1
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Boden JS, Zhong J, Anderson RE, Stüeken EE. Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics. Nat Commun 2024; 15:3703. [PMID: 38697988 PMCID: PMC11066067 DOI: 10.1038/s41467-024-47914-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life's origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS; <1 µM) appeared around the same time or in the Mesoarchean depending on the reconstruction method. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising pathways and hypophosphite-oxidising pathways. CP-lyases are particularly abundant in dissolved phosphate concentrations below 0.1 µM. Our results thus indicate at least local regions of declining phosphate levels through the Archean, possibly linked to phosphate-scavenging Fe(III), which may have limited productivity. However, reduced phosphorus species did not become widely used until after the Paleoproterozoic Great Oxidation Event (2.3 Ga), possibly linked to expansion of the biosphere at that time.
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Affiliation(s)
- Joanne S Boden
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom.
| | - Juntao Zhong
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Rika E Anderson
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Eva E Stüeken
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom
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2
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Mao Z, Fleming JR, Mayans O, Frey J, Schleheck D, Schink B, Müller N. AMP-dependent phosphite dehydrogenase, a phosphorylating enzyme in dissimilatory phosphite oxidation. Proc Natl Acad Sci U S A 2023; 120:e2309743120. [PMID: 37922328 PMCID: PMC10636320 DOI: 10.1073/pnas.2309743120] [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: 06/14/2023] [Accepted: 09/20/2023] [Indexed: 11/05/2023] Open
Abstract
Oxidation of phosphite (HPO32-) to phosphate (HPO42-) releases electrons at a very low redox potential (E0'= -690 mV) which renders phosphite an excellent electron donor for microbial energy metabolism. To date, two pure cultures of strictly anaerobic bacteria have been isolated that run their energy metabolism on the basis of phosphite oxidation, the Gram-negative Desulfotignum phosphitoxidans (DSM 13687) and the Gram-positive Phosphitispora fastidiosa (DSM 112739). Here, we describe the key enzyme for dissimilatory phosphite oxidation in these bacteria. The enzyme catalyzed phosphite oxidation in the presence of adenosine monophosphate (AMP) to form adenosine diphosphate (ADP), with concomitant reduction of oxidized nicotinamide adenine dinucleotide (NAD+) to reduced nicotinamide adenine dinucleotide (NADH). The enzyme of P. fastidiosa was heterologously expressed in Escherichia coli. It has a molecular mass of 35.2 kDa and a high affinity for phosphite and NAD+. Its activity was enhanced more than 100-fold by addition of ADP-consuming adenylate kinase (myokinase) to a maximal activity between 30 and 80 mU x mg protein-1. A similar NAD-dependent enzyme oxidizing phosphite to phosphate with concomitant phosphorylation of AMP to ADP is found in D. phosphitoxidans, but this enzyme could not be heterologously expressed. Based on sequence analysis, these phosphite-oxidizing enzymes are related to nucleotide-diphosphate-sugar epimerases and indeed represent AMP-dependent phosphite dehydrogenases (ApdA). A reaction mechanism is proposed for this unusual type of substrate-level phosphorylation reaction.
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Affiliation(s)
- Zhuqing Mao
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Jennifer R. Fleming
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Jasmin Frey
- Department of Biology, University of Konstanz, Constance78457, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Constance78457, Germany
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Constance78457, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance78457, Germany
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3
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Reyes-Umana V, Ewens SD, Meier DAO, Coates JD. Integration of molecular and computational approaches paints a holistic portrait of obscure metabolisms. mBio 2023; 14:e0043123. [PMID: 37855625 PMCID: PMC10746228 DOI: 10.1128/mbio.00431-23] [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] [Indexed: 10/20/2023] Open
Abstract
Microorganisms are essential drivers of earth's geochemical cycles. However, the significance of elemental redox cycling mediated by microorganisms is often underestimated beyond the most well-studied nutrient cycles. Phosphite, (per)chlorate, and iodate are each considered esoteric substrates metabolized by microorganisms. However, recent investigations have indicated that these metabolisms are widespread and ubiquitous, affirming a need to continue studying the underlying microbiology to understand their biogeochemical effects and their interface with each other and our biosphere. This review focuses on combining canonical techniques of culturing microorganisms with modern omic approaches to further our understanding of obscure metabolic pathways and elucidate their importance in global biogeochemical cycles. Using these approaches, marker genes of interest have already been identified for phosphite, (per)chlorate, and iodate using traditional microbial physiology and genetics. Subsequently, their presence was queried to reveal the distribution of metabolic pathways in the environment using publicly available databases. In conjunction with each other, computational and experimental techniques provide a more comprehensive understanding of the location of these microorganisms, their underlying biochemistry and genetics, and how they tie into our planet's geochemical cycles.
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Affiliation(s)
- Victor Reyes-Umana
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Sophia D. Ewens
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - David A. O. Meier
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - John D. Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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4
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Nicholls JWF, Chin JP, Williams TA, Lenton TM, O’Flaherty V, McGrath JW. On the potential roles of phosphorus in the early evolution of energy metabolism. Front Microbiol 2023; 14:1239189. [PMID: 37601379 PMCID: PMC10433651 DOI: 10.3389/fmicb.2023.1239189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.
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Affiliation(s)
- Jack W. F. Nicholls
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Jason P. Chin
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - John W. McGrath
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
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5
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Liu W, Zhang Y, Yu M, Xu J, Du H, Zhang R, Wu D, Xie X. Role of phosphite in the environmental phosphorus cycle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163463. [PMID: 37062315 DOI: 10.1016/j.scitotenv.2023.163463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/29/2023] [Accepted: 04/08/2023] [Indexed: 06/01/2023]
Abstract
In modern geochemistry, phosphorus (P) is considered synonymous with phosphate (Pi) because Pi controls the growth of organisms as a limiting nutrient in many ecosystems. The researchers therefore realised that a complete P cycle is essential. Limited by thermodynamic barriers, P was long believed to be incapable of redox reactions, and the role of the redox cycle of reduced P in the global P cycling system was thus not ascertained. Nevertheless, the phosphite (Phi) form of P is widely present in various environments and participates in the global P redox cycle. Herein, global quantitative evidences of Phi are enumerated and the early origin and modern biotic/abiotic sources of Phi are elaborated. Further, the Phi-based redox pathway for P reduction is analysed and global multienvironmental Phi redox cycle processes are proposed on the basis of this pathway. The possible role of Phi in controlling algae in eutrophic lakes and its ecological benefits to plants are proposed. In this manner, the important role of Phi in the P redox cycle and global P cycle is systematically and comprehensively identified and confirmed. This work will provide scientific guidance for the future production and use of Phi products and arouse attention and interest on clarifying the role of Phi in the environmental phosphorus cycle.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Yalan Zhang
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Mengqin Yu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Jinying Xu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Hu Du
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Ru Zhang
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China
| | - Daishe Wu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China; School of Materials and Chemical Engineering, Pingxiang University, Pingxiang 337000, China
| | - Xianchuan Xie
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resource and Environment, Nanchang University, Nanchang 330031, China.
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6
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Partipilo M, Claassens NJ, Slotboom DJ. A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells. ACS Synth Biol 2023; 12:947-962. [PMID: 37052416 PMCID: PMC10127272 DOI: 10.1021/acssynbio.3c00070] [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: 01/31/2023] [Indexed: 04/14/2023]
Abstract
The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.
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Affiliation(s)
- Michele Partipilo
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nico J. Claassens
- Laboratory
of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Jan Slotboom
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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7
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Abstract
Phosphite (Phi)-containing products are marketed for their antifungal and nutritional value. Substantial evidence of the anti-fungal properties of Phi on a wide variety of plants has been documented. Although Phi is readily absorbed by plant leaves and/or roots, the plant response to Phi used as a phosphorus (P) source is variable. Negative effects of Phi on plant growth are commonly observed under P deficiency compared to near adequate plant P levels. Positive responses to Phi may be attributed to some level of fungal disease control. While only a few studies have provided evidence of Phi oxidation through cellular enzymes genetically controlled in plant cells, increasing evidence exists for the potential to manipulate plant genes to enhance oxidation of Phi to phosphate (Pi) in plants. Advances in genetic engineering to sustain growth and yield with Phi + Pi potentially provides a dual fertilization and weed control system. Further advances in genetic manipulation of plants to utilize Phi are warranted. Since Phi oxidation occurs slowly in soils, additional information is needed to characterize Phi oxidation kinetics under variable soil and environmental conditions.
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8
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Ewens SD, Gomberg AFS, Barnum TP, Borton MA, Carlson HK, Wrighton KC, Coates JD. The diversity and evolution of microbial dissimilatory phosphite oxidation. Proc Natl Acad Sci U S A 2021; 118:e2020024118. [PMID: 33688048 PMCID: PMC7980464 DOI: 10.1073/pnas.2020024118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (Eo') of -650 mV for the PO43-/PO33- couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.
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Affiliation(s)
- Sophia D Ewens
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Energy & Biosciences Institute, University of California, Berkeley, CA 94720
| | - Alexa F S Gomberg
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Energy & Biosciences Institute, University of California, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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9
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Figueroa IA, Barnum TP, Somasekhar PY, Carlström CI, Engelbrektson AL, Coates JD. Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO 2 fixation pathway. Proc Natl Acad Sci U S A 2018; 115:E92-E101. [PMID: 29183985 PMCID: PMC5776814 DOI: 10.1073/pnas.1715549114] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dissimilatory phosphite oxidation (DPO), a microbial metabolism by which phosphite (HPO32-) is oxidized to phosphate (PO43-), is the most energetically favorable chemotrophic electron-donating process known. Only one DPO organism has been described to date, and little is known about the environmental relevance of this metabolism. In this study, we used 16S rRNA gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatment sludge enrichments performing DPO coupled to CO2 reduction. We identified an uncultivated DPO bacterium, Candidatus Phosphitivorax (Ca. P.) anaerolimi strain Phox-21, that belongs to candidate order GW-28 within the Deltaproteobacteria, which has no known cultured isolates. Genes for phosphite oxidation and for CO2 reduction to formate were found in the genome of Ca. P. anaerolimi, but it appears to lack any of the known natural carbon fixation pathways. These observations led us to propose a metabolic model for autotrophic growth by Ca. P. anaerolimi whereby DPO drives CO2 reduction to formate, which is then assimilated into biomass via the reductive glycine pathway.
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Affiliation(s)
- Israel A Figueroa
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Pranav Y Somasekhar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Charlotte I Carlström
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Anna L Engelbrektson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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10
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The molecular basis of phosphite and hypophosphite recognition by ABC-transporters. Nat Commun 2017; 8:1746. [PMID: 29170493 PMCID: PMC5700983 DOI: 10.1038/s41467-017-01226-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 08/30/2017] [Indexed: 11/10/2022] Open
Abstract
Inorganic phosphate is the major bioavailable form of the essential nutrient phosphorus. However, the concentration of phosphate in most natural habitats is low enough to limit microbial growth. Under phosphate-depleted conditions some bacteria utilise phosphite and hypophosphite as alternative sources of phosphorus, but the molecular basis of reduced phosphorus acquisition from the environment is not fully understood. Here, we present crystal structures and ligand binding affinities of periplasmic binding proteins from bacterial phosphite and hypophosphite ATP-binding cassette transporters. We reveal that phosphite and hypophosphite specificity results from a combination of steric selection and the presence of a P-H…π interaction between the ligand and a conserved aromatic residue in the ligand-binding pocket. The characterisation of high affinity and specific transporters has implications for the marine phosphorus redox cycle, and might aid the use of phosphite as an alternative phosphorus source in biotechnological, industrial and agricultural applications. Some bacteria can use inorganic phosphite and hypophosphite as sources of inorganic phosphorus. Here, the authors report crystal structures of the periplasmic proteins that bind these reduced phosphorus species and show that a P-H…π interaction between the ligand and binding site determines their specificity.
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11
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Taniguchi H, Okano K, Honda K. Modules for in vitro metabolic engineering: Pathway assembly for bio-based production of value-added chemicals. Synth Syst Biotechnol 2017; 2:65-74. [PMID: 29062963 PMCID: PMC5636945 DOI: 10.1016/j.synbio.2017.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/02/2017] [Indexed: 11/17/2022] Open
Abstract
Bio-based chemical production has drawn attention regarding the realization of a sustainable society. In vitro metabolic engineering is one of the methods used for the bio-based production of value-added chemicals. This method involves the reconstitution of natural or artificial metabolic pathways by assembling purified/semi-purified enzymes in vitro. Enzymes from distinct sources can be combined to construct desired reaction cascades with fewer biological constraints in one vessel, enabling easier pathway design with high modularity. Multiple modules have been designed, built, tested, and improved by different groups for different purpose. In this review, we focus on these in vitro metabolic engineering modules, especially focusing on the carbon metabolism, and present an overview of input modules, output modules, and other modules related to cofactor management.
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12
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Figueroa IA, Coates JD. Microbial Phosphite Oxidation and Its Potential Role in the Global Phosphorus and Carbon Cycles. ADVANCES IN APPLIED MICROBIOLOGY 2016; 98:93-117. [PMID: 28189156 DOI: 10.1016/bs.aambs.2016.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Phosphite [Formula: see text] is a highly soluble, reduced phosphorus compound that is often overlooked in biogeochemical analyses. Although the oxidation of phosphite to phosphate is a highly exergonic process (Eo'=-650mV), phosphite is kinetically stable and can account for 10-30% of the total dissolved P in various environments. There is also evidence that phosphite was more prevalent under the reducing conditions of the Archean period and may have been involved in the development of early life. Its role as a phosphorus source for a variety of extant microorganisms has been known since the 1950s, and the pathways involved in assimilatory phosphite oxidation have been well characterized. More recently, it was demonstrated that phosphite could also act as an electron donor for energy metabolism in a process known as dissimilatory phosphite oxidation (DPO). The bacterium described in this study, Desulfotignum phosphitoxidans strain FiPS-3, was isolated from brackish sediments and is capable of growing by coupling phosphite oxidation to the reduction of either sulfate or carbon dioxide. FiPS-3 remains the only isolated organism capable of DPO, and the prevalence of this metabolism in the environment is still unclear. Nonetheless, given the widespread presence of phosphite in the environment and the thermodynamic favorability of its oxidation, microbial phosphite oxidation may play an important and hitherto unrecognized role in the global phosphorus and carbon cycles.
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Affiliation(s)
- I A Figueroa
- University of California, Berkeley, CA, United States
| | - J D Coates
- University of California, Berkeley, CA, United States
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13
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Poehlein A, Freese H, Daniel R, Simeonova DD. Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna. Stand Genomic Sci 2016; 11:14. [PMID: 26865909 PMCID: PMC4748535 DOI: 10.1186/s40793-015-0129-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 12/30/2015] [Indexed: 11/10/2022] Open
Abstract
Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton Daphnia magna. Here we report the draft genome of this bacterium, which comprises 7,677,812 bp and 7505 predicted protein-coding genes.
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Affiliation(s)
- Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Heike Freese
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124 Braunschweig, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Diliana D Simeonova
- Laboratory of Microbial Ecology, University of Konstanz, D-78457 Constance, Germany ; Current Address: Laboratory of Microbial Biochemistry, Department of General Microbiology, Institute of Microbiology, Bulgarian Academy of Sciences, 26 Georgi Bonchev str., 1113 Sofia, Bulgaria
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14
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Poehlein A, Daniel R, Simeonova DD. Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna. Stand Genomic Sci 2015; 10:100. [PMID: 26566425 PMCID: PMC4642753 DOI: 10.1186/s40793-015-0086-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
The phosphite assimilating bacterium, P. glucosidilyticus DD6b, was isolated from the gut of the zooplankton Daphnia magna. Its 3,872,381 bp high-quality draft genome is arranged into 93 contigs containing 3311 predicted protein-coding and 41 RNA-encoding genes. This genome report presents the specific properties and common features of P. glucosidilyticus DD6b genome in comparison with the genomes of P. glucosidilyticus type strain DSM 23,534, and another five Pedobacter type strains with publicly available completely sequenced genomes. Here, we present the first journal report on P. glucosidilyticus genome sequence and provide information on a new specific physiological determinant of P. glucosidilyticus species.
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Affiliation(s)
- Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Diliana D Simeonova
- Laboratory of Microbial Ecology, Department of Biology, University of Konstanz, Universitaetsstr. 10, D-78457 Konstanz, Germany ; Current address: Laboratory of Microbial Biochemistry, Department of General Microbiology, Institute of Microbiology, Bulgarian Academy of Sciences, 26 Georgi Bonchev str., 1113 Sofia, Bulgaria
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15
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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16
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Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK, van Loosdrecht MCM, Chen GH. A review of biological sulfate conversions in wastewater treatment. WATER RESEARCH 2014; 65:1-21. [PMID: 25086411 DOI: 10.1016/j.watres.2014.06.043] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/26/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Treatment of waters contaminated with sulfur containing compounds (S) resulting from seawater intrusion, the use of seawater (e.g. seawater flushing, cooling) and industrial processes has become a challenging issue since around two thirds of the world's population live within 150 km of the coast. In the past, research has produced a number of bioengineered systems for remediation of industrial sulfate containing sewage and sulfur contaminated groundwater utilizing sulfate reducing bacteria (SRB). The majority of these studies are specific with SRB only or focusing on the microbiology rather than the engineered application. In this review, existing sulfate based biotechnologies and new approaches for sulfate contaminated waters treatment are discussed. The sulfur cycle connects with carbon, nitrogen and phosphorus cycles, thus a new platform of sulfur based biotechnologies incorporating sulfur cycle with other cycles can be developed, for the removal of sulfate and other pollutants (e.g. carbon, nitrogen, phosphorus and metal) from wastewaters. All possible electron donors for sulfate reduction are summarized for further understanding of the S related biotechnologies including rates and benefits/drawbacks of each electron donor. A review of known SRB and their environmental preferences with regard to bioreactor operational parameters (e.g. pH, temperature, salinity etc.) shed light on the optimization of sulfur conversion-based biotechnologies. This review not only summarizes information from the current sulfur conversion-based biotechnologies for further optimization and understanding, but also offers new directions for sulfur related biotechnology development.
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Affiliation(s)
- Tian-wei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peng-yu Xiang
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hamish R Mackey
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Kun Chi
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hui Lu
- SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China
| | - Ho-kwong Chui
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China.
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17
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Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00903-14. [PMID: 25212623 PMCID: PMC4161752 DOI: 10.1128/genomea.00903-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb.
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18
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Poehlein A, Daniel R, Schink B, Simeonova DD. Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans. BMC Genomics 2013; 14:753. [PMID: 24180241 PMCID: PMC4046663 DOI: 10.1186/1471-2164-14-753] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 10/30/2013] [Indexed: 12/02/2022] Open
Abstract
Background The Delta-Proteobacterium Desulfotignum phosphitoxidans is a type strain of the genus Desulfotignum, which comprises to date only three species together with D. balticum and D. toluenicum. D. phosphitoxidans oxidizes phosphite to phosphate as its only source of electrons, with either sulfate or CO2 as electron acceptor to gain its metabolic energy, which is of exclusive interest. Sequencing of the genome of this bacterium was undertaken to elucidate the genomic basis of this so far unique type of energy metabolism. Results The genome contains 4,998,761 base pairs and 4646 genes of which 3609 were assigned to a function, and 1037 are without function prediction. Metabolic reconstruction revealed that most biosynthetic pathways of Gram negative, autotrophic sulfate reducers were present. Autotrophic CO2 assimilation proceeds through the Wood-Ljungdahl pathway. Additionally, we have found and confirmed the ability of the strain to couple phosphite oxidation to dissimilatory nitrate reduction to ammonia, which in itself is a new type of energy metabolism. Surprisingly, only two pathways for uptake, assimilation and utilization of inorganic and organic phosphonates were found in the genome. The unique for D. phosphitoxidans Ptx-Ptd cluster is involved in inorganic phosphite oxidation and an atypical C-P lyase-coding cluster (Phn) is involved in utilization of organophosphonates. Conclusions We present the whole genome sequence of the first bacterium able to gain metabolic energy via phosphite oxidation. The data obtained provide initial information on the composition and architecture of the phosphite–utilizing and energy-transducing systems needed to live with phosphite as an unusual electron donor.
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Affiliation(s)
| | | | | | - Diliana D Simeonova
- Laboratory of Microbial Ecology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
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19
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Draft Genome Sequence of Desulfotignum phosphitoxidans DSM 13687 Strain FiPS-3. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00227-13. [PMID: 23704177 PMCID: PMC3662817 DOI: 10.1128/genomea.00227-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the 5.008-Mbp assembled draft genome sequence of Desulfotignum phosphitoxidans strain FiPS-3 (DSM 13687), which gains metabolic energy from the oxidation of phosphite to phosphate. Its genome provides insights into the composition and architecture of the phosphite-utilizing and energy-transducing systems required to live with phosphite as electron donor.
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20
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Isolation and characterization of a soluble and thermostable phosphite dehydrogenase from Ralstonia sp. strain 4506. J Biosci Bioeng 2011; 113:445-50. [PMID: 22197497 DOI: 10.1016/j.jbiosc.2011.11.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 11/21/2011] [Accepted: 11/24/2011] [Indexed: 11/21/2022]
Abstract
Phosphite dehydrogenase (PtxD), which catalyzes the nearly irreversible oxidation of phosphite to phosphate with the concomitant reduction of NAD(+) to NADH, has great potential for NADH regeneration in industrial biocatalysts. Here, we isolated a soil bacterium, Ralstonia sp. strain 4506, that grew at 45°C on a minimal medium containing phosphite as the sole source of phosphorus. A recombinant PtxD of Ralstonia sp. (PtxD(R4506)) appeared in the soluble fraction in Escherichia coli. The purified PtxD(R4506) showed 6.7-fold greater catalytic efficiency (V(max)/K(m)) than the first characterized PtxD of Pseudomonas stutzeri (PtxD(PS)). Moreover, the purified PtxD(R4506) showed maximum activity at 50°C, and its half-life of thermal inactivation at 45°C was 80.5h, which is approximately 3,450-fold greater than that of PtxD(PS). Therefore, we concluded that PtxD(R4506), which shows high catalytic efficiency, solubility, and thermostability, would be useful for NADH regeneration applications.
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21
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Stone BL, White AK. Most probable number quantification of hypophosphite and phosphite oxidizing bacteria in natural aquatic and terrestrial environments. Arch Microbiol 2011; 194:223-8. [DOI: 10.1007/s00203-011-0775-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 09/28/2011] [Accepted: 11/10/2011] [Indexed: 12/01/2022]
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22
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Martínez A, Osburne MS, Sharma AK, DeLong EF, Chisholm SW. Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301. Environ Microbiol 2011; 14:1363-77. [PMID: 22004069 DOI: 10.1111/j.1462-2920.2011.02612.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Primary productivity in the ocean's oligotrophic regions is often limited by phosphorus (P) availability. In low phosphate environments, the prevalence of many genes involved in P acquisition is elevated, suggesting that the ability to effectively access diverse P sources is advantageous for organisms inhabiting these regions. Prochlorococcus, the numerically dominant primary producer in the oligotrophic ocean, encodes high-affinity P transporters, P regulatory proteins and enzymes for organic phosphate utilization, but its ability to use reduced P compounds has not been previously demonstrated. Because Prochlorococcus strain MIT9301 encodes genes similar to phnY and phnZ, which constitute a novel marine bacterial 2-aminoethylphosphonate (2-AEPn) utilization pathway, it has been suggested that this organism might use 2-AEPn as an alternative P source. We show here that although MIT9301 was unable to use 2-AEPn as a sole P source under standard culture conditions, it was able to use phosphite. Phosphite utilization by MIT9301 appears to be mediated by an NAD-dependent phosphite dehydrogenase encoded by ptxD. We show that phosphite utilization genes are present in diverse marine microbes and that their abundance is higher in low-P waters. These results strongly suggest that phosphite represents a previously unrecognized component of the marine P cycle.
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Affiliation(s)
- Asunción Martínez
- Department of Civil and Environmental Engineering Division of Biological Engineering Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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23
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Rosen BP, Ajees AA, McDermott TR. Life and death with arsenic. Arsenic life: an analysis of the recent report "A bacterium that can grow by using arsenic instead of phosphorus". Bioessays 2011; 33:350-7. [PMID: 21387349 PMCID: PMC3801090 DOI: 10.1002/bies.201100012] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Arsenic and phosphorus are group 15 elements with similar chemical properties. Is it possible that arsenate could replace phosphate in some of the chemicals that are required for life? Phosphate esters are ubiquitous in biomolecules and are essential for life, from the sugar phosphates of intermediary metabolism to ATP to phospholipids to the phosphate backbone of DNA and RNA. Some enzymes that form phosphate esters catalyze the formation of arsenate esters. Arsenate esters hydrolyze very rapidly in aqueous solution, which makes it improbable that phosphorous could be completely replaced with arsenic to support life. Studies of bacterial growth at high arsenic:phosphorus ratios demonstrate that relatively high arsenic concentrations can be tolerated, and that arsenic can become involved in vital functions in the cell, though likely much less efficiently than phosphorus. Recently Wolfe-Simon et al. [1 ] reported the isolation of a microorganism that they maintain uses arsenic in place of phosphorus for growth. Here, we examine and evaluate their data and conclusions.
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Affiliation(s)
- Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
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