universidade de São Paulo , Rua do Matão 1226, 05508-090 São Paulo , Brazil
| | - Gertrudes Corção
- a Departamento de Microbiologia , Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul , Rua Sarmento Leite 500, 90050-170 Porto Alegre , Brazil
| | - Adriano Brandelli
- d Departamento de Ciência de Alimentos , Universidade Federal do Rio Grande do Sul , Av. Bento Gonçalves 9500, 91501-970 Porto Alegre , Brazil
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Dahl C. Cytoplasmic sulfur trafficking in sulfur-oxidizing prokaryotes. IUBMB Life 2015; 67:268-74. [DOI: 10.1002/iub.1371] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/27/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn; Bonn Germany
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Dahl C, Franz B, Hensen D, Kesselheim A, Zigann R. Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process. MICROBIOLOGY-SGM 2013; 159:2626-2638. [PMID: 24030319 DOI: 10.1099/mic.0.071019-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In phototrophic sulfur bacteria, sulfite is a well-established intermediate during reduced sulfur compound oxidation. Sulfite is generated in the cytoplasm by the reverse-acting dissimilatory sulfite reductase DsrAB. Many purple sulfur bacteria can even use externally available sulfite as a photosynthetic electron donor. Nevertheless, the exact mode of sulfite oxidation in these organisms is a long-standing enigma. Indirect oxidation in the cytoplasm via adenosine-5'-phosphosulfate (APS) catalysed by APS reductase and ATP sulfurylase is neither generally present nor essential. The inhibition of sulfite oxidation by tungstate in the model organism Allochromatium vinosum indicated the involvement of a molybdoenzyme, but homologues of the periplasmic molybdopterin-containing SorAB or SorT sulfite dehydrogenases are not encoded in genome-sequenced purple or green sulfur bacteria. However, genes for a membrane-bound polysulfide reductase-like iron-sulfur molybdoprotein (SoeABC) are universally present. The catalytic subunit of the protein is predicted to be oriented towards the cytoplasm. We compared the sulfide- and sulfite-oxidizing capabilities of A. vinosum WT with single mutants deficient in SoeABC or APS reductase and the respective double mutant, and were thus able to prove that SoeABC is the major sulfite-oxidizing enzyme in A. vinosum and probably also in other phototrophic sulfur bacteria. The genes also occur in a large number of chemotrophs, indicating a general importance of SoeABC for sulfite oxidation in the cytoplasm. Furthermore, we showed that the periplasmic sulfur substrate-binding protein SoxYZ is needed in parallel to the cytoplasmic enzymes for effective sulfite oxidation in A. vinosum and provided a model for the interplay between these systems despite their localization in different cellular compartments.
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Affiliation(s)
- Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Bettina Franz
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Daniela Hensen
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Anne Kesselheim
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Renate Zigann
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
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Ji B, Zhang SD, Arnoux P, Rouy Z, Alberto F, Philippe N, Murat D, Zhang WJ, Rioux JB, Ginet N, Sabaty M, Mangenot S, Pradel N, Tian J, Yang J, Zhang L, Zhang W, Pan H, Henrissat B, Coutinho PM, Li Y, Xiao T, Médigue C, Barbe V, Pignol D, Talla E, Wu LF. Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain. Environ Microbiol 2013; 16:525-44. [PMID: 23841906 DOI: 10.1111/1462-2920.12180] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/17/2013] [Accepted: 06/02/2013] [Indexed: 11/30/2022]
Abstract
Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts.
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Affiliation(s)
- Boyang Ji
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7283, F-13402, Marseille Cedex 20, France
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Kinetic enrichment of 34S during proteobacterial thiosulfate oxidation and the conserved role of SoxB in S-S bond breaking. Appl Environ Microbiol 2013; 79:4455-64. [PMID: 23686269 DOI: 10.1128/aem.00956-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During chemolithoautotrophic thiosulfate oxidation, the phylogenetically diverged proteobacteria Paracoccus pantotrophus, Tetrathiobacter kashmirensis, and Thiomicrospira crunogena rendered steady enrichment of (34)S in the end product sulfate, with overall fractionation ranging between -4.6‰ and +5.8‰. The fractionation kinetics of T. crunogena was essentially similar to that of P. pantotrophus, albeit the former had a slightly higher magnitude and rate of (34)S enrichment. In the case of T. kashmirensis, the only significant departure of its fractionation curve from that of P. pantotrophus was observed during the first 36 h of thiosulfate-dependent growth, in the course of which tetrathionate intermediate formation is completed and sulfate production starts. The almost-identical (34)S enrichment rates observed during the peak sulfate-producing stage of all three processes indicated the potential involvement of identical S-S bond-breaking enzymes. Concurrent proteomic analyses detected the hydrolase SoxB (which is known to cleave terminal sulfone groups from SoxYZ-bound cysteine S-thiosulfonates, as well as cysteine S-sulfonates, in P. pantotrophus) in the actively sulfate-producing cells of all three species. The inducible expression of soxB during tetrathionate oxidation, as well as the second leg of thiosulfate oxidation, by T. kashmirensis is significant because the current Sox pathway does not accommodate tetrathionate as one of its substrates. Notably, however, no other Sox protein except SoxB could be detected upon matrix-assisted laser desorption ionization mass spectrometry analysis of all such T. kashmirensis proteins as appeared to be thiosulfate inducible in 2-dimensional gel electrophoresis. Instead, several other redox proteins were found to be at least 2-fold overexpressed during thiosulfate- or tetrathionate-dependent growth, thereby indicating that there is more to tetrathionate oxidation than SoxB alone.
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Mislocalization of Rieske protein PetA predominantly accounts for the aerobic growth defect of Tat mutants in Shewanella oneidensis. PLoS One 2013; 8:e62064. [PMID: 23593508 PMCID: PMC3623810 DOI: 10.1371/journal.pone.0062064] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 03/17/2013] [Indexed: 02/04/2023] Open
Abstract
Shewanella oneidensis exhibits a remarkable versatility in respiration, which largely relies on its various respiratory pathways. Most of these pathways are composed of secretory terminal reductases and multiple associated electron transport proteins that contain cofactors such as Fe-S, molybdopterin, and NiFe. The majority of these cofactors are inserted enzymatically in the cytoplasm, and thus are substrates of the twin-arginine translocation (Tat) protein export system, which transports fully folded proteins. Using genomic array footprinting, we discovered that loss of TatA or TatC caused a reduction in the growth rate of S. oneidensis under aerobic conditions. Mutational analysis of the predicted Tat substrates revealed that PetA, the Rieske Fe-S subunit of the ubiquinol-cytochrome c reductase, predominantly dictates the aerobic growth defect of tat mutants in S. oneidensis. In addition, evidence is presented that the signal sequence in PetA appears to be resistant to cleavage after the protein is inserted into the cytoplasmic membrane.
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45
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Handley KM, VerBerkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, Frischkorn KR, Chourey K, Thomas BC, Shah MB, Long PE, Hettich RL, Banfield JF. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. THE ISME JOURNAL 2013; 7:800-16. [PMID: 23190730 PMCID: PMC3603403 DOI: 10.1038/ismej.2012.148] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/28/2012] [Accepted: 10/08/2012] [Indexed: 11/09/2022]
Abstract
Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used proteogenomics to test the hypothesis that excess input of acetate activates complex community functioning and syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer and recovered during microbial sulfate reduction. De novo reconstruction of community sequences yielded near-complete genomes of Desulfobacter (Deltaproteobacteria), Sulfurovum- and Sulfurimonas-like Epsilonproteobacteria and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen fixation and acetate oxidation to CO2 during amendment. Results indicate less abundant Desulfuromonadales, and possibly Bacteroidetes, also actively contributed to CO2 production via the tricarboxylic acid (TCA) cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. We infer that high acetate concentrations, aimed at stimulating anaerobic heterotrophy, led to the co-enrichment of, and carbon fixation in Epsilonproteobacteria. Results give an insight into ecosystem behavior following addition of simple organic carbon to the subsurface, and demonstrate a range of biological processes and community interactions were stimulated.
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Affiliation(s)
- Kim M Handley
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Nathan C VerBerkmoes
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Carl I Steefel
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
| | - Kenneth H Williams
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
| | - Itai Sharon
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Christopher S Miller
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Kyle R Frischkorn
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Karuna Chourey
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Brian C Thomas
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
| | - Manesh B Shah
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Philip E Long
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
| | - Robert L Hettich
- Chemical Sciences and Biosciences Divisions,
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN,
USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science,
University of California, Berkeley, CA,
USA
- Earth Science Division, Lawrence Berkeley
National Laboratory (LBNL), Berkeley, CA,
USA
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Kappler U, Maher MJ. The bacterial SoxAX cytochromes. Cell Mol Life Sci 2013; 70:977-92. [PMID: 22907414 PMCID: PMC11113948 DOI: 10.1007/s00018-012-1098-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 07/09/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
SoxAX cytochromes are heme-thiolate proteins that play a key role in bacterial thiosulfate oxidation, where they initiate the reaction cycle of a multi-enzyme complex by catalyzing the attachment of sulfur substrates such as thiosulfate to a conserved cysteine present in a carrier protein. SoxAX proteins have a wide phylogenetic distribution and form a family with at least three distinct types of SoxAX protein. The types of SoxAX cytochromes differ in terms of the number of heme groups present in the proteins (there are diheme and triheme versions) as well as in their subunit structure. While two of the SoxAX protein types are heterodimers, the third group contains an additional subunit, SoxK, that stabilizes the complex of the SoxA and SoxX proteins. Crystal structures are available for representatives of the two heterodimeric SoxAX protein types and both of these have shown that the cysteine ligand to the SoxA active site heme carries a modification to a cysteine persulfide that implicates this ligand in catalysis. EPR studies of SoxAX proteins have also revealed a high complexity of heme dependent signals associated with this active site heme; however, the exact mechanism of catalysis is still unclear at present, as is the exact number and types of redox centres involved in the reaction.
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Affiliation(s)
- Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Evidence for niche partitioning revealed by the distribution of sulfur oxidation genes collected from areas of a terrestrial sulfidic spring with differing geochemical conditions. Appl Environ Microbiol 2012; 79:1171-82. [PMID: 23220955 DOI: 10.1128/aem.02812-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. We analyzed the geographic distribution of 16S rRNA pyrosequences and soxB genes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of the soxB gene were naturally distributed within the spring outflow channel and to identify possible evidence for altered SoxB enzyme function in nature. Distinct compositional differences between bacteria that utilize their SoxB enzyme in the Paracoccus sulfide oxidation pathway (e.g., Bradyrhizobium, Paracoccus, and Rhodovulum) and bacteria that utilize their SoxB enzyme in the branched pathway (e.g., Chlorobium, Thiothrix, Thiobacillus, Halothiobacillus, and Thiomonas) were identified. Different variations of the soxB genes were present at different locations within the spring outflow channel in a manner that significantly corresponded to geochemical conditions. The distribution of the different soxB gene sequence variations suggests that the enzymes encoded by these genes are functionally different and could be optimized to specific geochemical conditions that define niche space for bacteria capable of oxidizing reduced sulfur compounds.
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Dai Y, Outten FW. The E. coli SufS-SufE sulfur transfer system is more resistant to oxidative stress than IscS-IscU. FEBS Lett 2012; 586:4016-22. [PMID: 23068614 DOI: 10.1016/j.febslet.2012.10.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 09/25/2012] [Accepted: 10/01/2012] [Indexed: 01/15/2023]
Abstract
During oxidative stress in Escherichiacoli, the SufABCDSE stress response pathway mediates iron-sulfur (Fe-S) cluster biogenesis rather than the Isc pathway. To determine why the Suf pathway is favored under stress conditions, the stress response SufS-SufE sulfur transfer pathway and the basal housekeeping IscS-IscU pathway were directly compared. We found that SufS-SufE cysteine desulfurase activity is significantly higher than IscS-IscU at physiological cysteine concentrations and after exposure to H(2)O(2). Mass spectrometry analysis demonstrated that IscS-IscU is more susceptible than SufS-SufE to oxidative modification by H(2)O(2). These important results provide biochemical insight into the stress resistance of the Suf pathway.
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Affiliation(s)
- Yuyuan Dai
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
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49
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Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle. Mol Biol Rep 2012; 39:10243-8. [PMID: 23053932 DOI: 10.1007/s11033-012-1900-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 09/30/2012] [Indexed: 10/27/2022]
Abstract
Microbial redox reactions of inorganic sulfur compounds are one of the important reactions for the recycling of sulfur to maintain the environmental sulfur balance. These reactions are carried out by phylogenetically diverse microorganisms. The sulfur oxidizing gene cluster (sox) of α-proteobacteria, Allochromatium vinosum comprises two divergently transcribed units. The central players of this process are SoxY, SoxZ and SoxL. SoxY is sulfur compound binder which binds to sulfur anions with the help of SoxZ. SoxL is a rhodanese like protein, which then cleaves off the sulfur substrate from the SoxYZ complex to recycle the SoxY and SoxZ. In the present work, homology modeling has been employed to build the three dimensional structures of SoxY, SoxZ and SoxL. With the help of docking simulations the amino acid residues of these proteins involved in the interactions have been identified. The interactions between the SoxY, SoxZ and SoxL proteins are mediated mainly through hydrogen bonding. Strong positive fields created by the SoxZ and SoxL proteins are found to be responsible for the binding and removal of the sulfur anion. The probable biochemical mechanism of sulfur anion oxidation process has been identified.
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50
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Bradley JM, Marritt SJ, Kihlken MA, Haynes K, Hemmings AM, Berks BC, Cheesman MR, Butt JN. Redox and chemical activities of the hemes in the sulfur oxidation pathway enzyme SoxAX. J Biol Chem 2012; 287:40350-9. [PMID: 23060437 DOI: 10.1074/jbc.m112.396192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND SoxAX enzymes initiate microbial oxidation of reduced inorganic sulfur compounds. Their catalytic mechanism is unknown. RESULTS Cyanide displaces the CysS(-) ligand to the active site heme following reduction by S(2)O(4)(2-) but not Eu(II). CONCLUSION An active site heme ligand becomes labile on exposure to substrate analogs. SIGNIFICANCE Elucidation of SoxAX mechanism is necessary to understand a widespread pathway for sulfur compound oxidation. SoxAX enzymes couple disulfide bond formation to the reduction of cytochrome c in the first step of the phylogenetically widespread Sox microbial sulfur oxidation pathway. Rhodovulum sulfidophilum SoxAX contains three hemes. An electrochemical cell compatible with magnetic circular dichroism at near infrared wavelengths has been developed to resolve redox and chemical properties of the SoxAX hemes. In combination with potentiometric titrations monitored by electronic absorbance and EPR, this method defines midpoint potentials (E(m)) at pH 7.0 of approximately +210, -340, and -400 mV for the His/Met, His/Cys(-), and active site His/CysS(-)-ligated heme, respectively. Exposing SoxAX to S(2)O(4)(2-), a substrate analog with E(m) ~-450 mV, but not Eu(II) complexed with diethylene triamine pentaacetic acid (E(m) ~-1140 mV), allows cyanide to displace the cysteine persulfide (CysS(-)) ligand to the active site heme. This provides the first evidence for the dissociation of CysS(-) that has been proposed as a key event in SoxAX catalysis.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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