1
|
Huang H, Lyu X, Xiao F, Fu J, Xu H, Wu J, Sun Y. Three-year field study on the temporal response of soil microbial communities and functions to PFOA exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135008. [PMID: 38943893 DOI: 10.1016/j.jhazmat.2024.135008] [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: 01/20/2024] [Revised: 06/13/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024]
Abstract
Contamination of per- and polyfluoroalkyl substances (PFAS) poses a significant threat to soil ecosystem health, yet there remains a lack of understanding regarding the responses of soil microbial communities to prolonged PFAS exposure in field conditions. This study involved a three-year field investigation to track changes in microbial communities and functions in soil subjected to the contamination of a primary PFAS, perfluorooctanoic acid (PFOA). Results showed that PFOA exposure altered soil bacterial and fungal communities in terms of diversity, composition, and structure. Notably, certain bacterial communities with a delayed reaction to PFOA contamination showed the most significant response after one year of exposure. Fungal communities were sensitive to PFOA in soil, exhibiting significant responses within just four months of exposure. After two years, the impact of PFOA on both bacterial and fungal communities was lessened, likely due to the long-term adaptation of microbial communities to PFOA. Moreover, PFOA exposure notably inhibited alkaline phosphatase activity and reduced certain phosphorus cycling-related functional genes after three years of exposure, suggesting potential disruptions in soil fertility. These new insights advance our understanding of the long-term effects of PFOA on soil microbial communities and functions at a field scale.
Collapse
Affiliation(s)
- Hai Huang
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China
| | - Xueyan Lyu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Feng Xiao
- Department of Civil and Environmental Engineering, University of Missouri, Columbia, MO 65211, USA
| | - Jiaju Fu
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China
| | - Hongxia Xu
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China
| | - Jichun Wu
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China; Technology Innovation Center for Ecological Monitoring & Restoration Project on Land (Arable), Nanjing 210018, China
| | - Yuanyuan Sun
- School of Earth Sciences and Engineering, Hydrosciences Department, Nanjing University, Nanjing 210023, China; Technology Innovation Center for Ecological Monitoring & Restoration Project on Land (Arable), Nanjing 210018, China.
| |
Collapse
|
2
|
Waggoner EM, Djaoudi K, Diaz JM, Duhamel S. Dissolved organic phosphorus bond-class utilization by Synechococcus. FEMS Microbiol Ecol 2024; 100:fiae099. [PMID: 39003239 PMCID: PMC11319936 DOI: 10.1093/femsec/fiae099] [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: 03/13/2024] [Revised: 05/14/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024] Open
Abstract
Dissolved organic phosphorus (DOP) contains compounds with phosphoester, phosphoanhydride, and phosphorus-carbon bonds. While DOP holds significant nutritional value for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by Synechococcus strains from open and coastal oceans. Both strains exhibited comparable growth rates when provided phosphate, a phosphoanhydride [3-polyphosphate and 45-polyphosphate], or a DOP compound with both phosphoanhydride and phosphoester bonds (adenosine 5'-triphosphate). Growth rates on phosphoesters [glucose-6-phosphate, adenosine 5'-monophosphate, bis(4-methylumbelliferyl) phosphate] were variable, and neither strain grew on selected phosphorus-carbon compounds. Both strains hydrolyzed 3-polyphosphate, then adenosine 5'-triphosphate, and lastly adenosine 5'-monophosphate, exhibiting preferential enzymatic hydrolysis of phosphoanhydride bonds. The strains' exoproteomes contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of phosphoanhydride bonds by these exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity toward the phosphoanhydride 3-polyphosphate, with varying affinities between strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition and highlight varied growth and enzymatic responses to molecular diversity within DOP bond-classes, thereby expanding our understanding of microbially mediated DOP cycling in marine ecosystems.
Collapse
Affiliation(s)
- Emily M Waggoner
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona, AZ 85721, United States
| | - Kahina Djaoudi
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona, AZ 85721, United States
| | - Julia M Diaz
- Geosciences Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, United States
| | - Solange Duhamel
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona, AZ 85721, United States
| |
Collapse
|
3
|
Riedel R, Commichau FM, Benndorf D, Hertel R, Holzer K, Hoelzle LE, Mardoukhi MSY, Noack LE, Martienssen M. Biodegradation of selected aminophosphonates by the bacterial isolate Ochrobactrum sp. BTU1. Microbiol Res 2024; 280:127600. [PMID: 38211497 DOI: 10.1016/j.micres.2024.127600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
Aminophosphonates, like glyphosate (GS) or metal chelators such as ethylenediaminetetra(methylenephosphonic acid) (EDTMP), are released on a large scale worldwide. Here, we have characterized a bacterial strain capable of degrading synthetic aminophosphonates. The strain was isolated from LC/MS standard solution. Genome sequencing indicated that the strain belongs to the genus Ochrobactrum. Whole-genome classification using pyANI software to compute a pairwise ANI and other metrics between Brucella assemblies and Ochrobactrum contigs revealed that the bacterial strain is designated as Ochrobactrum sp. BTU1. Degradation batch tests with Ochrobactrum sp. BTU1 and the selected aminophosphonates GS, EDTMP, aminomethylphosphonic acid (AMPA), iminodi(methylene-phosphonic) (IDMP) and ethylaminobis(methylenephosphonic) acid (EABMP) showed that the strain can use all phosphonates as sole phosphorus source during phosphorus starvation. The highest growth rate was achieved with AMPA, while EDTMP and GS were least supportive for growth. Proteome analysis revealed that GS degradation is promoted by C-P lyase via the sarcosine pathway, i.e., initial cleavage at the C-P bond. We also identified C-P lyase to be responsible for degradation of EDTMP, EABMP, IDMP and AMPA. However, the identification of the metabolite ethylenediaminetri(methylenephosphonic acid) via LC/MS analysis in the test medium during EDTMP degradation indicates a different initial cleavage step as compared to GS. For EDTMP, it is evident that the initial cleavage occurs at the C-N bond. The detection of different key enzymes at regulated levels, form the bacterial proteoms during EDTMP exposure, further supports this finding. This study illustrates that widely used and structurally more complex aminophosphonates can be degraded by Ochrobactrum sp. BTU1 via the well-known degradation pathways but with different initial cleavage strategy compared to GS.
Collapse
Affiliation(s)
- Ramona Riedel
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Technology, BTU Cottbus-Senftenberg, Cottbus, Germany.
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany; FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Dirk Benndorf
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Köthen, Germany; Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany; Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Katharina Holzer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Ludwig E Hoelzle
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Mohammad Saba Yousef Mardoukhi
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Technology, BTU Cottbus-Senftenberg, Cottbus, Germany; FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany; FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Emelie Noack
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Technology, BTU Cottbus-Senftenberg, Cottbus, Germany
| | - Marion Martienssen
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Technology, BTU Cottbus-Senftenberg, Cottbus, Germany
| |
Collapse
|
4
|
Riedel R, Krahl K, Buder K, Böllmann J, Braun B, Martienssen M. Novel standard biodegradation test for synthetic phosphonates. J Microbiol Methods 2023; 212:106793. [PMID: 37543110 DOI: 10.1016/j.mimet.2023.106793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Determination of biodegradation of synthetic phosphonates such as aminotris(methylenephosphonic acid) (ATMP), ethylenediamine tetra(methylenephosphonic acid) (EDTMP), or diethylenetriamine penta(methylenephosphonic acid) (DTPMP) is a great challenge. Commonly, ready biodegradability of organic substances is assessed by OECD 301 standard tests. However, due to the chemical imbalance of carbon to phosphorus synthetic phosphonates do not promote microbial growth and, thus, limiting its biodegradation. Therefore, standard OECD test methods are not always reliable to predict the real biodegradability of phosphonates. In the presented study, we report the development of a standardized batch system suitable to synthetic phosphonates such as ATMP, EDTMP, DTPMP and others. The novel standard batch test is applicable with pure strains, activated sludge from different wastewater treatment plants (i.e., municipal and industrial), and with tap water as inoculum. We optimized the required calcium and magnesium exposure levels as well as the amount of the start inoculum biomass. We demonstrated that our test also allows to determine several parameters including ortho-phosphate (o-PO43-), total phosphorus (TP), ammonium (NH4+) and total organic carbon (TOC). In addition, also LC/MS analyses of cell-free medium is applicable for determining the mother compounds and metabolites. We applied our optimized standardized batch with selected phosphonates and evidenced that the chemical structure has a major influence of the microbial growth rates. Thus, our novel batch test overcomes drawbacks of the OECD 301 test series for determination of easy biodegradability for stoichiometric imbalanced organic compounds such as phosphonates.
Collapse
Affiliation(s)
- Ramona Riedel
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, Biotechnology of Water Treatment, 03046 Cottbus, Germany.
| | - Kathrin Krahl
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, Biotechnology of Water Treatment, 03046 Cottbus, Germany
| | - Kai Buder
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, Biotechnology of Water Treatment, 03046 Cottbus, Germany
| | - Jörg Böllmann
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, Biotechnology of Water Treatment, 03046 Cottbus, Germany
| | - Burga Braun
- University of Technology Berlin, Department of Environmental Microbiology, 10587 Berlin, Germany
| | - Marion Martienssen
- Brandenburg University of Technology Cottbus-Senftenberg, Institute of Environmental Technology, Biotechnology of Water Treatment, 03046 Cottbus, Germany
| |
Collapse
|
5
|
Zhang W, Chen WJ, Chen SF, Lei Q, Li J, Bhatt P, Mishra S, Chen S. Cellular Response and Molecular Mechanism of Glyphosate Degradation by Chryseobacterium sp. Y16C. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6650-6661. [PMID: 37084257 DOI: 10.1021/acs.jafc.2c07301] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glyphosate is one of the most widely used herbicides worldwide. Unfortunately, the continuous use of glyphosate has resulted in serious environmental contamination and raised public concern about its impact on human health. In our previous study, Chryseobacterium sp. Y16C was isolated and characterized as an efficient degrader that can completely degrade glyphosate. However, the biochemical and molecular mechanisms underlying its glyphosate biodegradation ability remain unclear. In this study, the physiological response of Y16C to glyphosate stimulation was characterized at the cellular level. The results indicated that, in the process of glyphosate degradation, Y16C induced a series of physiological responses in the membrane potential, reactive oxygen species levels, and apoptosis. The antioxidant system of Y16C was activated to alleviate the oxidative damage caused by glyphosate. Furthermore, a novel gene, goW, was expressed in response to glyphosate. The gene product, GOW, is an enzyme that catalyzes glyphosate degradation, with putative structural similarities to glycine oxidase. GOW encodes 508 amino acids, with an isoelectric point of 5.33 and a molecular weight of 57.2 kDa, which indicates that it is a glycine oxidase. GOW displays maximum enzyme activity at 30 °C and pH 7.0. Additionally, most of the metal ions exhibited little influence on the enzyme activity except for Cu2+. Finally, with glyphosate as the substrate, the catalytic efficiency of GOW was higher than that of glycine, although opposite results were observed for the affinity. Taken together, the current study provides new insights to deeply understand and reveal the mechanisms of glyphosate degradation in bacteria.
Collapse
Affiliation(s)
- Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Wen-Juan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Shao-Fang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette 47906, United States
| | - Sandhya Mishra
- Environmental Technologies Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
6
|
Gao Z, Yi S, Xue M, Zhu K, Yang R, Wang T, Sun H, Zhu L. Microbial biotransformation mechanisms of PFPiAs in soil unveiled by metagenomic analysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130896. [PMID: 36764254 DOI: 10.1016/j.jhazmat.2023.130896] [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: 11/23/2022] [Revised: 01/15/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
As alternatives of long-chain PFASs (Poly- and perfluoroalkyl substances), perfluoroalkyl phosphinic acids (PFPiAs) are increasingly observed in the environment, but their environmental behaviors have not been well understood. Here, the microbial biotransformation of C6/C6 and C8/C8 PFPiA in two soils (Soil N and Y) was investigated. After 252 d and 330 d of incubation with PFPiAs in Soil N and Y respectively, the levels of PFPiAs decreased distinctly, accompanied by the increasing perfluorohexaphosphonic acid (PFHxPA) or perfluorooctanophosphonic acid (PFOPA) formation, magnifying PFPiAs were susceptible to C-P cleavage, which was also confirmed by the density functional theory calculations. The half-lives of the PFPiAs were longer than one year, while generally shorter in Soil N than in Soil Y and that of C6/C6 was shorter than C8/C8 PFPiA (392 d and 746 d in Soil N, and 603 and 1155 d in Soil Y, respectively). Metagenomic sequencing analysis revealed that Proteobacteria as the primary host of the potential functional genes related to CP bond cleavage might be the crucial phyla contributing to the biotransformation of PFPiAs. Meanwhile, the more intensive interactions between the microbes in Soil N consistently contribute to its greater capacity for transforming PFPiAs.
Collapse
Affiliation(s)
- Zhuo Gao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Shujun Yi
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China
| | - Mengzhu Xue
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Kecheng Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Rongyan Yang
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Hongwen Sun
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China.
| |
Collapse
|
7
|
Schultz CR, Johnson M, Wallace JG. Effects of Inbreeding on Microbial Community Diversity of Zea mays. Microorganisms 2023; 11:microorganisms11040879. [PMID: 37110300 PMCID: PMC10145435 DOI: 10.3390/microorganisms11040879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.
Collapse
|
8
|
The functional importance of bacterial oxidative phosphonate pathways. Biochem Soc Trans 2023; 51:487-499. [PMID: 36892197 DOI: 10.1042/bst20220479] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Organophosphonates (Pns) are a unique class of natural products characterized by a highly stable C-P bond. Pns exhibit a wide array of interesting structures as well as useful bioactivities ranging from antibacterial to herbicidal. More structurally simple Pns are scavenged and catabolized by bacteria as a source of phosphorus. Despite their environmental and industrial importance, the pathways involved in the metabolism of Pns are far from being fully elucidated. Pathways that have been characterized often reveal unusual chemical transformations and new enzyme mechanisms. Among these, oxidative enzymes play an outstanding role during the biosynthesis and degradation of Pns. They are to a high extent responsible for the structural diversity of Pn secondary metabolites and for the break-down of both man-made and biogenic Pns. Here, we review our current understanding of the importance of oxidative enzymes for microbial Pn metabolism, discuss the underlying mechanistic principles, similarities, and differences between pathways. This review illustrates Pn biochemistry to involve a mix of classical redox biochemistry and unique oxidative reactions, including ring formations, rearrangements, and desaturations. Many of these reactions are mediated by specialized iron-dependent oxygenases and oxidases. Such enzymes are the key to both early pathway diversification and late-stage functionalization of complex Pns.
Collapse
|
9
|
The Microbiome Structure of the Symbiosis between the Desert Truffle Terfezia boudieri and Its Host Plant Helianthemum sessiliflorum. J Fungi (Basel) 2022; 8:jof8101062. [PMID: 36294627 PMCID: PMC9605525 DOI: 10.3390/jof8101062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
The desert truffle Terfezia boudieri is an ascomycete fungus that forms ect-endomycorrhiza in the roots of plants belonging to Cistaceae. The fungus forms hypogeous edible fruit bodies, appreciated as gourmet food. Truffles and host plants are colonized by various microbes, which may contribute to their development. However, the diversity and composition of the bacterial community under field conditions in the Negev desert are still unknown. The overall goal of this research was to identify the rhizosphere microbial community supporting the establishment of a symbiotic association between T. boudieri and Helianthemum sessiliflorum. The bacterial community was characterized by fruiting bodies, mycorrhized roots, and rhizosphere soil. Based on next-generation sequencing meta-analyses of the 16S rRNA gene, we discovered diverse bacterial communities of fruit bodies that differed from those found in the roots and rhizosphere. Families of Proteobacteria, Planctomycetes, and Actinobacteria were present in all four samples. Alpha diversity analysis revealed that the rhizosphere and roots contain significantly higher bacterial species numbers compared to the fruit. Additionally, ANOSIM and PCoA provided a comparative analysis of the bacterial taxa associated with fruiting bodies, roots, and rhizosphere. The core microbiome described consists of groups whose biological role triggers important traits supporting plant growth and fruit body development.
Collapse
|
10
|
Wackett LP. Strategies for the Biodegradation of Polyfluorinated Compounds. Microorganisms 2022; 10:microorganisms10081664. [PMID: 36014082 PMCID: PMC9415301 DOI: 10.3390/microorganisms10081664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 01/01/2023] Open
Abstract
Many cite the strength of C–F bonds for the poor microbial biodegradability of polyfluorinated organic compounds (PFCs). However, commercial PFCs almost invariably contain more functionality than fluorine. The additional functionality provides a weak entry point for reactions that activate C–F bonds and lead to their eventual cleavage. This metabolic activation strategy is common in microbial biodegradation pathways and is observed with aromatic hydrocarbons, chlorinated compounds, phosphonates and many other compounds. Initial metabolic activation precedes critical bond breakage and assimilation of nutrients. A similar strategy with commercial PFCs proceeds via initial attack at the non-fluorinated functionalities: sulfonates, carboxylates, chlorines, phenyl rings, or phosphonates. Metabolic transformation of these non-fluorinated groups can activate the C–F bonds, allowing more facile cleavage than a direct attack on the C–F bonds. Given that virtually all compounds denoted as “PFAS” are not perfluorinated and are not alkanes, it is posited here that considering their individual chemical classes is more useful for both chemical and microbiological considerations of their fate.
Collapse
Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
11
|
Cooper ZS, Rapp JZ, Shoemaker AMD, Anderson RE, Zhong ZP, Deming JW. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Front Microbiol 2022; 13:879116. [PMID: 35733954 PMCID: PMC9207381 DOI: 10.3389/fmicb.2022.879116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
Collapse
Affiliation(s)
- Zachary S. Cooper
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
- *Correspondence: Zachary S. Cooper, , orcid.org/0000-0001-6515-7971
| | - Josephine Z. Rapp
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
- Institute of Integrative Biology and Systems (IBIS), Université Laval, Québec, QC, Canada
| | - Anna M. D. Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, United States
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W. Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
| |
Collapse
|
12
|
Song X, Liu J, Wang B. Emergence of Function from Nonheme Diiron Oxygenases: A Quantum Mechanical/Molecular Mechanical Study of Oxygen Activation and Organophosphonate Catabolism Mechanisms by PhnZ. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xitong Song
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| |
Collapse
|
13
|
Jin H, Wang Y, Fu Y, Bhaya D. The role of three-tandem Pho Boxes in the control of the C-P lyase operon in a thermophilic cyanobacterium. Environ Microbiol 2021; 23:6433-6449. [PMID: 34472186 DOI: 10.1111/1462-2920.15750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria have an inherited advantage in phosphonate phytoremediation. However, studies on phosphonate metabolism in cyanobacteria are rare and mostly focus on physiology and ecology. Here, C-P lyase gene cluster regulation in an undomesticated thermophilic Synechococcus OS-B' was examined in Synechocystis sp. PCC6803, a unicellular cyanobacterial model. Phylogenetic and cluster synteny analysis of C-P lyase genes revealed a closer relationship between Syn OS-B' and Thermus thermophilus, than with other cyanobacteria. Pho boxes were identified in the 5'-end-flanking region of the C-P lyase gene cluster, through which the downstream gene expression was regulated in a phosphate concentration-dependent manner. Unexpectedly, the phosphate concentration that thoroughly inhibited Pho boxes was almost two orders of magnitude higher than that of any natural or anthropogenic wastewater reported so far. The Pho boxes mediated regulation was achieved through the Pho regulon two-component system, and the absence of either SphS or SphR ablated the cell's ability to sense ambient phosphate changes. The three tandems of Pho boxes maintained inequivalent roles, of which the third tandem was not essential; however, it played a role in adjusting Pho boxes response in both positive and negative manner under phosphorus limitation.
Collapse
Affiliation(s)
- Haojie Jin
- College of Forestry, Beijing Forestry University, Beijing, 100083, China.,Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Yan Wang
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Yujie Fu
- College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| |
Collapse
|
14
|
Gama SR, Stankovic T, Hupp K, Al Hejami A, McClean M, Evans A, Beauchemin D, Hammerschmidt F, Pallitsch K, Zechel DL. Biosynthesis of the Fungal Organophosphonate Fosfonochlorin Involves an Iron(II) and 2-(Oxo)glutarate Dependent Oxacyclase. Chembiochem 2021; 23:e202100352. [PMID: 34375042 DOI: 10.1002/cbic.202100352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Indexed: 11/07/2022]
Abstract
The fungal metabolite Fosfonochlorin features a chloroacetyl moiety that is unusual within known phosphonate natural product biochemistry. Putative biosynthetic genes encoding Fosfonochlorin in Fusarium and Talaromyces spp. were investigated through reactions of encoded enzymes with synthetic substrates and isotope labelling studies. We show that early biosynthetic steps for Fosfonochlorin involves the reduction of phosphonoacetaldehyde to form 2-hydroxyethylphosphonic acid, followed by oxidative intramolecular cyclization of the resulting alcohol to form ( S )-epoxyethylphosphonic acid. The latter reaction is catalyzed by FfnD, a rare example of a non-heme iron / 2-(oxo)glutarate dependent oxacyclase. In contrast, FfnD behaves as a more typical oxygenase with ethylphosphonic acid, producing ( S )-1-hydroxyethylphosphonic acid. FfnD thus represents a new example of a ferryl generating enzyme that can suppress the typical oxygen rebound reaction that follows abstraction of a substrate hydrogen by a ferryl oxygen, thereby directing the substrate radical towards a fate other than hydroxylation.
Collapse
Affiliation(s)
- Simanga R Gama
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Toda Stankovic
- Institut für Organische Chemie, Universität Wien, 1090, Wien, Österreich
| | - Kendall Hupp
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Ahmed Al Hejami
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Mimi McClean
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Alysa Evans
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - Diane Beauchemin
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | | | | | - David L Zechel
- Department of Chemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| |
Collapse
|
15
|
Jia H, Chen Y, Chen Y, Liu R, Zhang Q, Bartlam M. Structural characterization of a 2-aminoethylphosphonate:pyruvate aminotransferase from Pseudomonas aeruginosa PAO1. Biochem Biophys Res Commun 2021; 552:114-119. [PMID: 33743347 DOI: 10.1016/j.bbrc.2021.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
2-aminoethylphosphonate:pyruvate aminotransferase (AEPT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that mediates the first step in the AEP degradation pathway. It catalyzes the transamination of 2-aminoethylphosphonate (AEP) with pyruvate to phosphonoacetaldehyde and l-alanine respectively. Although the enzyme is widely present in microorganisms, there are few reports on the structure and function of AEPT to date. Here we report the crystal structure of AEPT from Pseudomonas aeruginosa PAO1 (PaAEPT) to 2.35 Å resolution in the absence of the PLP cofactor. PaAEPT crystallizes in space group P21212 with one monomer per asymmetric unit. Analytical ultracentrifugation analysis shows that PaAEPT forms a stable dimer in solution. Our work provides a valuable starting point for further functional and mechanistic studies of the AEP degradation pathway.
Collapse
Affiliation(s)
- Haizhu Jia
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yuan Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yujing Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| |
Collapse
|
16
|
Coward C, Dharmalingham G, Abdulle O, Avis T, Beisken S, Breidenstein E, Carli N, Figueiredo L, Jones D, Khan N, Malara S, Martins J, Nagalingam N, Turner K, Wain J, Williams D, Powell D, Mason C. High-density transposon libraries utilising outward-oriented promoters identify mechanisms of action and resistance to antimicrobials. FEMS Microbiol Lett 2020; 367:fnaa185. [PMID: 33186989 PMCID: PMC7735965 DOI: 10.1093/femsle/fnaa185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/11/2020] [Indexed: 01/07/2023] Open
Abstract
The use of bacterial transposon mutant libraries in phenotypic screens is a well-established technique for determining which genes are essential or advantageous for growth in conditions of interest. Standard, inactivating, transposon libraries cannot give direct information about genes whose over-expression gives a selective advantage. We report the development of a system wherein outward-oriented promoters are included in mini-transposons, generation of transposon mutant libraries in Escherichia coli and Pseudomonas aeruginosa and their use to probe genes important for growth under selection with the antimicrobial fosfomycin, and a recently-developed leucyl-tRNA synthase inhibitor. In addition to the identification of known mechanisms of action and resistance, we identify the carbon-phosphorous lyase complex as a potential resistance liability for fosfomycin in E. coli and P. aeruginosa. The use of this technology can facilitate the development of novel mechanism-of-action antimicrobials that are urgently required to combat the increasing threat worldwide from antimicrobial-resistant pathogenic bacteria.
Collapse
Affiliation(s)
- Chris Coward
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Gopujara Dharmalingham
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Omar Abdulle
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Tim Avis
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Stephan Beisken
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Elena Breidenstein
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Natasha Carli
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Luis Figueiredo
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - David Jones
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Nawaz Khan
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Sara Malara
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Joana Martins
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Nabeetha Nagalingam
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Keith Turner
- Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - John Wain
- Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - David Williams
- Nanna Therapeutics, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - David Powell
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Clive Mason
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| |
Collapse
|
17
|
Stosiek N, Talma M, Klimek-Ochab M. Carbon-Phosphorus Lyase-the State of the Art. Appl Biochem Biotechnol 2020; 190:1525-1552. [PMID: 31792787 DOI: 10.1007/s12010-019-03161-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 10/23/2019] [Indexed: 11/27/2022]
Abstract
Organophosphonates are molecules that contain a very chemically stable carbon-phosphorus (C-P) bond. Microorganisms can utilize phosphonates as potential source of crucial elements for their growth, as developed several pathways to metabolize these compounds. One among these pathways is catalyzed by C-P lyase complex, which has a broad substrate specifity; therefore, it has a wide application in degradation of herbicides deposited in the environment, such as glyphosate. This multi-enzyme system accurately recognized in Escherichia coli and genetic studies have demonstrated that it is encoded by phn operon containing 14 genes (phnC-phnP). The phn operon is a member of the Pho regulon induced by phosphate starvation. Ability to degradation of phosphonates is also found in other microorganisms, especially soil and marine bacteria, that have homologous genes to those in E. coli. Despite the existence of differences in structure and composition of phn gene cluster, each of these strains contains phnGHIJKLM genes necessary in the C-P bond cleavage mechanism. The review provides a detailed description and summary of achievements on the C-P lyase enzymatic pathway over the last 50 years.
Collapse
Affiliation(s)
- Natalia Stosiek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Michał Talma
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Magdalena Klimek-Ochab
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| |
Collapse
|
18
|
Mosquito S, Bertani I, Licastro D, Compant S, Myers MP, Hinarejos E, Levy A, Venturi V. In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:349-363. [PMID: 31609645 DOI: 10.1094/mpmi-09-19-0256-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant-bacteria interaction.
Collapse
Affiliation(s)
- Susan Mosquito
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Iris Bertani
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Danilo Licastro
- CBM S.c.r.l., Area Science Park-Basovizza, 34149 Trieste, Italy
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Vienna, Austria
| | - Michael P Myers
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | | | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| |
Collapse
|
19
|
Brown CJ, Mtui D, Oswald BP, Van Leuven JT, Vallender EJ, Schultz‐Darken N, Ross CN, Tardif SD, Austad SN, Forney LJ. Comparative genomics of Bifidobacterium species isolated from marmosets and humans. Am J Primatol 2019; 81:e983. [PMID: 31062394 PMCID: PMC6900142 DOI: 10.1002/ajp.22983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/08/2019] [Accepted: 04/14/2019] [Indexed: 12/15/2022]
Abstract
The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.
Collapse
Affiliation(s)
- Celeste J. Brown
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
- Center for Modeling Complex InteractionsUniversity of IdahoMoscowIdaho
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
| | - Dorah Mtui
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
| | - Benjamin P. Oswald
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
| | | | - Eric J. Vallender
- New England Primate Research CenterHarvard Medical SchoolSouthboroughMassachusetts
| | - Nancy Schultz‐Darken
- Wisconsin National Primate Research CenterUniversity of WisconsinMadisonWisconsin
| | - Corinna N. Ross
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexas
- Department of Science and MathematicsTexas A&M UniversitySan AntonioTexas
| | - Suzette D. Tardif
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexas
| | - Steven N. Austad
- Department of Cellular and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTexas
| | - Larry J. Forney
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
| |
Collapse
|
20
|
Manav MC, Sofos N, Hove-Jensen B, Brodersen DE. The Abc of Phosphonate Breakdown: A Mechanism for Bacterial Survival. Bioessays 2018; 40:e1800091. [DOI: 10.1002/bies.201800091] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/13/2018] [Indexed: 12/11/2022]
Affiliation(s)
- M. Cemre Manav
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
| | - Nicholas Sofos
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
| | - Bjarne Hove-Jensen
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
| | - Ditlev E. Brodersen
- Department of Molecular Biology and Genetics; Aarhus University; DK-8000 Aarhus Denmark
| |
Collapse
|
21
|
A novel pseudo-centrosymmetric P O⋯H O H⋯O P synthon in crystal structures of azaheterocyclic phosphonates. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
22
|
Rivas M, del Valle LJ, Rodríguez-Rivero AM, Turon P, Puiggalí J, Alemán C. Loading of Antibiotic into Biocoated Hydroxyapatite Nanoparticles: Smart Antitumor Platforms with Regulated Release. ACS Biomater Sci Eng 2018; 4:3234-3245. [DOI: 10.1021/acsbiomaterials.8b00353] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Manuel Rivas
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, 08019, Barcelona, Spain
| | - Luís J. del Valle
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, 08019, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, Barcelona E-08028, Spain
| | | | - Pau Turon
- B. Braun Surgical, S.A. Carretera de Terrasa 121, 08191 Rubí (Barcelona), Spain
| | - Jordi Puiggalí
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, 08019, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, Barcelona E-08028, Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, 08019, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, Barcelona E-08028, Spain
| |
Collapse
|
23
|
Zhan H, Feng Y, Fan X, Chen S. Recent advances in glyphosate biodegradation. Appl Microbiol Biotechnol 2018; 102:5033-5043. [PMID: 29705962 DOI: 10.1007/s00253-018-9035-0] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 02/01/2023]
Abstract
Glyphosate has emerged as the most widespread herbicide to control annual and perennial weeds. Massive use of glyphosate for decades has resulted in its ubiquitous presence in the environment, and poses a threat to humans and ecosystem. Different approaches such as adsorption, photocatalytic degradation, and microbial degradation have been studied to break down glyphosate in the environment. Among these, microbial degradation is the most effective and eco-friendly method. During its degradation, various microorganisms can use glyphosate as a sole source of phosphorus, carbon, and nitrogen. Major glyphosate degradation pathways and its metabolites have been frequently investigated, but the related enzymes and genes have been rarely studied. There are many reviews about the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid. However, there is lack of reviews on biodegradation and bioremediation of glyphosate. The aims of this review are to summarize the microbial degradation of glyphosate and discuss the potential of glyphosate-degrading microorganisms to bioremediate glyphosate-contaminated environments. This review will provide an instructive direction to apply glyphosate-degrading microorganisms in the environment for bioremediation.
Collapse
Affiliation(s)
- Hui Zhan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yanmei Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Xinghui Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| |
Collapse
|
24
|
Rivas M, del Valle LJ, Armelin E, Bertran O, Turon P, Puiggalí J, Alemán C. Hydroxyapatite with Permanent Electrical Polarization: Preparation, Characterization, and Response against Inorganic Adsorbates. Chemphyschem 2018; 19:1746-1755. [DOI: 10.1002/cphc.201800196] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Manuel Rivas
- Department of Chemical EngineeringUniversitat Politècnica de Catalunya EEBE, C/Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
| | - Luis J. del Valle
- Department of Chemical EngineeringUniversitat Politècnica de Catalunya EEBE, C/Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and EngineeringUniversitat Politècnica de Catalunya Institution EEBE, C/ Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
| | - Elaine Armelin
- Department of Chemical EngineeringUniversitat Politècnica de Catalunya EEBE, C/Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and EngineeringUniversitat Politècnica de Catalunya Institution EEBE, C/ Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
| | - Oscar Bertran
- Department of PhysicsUniversitat Politècnica de Catalunya EEI, Av. Pla de la Massa, 8 08700 Igualada Spain
| | - Pau Turon
- Department of Chemical EngineeringUniversitat Politècnica de Catalunya EEBE, C/Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
- B. Braun Surgical, S.A Carretera de Terrassa 121 08191 Rubí (Barcelona) Spain
| | - Jordi Puiggalí
- Department of Chemical EngineeringUniversitat Politècnica de Catalunya EEBE, C/Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and EngineeringUniversitat Politècnica de Catalunya Institution EEBE, C/ Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
| | - Carlos Alemán
- Department of Chemical EngineeringUniversitat Politècnica de Catalunya EEBE, C/Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
- Barcelona Research Center for Multiscale Science and EngineeringUniversitat Politècnica de Catalunya Institution EEBE, C/ Eduard Maristany 10–14, Ed. I2 08019 Barcelona Spain
| |
Collapse
|
25
|
Iyer R, Iken B, Damania A, Krieger J. Whole genome analysis of six organophosphate-degrading rhizobacteria reveals putative agrochemical degradation enzymes with broad substrate specificity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:13660-13675. [PMID: 29502257 DOI: 10.1007/s11356-018-1435-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Six organophosphate-degrading bacterial strains collected from farm and ranch soil rhizospheres across the Houston-metropolitan area were identified as strains of Pseudomonas putida (CBF10-2), Pseudomonas stutzeri (ODKF13), Ochrobactrum anthropi (FRAF13), Stenotrophomonas maltophilia (CBF10-1), Achromobacter xylosoxidans (ADAF13), and Rhizobium radiobacter (GHKF11). Whole genome sequencing data was assessed for relevant genes, proteins, and pathways involved in the breakdown of agrochemicals. For comparative purposes, this analysis was expanded to also include data from deposited strains in the National Center for Biotechnology Information's (NCBI) database. This study revealed Zn-dependent metallo-β-lactamase (MBL)-fold proteins similar to OPHC2 first identified in P. pseudoalcaligenes as the likely agents of organophosphate (OP) hydrolysis in A. xylosoxidans ADAF13, S. maltophilia CBF10-1, O. anthropi FRAF13, and R. radiobacter GHKF11. A search of similar proteins within NCBI identified over 200 hits for bacterial genera and species with a similar OPHC2 domain. Taken together, we conclude from this data that intrinsic low-level OP hydrolytic activity is likely prevalent across the rhizosphere stemming from widespread OPHC2-like metalloenzymes. In addition, P. stutzeri ODKF13, P. putida CBF10-2, O. anthropi FRAF13, and R. radiobacter GHKF11 were found to harbor glycine oxidase (GO) enzymes that putatively possess low-level activity against the herbicide glyphosate. These bacterial GOs are reported to catalyze the degradation of glyphosate to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and suggest a possible link to AMPA that can be found in glyphosate-contaminated agricultural soil. The presence of aromatic degradation proteins were also detected in five of six study strains, but are attributed primarily to components of the widely distributed β-ketoadipate pathway found in many soil bacteria.
Collapse
Affiliation(s)
- Rupa Iyer
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX, 77204, USA.
| | - Brian Iken
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX, 77204, USA
| | - Ashish Damania
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jerry Krieger
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston, TX, 77204, USA
| |
Collapse
|
26
|
Rott E, Steinmetz H, Metzger JW. Organophosphonates: A review on environmental relevance, biodegradability and removal in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:1176-1191. [PMID: 29751423 DOI: 10.1016/j.scitotenv.2017.09.223] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/18/2017] [Accepted: 09/21/2017] [Indexed: 05/24/2023]
Abstract
The worldwide increasing consumption of the phosphonates 2-phosphonobutane-1,2,4-tricarboxylic acid [PBTC], 1-hydroxyethane 1,1-diphosphonic acid [HEDP], nitrilotris(methylene phosphonic acid) [NTMP], ethylenediamine tetra(methylene phosphonic acid) [EDTMP] and diethylenetriamine penta(methylene phosphonic acid) [DTPMP] over the past decades put phosphonates into focus of environmental scientists and agencies, as they are increasingly discussed in the context of various environmental problems. The hitherto difficult analysis of phosphonates contributed to the fact that very little is known about their concentrations and behavior in the environment. This work critically reviews the existing literature up to the year 2016 on the potential environmental relevance of phosphonates, their biotic and abiotic degradability, and their removal in wastewater treatment plants (WWTPs). Accordingly, despite their stability against biological degradation, phosphonates can be removed with relatively high efficiency (>80%) in WWTPs operated with chemical phosphate precipitation. In the literature, however, to our knowledge, there is no information as to whether an enhanced biological phosphorus removal alone is sufficient for such high removal rates and whether the achievable phosphonate concentrations in effluents are sufficiently low to prevent eutrophication. It is currently expected that phosphonates, although being complexing agents, do not remobilize heavy metals from sediments in a significant amount since the phosphonate concentrations required for this (>50μg/L) are considerably higher than the concentrations determined in surface waters. Various publications also point out that phosphonates are harmless to a variety of aquatic organisms. Moreover, degradation products thereof such as N-(phosphonomethyl)glycine and aminomethylphosphonic acid are regarded as being particularly critical. Despite their high stability against biological degradation, phosphonates contribute to eutrophication due to abiotic degradation (mainly photolysis). Furthermore, the literature reports on the fact that phosphonates in high concentrations interfere with phosphate precipitation in WWTPs. Thus, it is recommended to remove phosphonates, in particular from industrial wastewaters, before discharging them into water bodies or WWTPs.
Collapse
Affiliation(s)
- Eduard Rott
- Institute for Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Bandtäle 2, 70569 Stuttgart, Germany.
| | - Heidrun Steinmetz
- Chair of Resource Efficient Wastewater Technology, University of Kaiserslautern, Paul-Ehrlich-Str. 14, 67663 Kaiserslautern, Germany
| | - Jörg W Metzger
- Institute for Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Bandtäle 2, 70569 Stuttgart, Germany
| |
Collapse
|
27
|
Ulrich EC, Kamat SS, Hove-Jensen B, Zechel DL. Methylphosphonic Acid Biosynthesis and Catabolism in Pelagic Archaea and Bacteria. Methods Enzymol 2018; 605:351-426. [DOI: 10.1016/bs.mie.2018.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
28
|
Ermakova IT, Shushkova TV, Sviridov AV, Zelenkova NF, Vinokurova NG, Baskunov BP, Leontievsky AA. Organophosphonates utilization by soil strains of Ochrobactrum anthropi and Achromobacter sp. Arch Microbiol 2017; 199:665-675. [PMID: 28184965 DOI: 10.1007/s00203-017-1343-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/12/2017] [Accepted: 01/19/2017] [Indexed: 10/20/2022]
Abstract
Four bacterial strains from glyphosate- or alkylphosphonates-contaminated soils were tested for ability to utilize different organophosphonates. All studied strains readily utilized methylphosphonic acid and a number of other phosphonates, but differed in their ability to degrade glyphosate. Only strains Ochrobactrum anthropi GPK 3 and Achromobacter sp. Kg 16 utilized this compound after isolation from enrichment cultures with glyphosate. Achromobacter sp. MPK 7 from the same enrichment culture, similar to Achromobacter sp. MPS 12 from methylphosphonate-polluted source, required adaptation to growth on GP. Studied strains varied significantly in their growth parameters, efficiency of phosphonates degradation and characteristic products of this process, as well as in their energy metabolism. These differences give grounds to propose a possible model of interaction between these strains in microbial consortium in phosphonate-contaminated soils.
Collapse
Affiliation(s)
- Inna T Ermakova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, Pushchino, Moscow, 142290, Russia
| | - Tatyana V Shushkova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, Pushchino, Moscow, 142290, Russia
| | - Alexey V Sviridov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, Pushchino, Moscow, 142290, Russia.
| | - Nina F Zelenkova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, Pushchino, Moscow, 142290, Russia
| | - Natalya G Vinokurova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, Pushchino, Moscow, 142290, Russia
| | - Boris P Baskunov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, Pushchino, Moscow, 142290, Russia
| | - Alexey A Leontievsky
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospect Nauki, Pushchino, Moscow, 142290, Russia
| |
Collapse
|
29
|
Zhao C, Chen H. Mechanism of Organophosphonate Catabolism by Diiron Oxygenase PhnZ: A Third Iron-Mediated O–O Activation Scenario in Nature. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chongyang Zhao
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| |
Collapse
|
30
|
Pallitsch K, Schweifer A, Roller A, Hammerschmidt F. Towards the biodegradation pathway of fosfomycin. Org Biomol Chem 2017; 15:3276-3285. [PMID: 28352915 DOI: 10.1039/c7ob00546f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Three functionalised propylphosphonic acids were synthesised to study C-P bond cleavage in R. huakuii PMY1. (R)-1-Hydroxy-2-oxopropylphosphonic acid [(R)-5] was prepared by chiral resolution of (±)-dimethyl 1-hydroxy-2-methylallyllphosphonate [(±)-12], followed by ozonolysis and deprotection. The N-(l-alanyl)-substituted (1R,2R)-2-amino-1-hydroxypropylphosphonic acid 10, a potential precursor for 2-oxopropylphosphonic acid (5) in cells, was obtained by coupling the aminophosphonic acid with benzotriazole-activated Z-l-alanine and hydrogenolytic deprotection. (1R*,2R*)-1,2-Dihydroxy-3,3,3-trifluoropropylphosphonic acid, a potential inhibitor of C-P bond cleavage after conversion into its 2-oxo derivative in the cell, was accessed from trifluoroacetaldehyde hydrate via hydroxypropanenitrile 21, which was silylated and reduced to the aldehyde (±)-23. Diastereoselective addition of diethyl trimethylsilyl phosphite furnished diastereomeric α-siloxyphosphonates. The less polar one was converted to the desired racemic phosphonic acid (±)-(1R*,2R*)-9 as its ammonium salt.
Collapse
Affiliation(s)
- K Pallitsch
- University of Vienna, Institute of Organic Chemistry, Währingerstrasse 38, 1090, Vienna, Austria.
| | | | | | | |
Collapse
|
31
|
Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
Collapse
Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
| |
Collapse
|
32
|
Freshwater bacteria release methane as a byproduct of phosphorus acquisition. Appl Environ Microbiol 2016; 82:6994-7003. [PMID: 27694233 DOI: 10.1128/aem.02399-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Freshwater lakes emit large amounts of methane, some of which is produced in oxic surface waters. Two potential pathways for aerobic methane production exist: methanogenesis in oxygenated water, which has been observed in some lakes, or demethylation of small organic molecules. Although methane is produced via demethylation in oxic marine environments, this mechanism of methane release has not yet been demonstrated in freshwater systems. Genes related to the C-P lyase pathway, which cleaves C-P bonds in phosphonate compounds, were found in a metagenomic survey of the surface water of Lake Matano, which is chronically P-starved and methane-rich. We demonstrate that four bacterial isolates from Lake Matano obtain P from methylphosphonate and release methane, and that this activity is repressed by phosphate. We further demonstrate that expression of phnJ, which encodes the enzyme that releases methane, is higher in the presence of methylphosphonate and lower when both methylphosphonate and phosphate are added. This gene is also found in most of the metagenomic data sets from freshwater environments. These experiments link methylphosphonate degradation and methane production with gene expression and phosphate availability in freshwater organisms, and suggest that some of the excess methane in the Lake Matano surface water, and in other methane-rich lakes, may be produced by P-starved bacteria. IMPORTANCE Methane is an important greenhouse gas, and contributes substantially to global warming. Although freshwater environments are known to release methane into the atmosphere, estimates of the amount of methane emitted by freshwater lakes vary from 8 to 73 Tg per year. Methane emissions are difficult to predict in part because the source of the methane can vary: it is the end product of the energy-conserving pathway in methanogenic archaea, which predominantly live in anoxic sediments or waters, but have also been identified in some oxic freshwater environments. More recently, methane release from small organic molecules has been observed in oxic marine environments. Here we show that demethylation of methylphosphonate may also contribute to methane release from lakes, and that phosphate can repress this activity. Since lakes are typically phosphorus-limited, some methane release in these environments may be a byproduct of phosphorus metabolism, rather than carbon or energy metabolism. Methane emissions from lakes are currently predicted using primary production, eutrophication status, extent of anoxia, and the shape and size of the lake; to improve prediction of methane emissions, phosphorus availability and sources may also need to be included in these models.
Collapse
|
33
|
Chin JP, McGrath JW, Quinn JP. Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling. Curr Opin Chem Biol 2016; 31:50-7. [DOI: 10.1016/j.cbpa.2016.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
|
34
|
Ren Z, Ranganathan S, Zinnel NF, Russell WK, Russell DH, Raushel FM. Subunit Interactions within the Carbon-Phosphorus Lyase Complex from Escherichia coli. Biochemistry 2015; 54:3400-11. [PMID: 25954983 DOI: 10.1021/acs.biochem.5b00194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphonates are a large class of organophosphorus compounds with a characteristic carbon-phosphorus bond. The genes responsible for phosphonate utilization in Gram-negative bacteria are arranged in an operon of 14 genes. The carbon-phosphorus lyase complex, encoded by the genes phnGHIJKLM, catalyzes the cleavage of the stable carbon-phosphorus bond of organophosphonates to the corresponding hydrocarbon and inorganic phosphate. Recently, complexes of this enzyme containing five subunits (PhnG-H-I-J-K), four subunits (PhnG-H-I-J), and two subunits (PhnG-I) were purified after expression in Escherichia coli ( Proc. Natl. Acad. Sci., U. S. A. 2011 , 108 , 11393 ). Here we demonstrated using mass spectrometry, ultracentrifugation, and chemical cross-linking experiments that these complexes are formed from a PhnG2I2 core that is further elaborated by the addition of two copies each of PhnH and PhnJ to generate PhnG2H2I2J2. This complex adds an additional subunit of PhnK to form PhnG2H2I2J2K. Chemical cross-linking of the five-component complex demonstrated that PhnJ physically interacts with both PhnG and PhnI. We were unable to demonstrate the interaction of PhnH or PhnK with any other subunits by chemical cross-linking. Hydrogen-deuterium exchange was utilized to probe for alterations in the dynamic properties of individual subunits within the various complexes. Significant regions of PhnG become less accessible to hydrogen/deuterium exchange from solvent within the PhnG2I2 complex compared with PhnG alone. Specific regions of PhnI exhibited significant differences in the H/D exchange rates in PhnG2I2 and PhnG2H2I2J2K.
Collapse
|
35
|
Rivas M, Casanovas J, del Valle LJ, Bertran O, Revilla-López G, Turon P, Puiggalí J, Alemán C. An experimental-computer modeling study of inorganic phosphates surface adsorption on hydroxyapatite particles. Dalton Trans 2015; 44:9980-91. [DOI: 10.1039/c5dt00209e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The adsorption of different phosphates and a triphosphonate onto hydroxyapatite has been highlighted combining experiments and theoretical calculations.
Collapse
Affiliation(s)
- Manuel Rivas
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Jordi Casanovas
- Departament de Química
- Escola Politècnica Superior
- Universitat de Lleida
- Lleida E-25001
- Spain
| | - Luis J. del Valle
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Oscar Bertran
- Departament de Física Aplicada
- EEI
- Universitat Politècnica de Catalunya
- 08700 Igualada
- Spain
| | - Guillermo Revilla-López
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Pau Turon
- B. Braun Surgical
- 08191 Rubí (Barcelona)
- Spain
| | - Jordi Puiggalí
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| |
Collapse
|
36
|
van Staalduinen LM, McSorley FR, Schiessl K, Séguin J, Wyatt PB, Hammerschmidt F, Zechel DL, Jia Z. Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates. Proc Natl Acad Sci U S A 2014; 111:5171-6. [PMID: 24706911 PMCID: PMC3986159 DOI: 10.1073/pnas.1320039111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enzymes PhnY and PhnZ comprise an oxidative catabolic pathway that enables marine bacteria to use 2-aminoethylphosphonic acid as a source of inorganic phosphate. PhnZ is notable for catalyzing the oxidative cleavage of a carbon-phosphorus bond using Fe(II) and dioxygen, despite belonging to a large family of hydrolytic enzymes, the HD-phosphohydrolase superfamily. We have determined high-resolution structures of PhnZ bound to its substrate, (R)-2-amino-1-hydroxyethylphosphonate (2.1 Å), and a buffer additive, l-tartrate (1.7 Å). The structures reveal PhnZ to have an active site containing two Fe ions coordinated by four histidines and two aspartates that is strikingly similar to the carbon-carbon bond cleaving enzyme, myo-inositol-oxygenase. The exception is Y24, which forms a transient ligand interaction at the dioxygen binding site of Fe2. Site-directed mutagenesis and kinetic analysis with substrate analogs revealed the roles of key active site residues. A fifth histidine that is conserved in the PhnZ subclade, H62, specifically interacts with the substrate 1-hydroxyl. The structures also revealed that Y24 and E27 mediate a unique induced-fit mechanism whereby E27 specifically recognizes the 2-amino group of the bound substrate and toggles the release of Y24 from the active site, thereby creating space for molecular oxygen to bind to Fe2. Structural comparisons of PhnZ reveal an evolutionary connection between Fe(II)-dependent hydrolysis of phosphate esters and oxidative carbon-phosphorus or carbon-carbon bond cleavage, thus uniting the diverse chemistries that are found in the HD superfamily.
Collapse
Affiliation(s)
- Laura M. van Staalduinen
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada K7L 3N6
| | - Fern R. McSorley
- Department of Chemistry, Queen’s University, Kingston, ON, Canada K7L 3N6
| | - Katharina Schiessl
- Institute of Organic Chemistry, University of Vienna, A-1090 Vienna, Austria; and
| | - Jacqueline Séguin
- Department of Chemistry, Queen’s University, Kingston, ON, Canada K7L 3N6
| | - Peter B. Wyatt
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | | | - David L. Zechel
- Department of Chemistry, Queen’s University, Kingston, ON, Canada K7L 3N6
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada K7L 3N6
| |
Collapse
|
37
|
Organophosphonate-degrading PhnZ reveals an emerging family of HD domain mixed-valent diiron oxygenases. Proc Natl Acad Sci U S A 2013; 110:18874-9. [PMID: 24198335 DOI: 10.1073/pnas.1315927110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The founding members of the HD-domain protein superfamily are phosphohydrolases, and newly discovered members are generally annotated as such. However, myo-inositol oxygenase (MIOX) exemplifies a second, very different function that has evolved within the common scaffold of this superfamily. A recently discovered HD protein, PhnZ, catalyzes conversion of 2-amino-1-hydroxyethylphosphonate to glycine and phosphate, culminating a bacterial pathway for the utilization of environmentally abundant 2-aminoethylphosphonate. Using Mössbauer and EPR spectroscopies, X-ray crystallography, and activity measurements, we show here that, like MIOX, PhnZ employs a mixed-valent Fe(II)/Fe(III) cofactor for the O2-dependent oxidative cleavage of its substrate. Phylogenetic analysis suggests that many more HD proteins may catalyze yet-unknown oxygenation reactions using this hitherto exceptional Fe(II)/Fe(III) cofactor. The results demonstrate that the catalytic repertoire of the HD superfamily extends well beyond phosphohydrolysis and suggest that the mechanism used by MIOX and PhnZ may be a common strategy for oxidative C-X bond cleavage.
Collapse
|
38
|
Kamat SS, Burgos ES, Raushel FM. Potent inhibition of the C-P lyase nucleosidase PhnI by Immucillin-A triphosphate. Biochemistry 2013; 52:7366-8. [PMID: 24111876 DOI: 10.1021/bi4013287] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The C-P lyase complex in bacteria catalyzes the transformation of phosphonates to orthophosphate under conditions of phosphate starvation. The first committed step in the C-P lyase-catalyzed reaction is the displacement of adenine from MgATP by phosphonate substrates, yielding ribose-1-phosphonate-5-triphosphate. In the C-P lyase complex, this reaction is catalyzed by the nucleosidase PhnI and modulated by the addition of PhnG, PhnH, and PhnL. Here we describe the synthesis of Immucillin-A triphosphate, a mimic of the transition state structure for the nucleosidase reaction catalyzed by PhnI. This compound inhibits PhnI with a dissociation constant of 20 nM at pH 7.5.
Collapse
Affiliation(s)
- Siddhesh S Kamat
- Department of Chemistry, Texas A&M University , College Station, Texas 77840, United States
| | | | | |
Collapse
|