1
|
Ruszczycky MW, Liu HW. Initiation, Propagation, and Termination in the Chemistry of Radical SAM Enzymes. Biochemistry 2024; 63:3161-3183. [PMID: 39626071 DOI: 10.1021/acs.biochem.4c00518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes catalyze radical mediated chemical transformations notable for their diversity. The radical mediated reactions that take place in their catalytic cycles can be characterized with respect to one or more phases of initiation, propagation, and termination. Mechanistic models abound regarding these three phases of catalysis being regularly informed and updated by new discoveries that offer insights into their detailed workings. However, questions continue to be raised that touch on fundamental aspects of their mechanistic enzymology. Radical SAM enzymes are consequently far from fully understood, and this Perspective aims to outline some of the current models of radical SAM chemistry with an emphasis on lines of investigation that remain to be explored.
Collapse
Affiliation(s)
- Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
2
|
Zepernick BN, Hart LN, Chase EE, Natwora KE, Obuya JA, Olokotum M, Houghton KA, Kiledal EA, Sheik CS, Sherman DH, Dick GJ, Wilhelm SW, Sitoki L, Otiso KM, McKay RML, Bullerjahn GS. Molecular investigation of harmful cyanobacteria reveals hidden risks and niche partitioning in Kenyan Lakes. HARMFUL ALGAE 2024; 140:102757. [PMID: 39613370 DOI: 10.1016/j.hal.2024.102757] [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: 08/29/2024] [Revised: 11/04/2024] [Accepted: 11/09/2024] [Indexed: 12/01/2024]
Abstract
Despite the global expansion of cyanobacterial harmful algal blooms (cHABs), research is biased to temperate systems within the global north, such as the Laurentian Great Lakes. This lack of diversity represents a significant gap in the field and jeopardizes the health of those who reside along at-risk watersheds in the global south. The African Great Lake, Lake Victoria, is understudied despite serving as the second largest lake by surface area and demonstrating year-round cHABs. Here, we address this knowledge gap by performing a molecular survey of cHAB communities in three anthropogenically and ecologically important freshwater systems of Victoria's Kenyan watershed: Winam Gulf (Lake Victoria), Lake Simbi and Lake Naivasha. We identified a bloom of non-toxic Dolichospermum and toxic Microcystis in the Winam Gulf, with data suggesting sulfur limitation shapes competition dynamics between these two bloom-formers. Though we did not detect a bloom in Naivasha, it contained the largest diversity of cHAB genera amongst the three lakes. In turn, our results indicated methane metabolism may allow non-toxic picoplankton to outcompete cHAB genera, while suggesting Synechococcus spp. serves as a methane source and sink in this system. Lake Simbi exhibited a non-toxic Limnospira bloom at the time of sampling with very low abundances of cHAB genera present. Subsequently, these results were employed to design a cHAB screening and risk assessment framework for local stakeholders. Cumulatively, this work serves to increase cHAB research efforts on the international scale while serving as an impetus for cHAB monitoring on the local scale.
Collapse
Affiliation(s)
- Brittany N Zepernick
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA; NSF-IRES 2022 Lake Victoria Research Consortium, USA
| | - Lauren N Hart
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA; Life Sciences Institute, University of Michigan, MI, USA
| | - Emily E Chase
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Kaela E Natwora
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, USA
| | - Julia A Obuya
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; Kenya Marine and Fisheries Research Institute, Kisumu, Kenya
| | - Mark Olokotum
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; National Fisheries Resources Research Institute (NaFIRRI), Jinja, Uganda
| | - Katelyn A Houghton
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - E Anders Kiledal
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Cody S Sheik
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, USA
| | | | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, USA; Great Lakes Center for Fresh Waters and Human Health, Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA; Great Lakes Center for Fresh Waters and Human Health, Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Lewis Sitoki
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; Technical University of Kenya, Nairobi, Kenya
| | - Kefa M Otiso
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; School of Earth, Environment and Society, Bowling Green State University, Bowling Green, Ohio, USA
| | - R Michael L McKay
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; Great Lakes Center for Fresh Waters and Human Health, Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA; Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, CA
| | - George S Bullerjahn
- NSF-IRES 2022 Lake Victoria Research Consortium, USA; Great Lakes Center for Fresh Waters and Human Health, Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA; Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA.
| |
Collapse
|
3
|
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
|
4
|
Riedel R, Meißner K, Kaschubowski A, Benndorf D, Martienssen M, Braun B. Laundry Isolate Delftia sp. UBM14 Capable of Biodegrading Industrially Relevant Aminophosphonates. Microorganisms 2024; 12:1664. [PMID: 39203506 PMCID: PMC11356716 DOI: 10.3390/microorganisms12081664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
Phosphonates such as ethylenediaminetetra (methylenephosphonic acid) (EDTMP) and aminotris (methylenephosphonic acid) (ATMP) are used every day in water treatment processes or in household products. Their consumption is still increasing, regardless of the debates on their environmental impact. Here, the microbial characterisation and determination of the biodegradation potential of selected industrially relevant phosphonates for the isolate Delftia sp. UMB14 is reported. The opportunistic strain was isolated from a biofilm that was derived from a conventional washing machine using conventional detergents containing phosphonates. In antimicrobial susceptibility testing, the strain was only susceptible to sulfonamide, tetracycline, and chloramphenicol. Physiological and biochemical characteristics were determined using the BIOLOG EcoPlate assay. Most importantly, the strain was shown to convert D-malic acid and D-mannitol, as confirmed for strains of Delftia lacustris, and thus the new isolate could be closely related. Biodegradation tests with different phosphonates showed that the strain preferentially degrades ATMP and EDTMP but does not degrade glyphosate (GS) and amino (methylphosphonic acid) (AMPA). A specific gene amplification confirmed the presence of phnX (phosphonoacetaldehyde hydrolase) and the absence of PhnJ (the gene for the core component of C-P lyase). The presence of PhnCDE is strongly suggested for the strain, as it is common in Delftia lacustris species.
Collapse
Affiliation(s)
- Ramona Riedel
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Science and Environmental Technology, BTU Cottbus-Senftenberg, 03046 Cottbus, Germany;
| | - Karsten Meißner
- German Environment Agency (UBA), Section II 3.3, 14195 Berlin, Germany;
- Department of Environmental Microbiomics, University of Technology Berlin, 10587 Berlin, Germany; (A.K.); (B.B.)
| | - Arne Kaschubowski
- Department of Environmental Microbiomics, University of Technology Berlin, 10587 Berlin, Germany; (A.K.); (B.B.)
| | - Dirk Benndorf
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, 06366 Köthen, Germany;
- Chair of Bioprocess Engineering, Otto von Guericke University, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Marion Martienssen
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Science and Environmental Technology, BTU Cottbus-Senftenberg, 03046 Cottbus, Germany;
| | - Burga Braun
- Department of Environmental Microbiomics, University of Technology Berlin, 10587 Berlin, Germany; (A.K.); (B.B.)
| |
Collapse
|
5
|
Zou C, Yi X, Li H, Bizic M, Berman-Frank I, Gao K. Correlation of methane production with physiological traits in Trichodesmium IMS 101 grown with methylphosphonate at different temperatures. Front Microbiol 2024; 15:1396369. [PMID: 38894967 PMCID: PMC11184136 DOI: 10.3389/fmicb.2024.1396369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The diazotrophic cyanobacterium Trichodesmium has been recognized as a potentially significant contributor to aerobic methane generation via several mechanisms including the utilization of methylphophonate (MPn) as a source of phosphorus. Currently, there is no information about how environmental factors regulate methane production by Trichodesmium. Here, we grew Trichodesmium IMS101 at five temperatures ranging from 16 to 31°C, and found that its methane production rates increased with rising temperatures to peak (1.028 ± 0.040 nmol CH4 μmol POC-1 day-1) at 27°C, and then declined. Its specific growth rate changed from 0.03 ± 0.01 d-1 to 0.34 ± 0.02 d-1, with the optimal growth temperature identified between 27 and 31°C. Within the tested temperature range the Q10 for the methane production rate was 4.6 ± 0.7, indicating a high sensitivity to thermal changes. In parallel, the methane production rates showed robust positive correlations with the assimilation rates of carbon, nitrogen, and phosphorus, resulting in the methane production quotients (molar ratio of carbon, nitrogen, or phosphorus assimilated to methane produced) of 227-494 for carbon, 40-128 for nitrogen, and 1.8-3.4 for phosphorus within the tested temperature range. Based on the experimental data, we estimated that the methane released from Trichodesmium can offset about 1% of its CO2 mitigation effects.
Collapse
Affiliation(s)
- Chuze Zou
- State Key Laboratory of Marine Environmental Science, College of the Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiangqi Yi
- Polar and Marine Research Institute, College of Harbor and Coastal Engineering, Jimei University, Xiamen, China
| | - He Li
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Mina Bizic
- Department of Environmental Microbiomics, Institute of Environmental Technology, Technical University of Berlin, Berlin, Germany
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science, College of the Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| |
Collapse
|
6
|
von Arx JN, Kidane AT, Philippi M, Mohr W, Lavik G, Schorn S, Kuypers MMM, Milucka J. Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic. Nat Commun 2023; 14:6529. [PMID: 37845220 PMCID: PMC10579326 DOI: 10.1038/s41467-023-42304-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.
Collapse
Affiliation(s)
- Jan N von Arx
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Miriam Philippi
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| |
Collapse
|
7
|
Ruffolo F, Dinhof T, Murray L, Zangelmi E, Chin JP, Pallitsch K, Peracchi A. The Microbial Degradation of Natural and Anthropogenic Phosphonates. Molecules 2023; 28:6863. [PMID: 37836707 PMCID: PMC10574752 DOI: 10.3390/molecules28196863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They are environmentally ubiquitous: some of them are produced by microorganisms and invertebrates, whereas others derive from anthropogenic activities. Because of their chemical stability and potential toxicity, man-made phosphonates pose pollution problems, and many studies have tried to identify biocompatible systems for their elimination. On the other hand, phosphonates are a resource for microorganisms living in environments where the availability of phosphate is limited; thus, bacteria in particular have evolved systems to uptake and catabolize phosphonates. Such systems can be either selective for a narrow subset of compounds or show a broader specificity. The role, distribution, and evolution of microbial genes and enzymes dedicated to phosphonate degradation, as well as their regulation, have been the subjects of substantial studies. At least three enzyme systems have been identified so far, schematically distinguished based on the mechanism by which the C-P bond is ultimately cleaved-i.e., through either a hydrolytic, radical, or oxidative reaction. This review summarizes our current understanding of the molecular systems and pathways that serve to catabolize phosphonates, as well as the regulatory mechanisms that govern their activity.
Collapse
Affiliation(s)
- Francesca Ruffolo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
| | - Tamara Dinhof
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Vienna, Austria;
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, A-1090 Vienna, Austria
| | - Leanne Murray
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
| | - Jason P. Chin
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Katharina Pallitsch
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Vienna, Austria;
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
| |
Collapse
|
8
|
Zhao L, Lin LZ, Zeng Y, Teng WK, Chen MY, Brand JJ, Zheng LL, Gan NQ, Gong YH, Li XY, Lv J, Chen T, Han BP, Song LR, Shu WS. The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance. MICROBIOME 2023; 11:142. [PMID: 37365664 DOI: 10.1186/s40168-023-01582-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria are often the dominant primary producers in freshwaters; yet, only a few strains of cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere is defined as the microenvironment in which extensive phytoplankton and heterotrophic bacteria interactions occur. It has been demonstrated that phytoplankton may recruit phycospheric bacteria based on their own needs. Therefore, the establishment of a phycospheric community rich in phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially in waters with scarce phosphorus. We characterized the distribution of heterotrophic phosphonate-degrading bacteria in field Microcystis bloom samples and in laboratory cyanobacteria "phycospheres" by qPCR and metagenomic analyses. The role of phosphonate-degrading phycospheric bacteria in cyanobacterial proliferation was determined through coculturing of heterotrophic bacteria with an axenic Microcystis aeruginosa strain and by metatranscriptomic analysis using field Microcystis aggregate samples. RESULTS Abundant bacteria that carry C-P lyase clusters were identified in plankton samples from freshwater Lakes Dianchi and Taihu during Microcystis bloom periods. Metagenomic analysis of 162 non-axenic laboratory strains of cyanobacteria (consortia cultures containing heterotrophic bacteria) showed that 20% (128/647) of high-quality bins from eighty of these consortia encode intact C-P lyase clusters, with an abundance ranging up to nearly 13%. Phycospheric bacterial phosphonate catabolism genes were expressed continually across bloom seasons, as demonstrated through metatranscriptomic analysis using sixteen field Microcystis aggregate samples. Coculturing experiments revealed that although Microcystis cultures did not catabolize methylphosphonate when axenic, they demonstrated sustained growth when cocultured with phosphonate-utilizing phycospheric bacteria in medium containing methylphosphonate as the sole source of phosphorus. CONCLUSIONS The recruitment of heterotrophic phosphonate-degrading phycospheric bacteria by cyanobacteria is a hedge against phosphorus scarcity by facilitating phosphonate availability. Cyanobacterial consortia are likely primary contributors to aquatic phosphonate mineralization, thereby facilitating sustained cyanobacterial growth, and even bloom maintenance, in phosphate-deficient waters. Video Abstract.
Collapse
Affiliation(s)
- Liang Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Li-Zhou Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ying Zeng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Wen-Kai Teng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Meng-Yun Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jerry J Brand
- Department of Molecular Biosciences and the Culture Collection of Algae, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ling-Ling Zheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
- National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Nan-Qin Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China
| | - Yong-Hui Gong
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Xin-Yi Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jin Lv
- Analysis and Testing Center, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Ting Chen
- Institute for Artificial Intelligence and Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510632, People's Republic of China.
| | - Li-Rong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People's Republic of China.
- National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China.
| | - Wen-Sheng Shu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
- Guangdong Magigene Biotechnology Co., Ltd., Shenzhen, 518081, People's Republic of China.
| |
Collapse
|
9
|
Amstrup SK, Ong SC, Sofos N, Karlsen JL, Skjerning RB, Boesen T, Enghild JJ, Hove-Jensen B, Brodersen DE. Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase. Nat Commun 2023; 14:1001. [PMID: 36813778 PMCID: PMC9947105 DOI: 10.1038/s41467-023-36604-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part of a complex, multi-step pathway, the PhnJ subunit was shown to cleave the C-P bond via a radical mechanism, however, the details of the reaction could not immediately be reconciled with the crystal structure of a 220 kDa PhnGHIJ C-P lyase core complex, leaving a significant gap in our understanding of phosphonate breakdown in bacteria. Here, we show using single-particle cryogenic electron microscopy that PhnJ mediates binding of a double dimer of the ATP-binding cassette proteins, PhnK and PhnL, to the core complex. ATP hydrolysis induces drastic structural remodelling leading to opening of the core complex and reconfiguration of a metal-binding and putative active site located at the interface between the PhnI and PhnJ subunits.
Collapse
Affiliation(s)
- Søren K Amstrup
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Sui Ching Ong
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Nicholas Sofos
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Jesper L Karlsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Ragnhild B Skjerning
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Centre (iNANO) Aarhus University, Gustav Wieds Vej 14, DK-8000, Aarhus C, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Bjarne Hove-Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.
| |
Collapse
|
10
|
Li J, Liu H, Liu Z, Zhang X, Blake RE, Huang Z, Cai M, Wang F, Yu C. Transformation mechanism of methylphosphonate to methane by Burkholderia sp: Insight from multi-labeled water isotope probing and transcriptomic. ENVIRONMENTAL RESEARCH 2023; 218:114970. [PMID: 36470350 DOI: 10.1016/j.envres.2022.114970] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Methylphosphonate (MPn), has been identified as a likely source of methane in aerobic ocean and may be responsible for the "ocean methane paradox", that is oversaturation of dissolved methane in oxic sea waters. However, the mechanism underlying the cleavage of C-P bonds during microbial degradation is not well understood. Using multi-labeled water isotope probing (MLWIP) and transcriptome analysis, we investigated the phosphate oxygen isotope systematics and mechanisms of microbial-mediated degradation of MPn in this study. In the aerobic culture containing MPn as the only phosphorus source, there was a significant release of inorganic phosphate (149.4 μmol/L) and free methane (268.3 mg/L). The oxygen isotopic composition of inorganic phosphorus (δ18OP) of accumulated released phosphate was 4.50‰, 23.96‰, and 40.88‰, respectively, in the corresponding 18O-labeled waters of -10.3‰, 9.9‰, and 30.6‰, and the slope obtained in plots of δ18OP versus the oxygen isotopic composition of water (δ18OW) was 0.89. Consequently, 89% of the oxygen atoms (Os) in phosphate (PO4) were exchanged with 18O-labeled waters in the medium, while the rest were exchanged with intracellular metabolic water. It has been confirmed that the C-P bond cleavage of MPn occurs in the cell with both ambient and metabolic water participation. Moreover, phn gene clusters play significant roles to cleave the C-P bond of MPn for Burkholderia sp. HQL1813, in which phnJ, phnM and phnI genes are significantly up-regulated during MPn decomposition to methane. In conclusion, the aerobic biotransformation of MPn to free methane by Burkholderia sp. HQL1813 has been elucidated, providing new insights into the mechanism that bio-cleaves C-P bonds to produce methane aerobically in aqueous environments for representative phosphonates.
Collapse
Affiliation(s)
- Junhong Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Houquan Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Zeqin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Ruth Elaine Blake
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, 06520-8109, USA
| | - Zhiyong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, 300308, Tianjin, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Centre of Microbial Pesticides, Huazhong Agricultural University, 430070, Wuhan, China
| | - Fei Wang
- School of Environment, Beijing Normal University, 19 Xinjiekouwai, Haidian District, 100875, Beijing, China.
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China.
| |
Collapse
|
11
|
Li J, Yu C, Liu Z, Wang Y, Wang F. Microplastic accelerate the phosphorus-related metabolism of bacteria to promote the decomposition of methylphosphonate to methane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160020. [PMID: 36356736 DOI: 10.1016/j.scitotenv.2022.160020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) contaminants in marine water have become a global public health concern because of their persistence and potentially adverse effects on organisms. MP can affect the growth and metabolism of marine microorganisms and further impact the microbial environmental functions. The molecular impact mechanisms of MP on specific functional microbes with the capability of decomposing methylphosphonate (MPn) to release methane (CH4) in oxygenated water have rarely been reported upon. Herein, we investigated the effects of MP on microbes and concomitant methanogenesis via the microbial degradation of MPn. Furthermore, the specific perturbation was revealed at the molecular level combined with transcriptomics and metabolomics. The results showed that intracellular phosphorus utilization by MPn-degrading strain Burkholderia sp. HQL1813 was enhanced by accelerating the catabolism of MPn. Phosphorus transport-related genes (phnG-M, pstSCAB, phnCDE) were upregulated in the MP exposure groups. Amino acid metabolism, the phosphotransferase system and nucleotide metabolism were also perturbed after MP exposure. Notably, released CH4 increased by 24 %, 29 % and 14 % in the exposure group. In addition, the responses of the strain were dose-independent with increasing MP doses. These findings are beneficial for clarifying the effect of MP on specific functional microbes at the molecular level and their degradation of CH4 by MPn.
Collapse
Affiliation(s)
- Junhong Li
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, 100083 Beijing, China; School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, 100875 Beijing, China
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062 Wuhan, China
| | - Zeqin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062 Wuhan, China
| | - Yan Wang
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, 100083 Beijing, China
| | - Fei Wang
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, 100875 Beijing, China.
| |
Collapse
|
12
|
Jiang Y, Wang Z, Liu Y, Han Y, Wang Y, Wang Q, Liu T. Nematodes and their bacterial prey improve phosphorus acquisition by wheat. THE NEW PHYTOLOGIST 2023; 237:974-986. [PMID: 36285379 DOI: 10.1111/nph.18569] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Plant growth is greatly influenced by the rhizosphere microbiome, which has been traditionally investigated from a bottom-up perspective assessing how resources such as root exudates stimulate microbial growth and drive microbiome assembly. However, the importance of predation as top-down force on the soil microbiome remains largely underestimated. Here, we planted wheat both in natural and in sterilized soils inoculated with the key microbiome predators - bacterivorous nematodes - to assess how plant performance responds to top-down predation of the soil microbiome and specific plant growth-promoting bacteria, namely phosphate-solubilizing bacteria. We found that nematodes enriched certain groups (e.g. Actinobacteria, Chloroflexi, and Firmicutes) and strengthened microbial connectance (e.g. Actinobacteria and Proteobacteria). These changes in microbiome structure were associated with phosphate-solubilizing bacteria that facilitated phosphorus (P) cycling, leading to greater P uptake and biomass of wheat in both soils. However, the enhancement varied between nematode species, which may be attributed to the divergence of feeding behavior, as nematodes with weaker grazing intensity supported greater abundance of phosphate-solubilizing bacteria and better plant performance compared with nematodes with greater grazing intensity. These results confirmed the ecological importance of soil nematodes for ecosystem functions via microbial co-occurrence networks and suggested that the predation strength of nematodes determines the soil bacteria contribution to P biogeochemical cycling and plant growth.
Collapse
Affiliation(s)
- Ying Jiang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhonghua Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ye Liu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yanlai Han
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yi Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiang Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ting Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
13
|
Mo S, He S, Sang Y, Li J, Kashif M, Zhang Z, Su G, Jiang C. Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion. MICROBIAL ECOLOGY 2023; 85:478-494. [PMID: 35157108 DOI: 10.1007/s00248-022-01979-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.
Collapse
Affiliation(s)
- Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Sheng He
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defect prevention, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, 530033, China
| | - Yimeng Sang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jinhui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Muhammad Kashif
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Zufan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Guijiao Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
| |
Collapse
|
14
|
Nano Ag/Co 3O 4 Catalyzed Rapid Decomposition of Robinia pseudoacacia Bark for Production Biofuels and Biochemicals. Polymers (Basel) 2022; 15:polym15010114. [PMID: 36616464 PMCID: PMC9824563 DOI: 10.3390/polym15010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/12/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022] Open
Abstract
Biomass energy has attracted widespread attention due to its renewable, storage, huge production and clean and pollution-free advantages. Using Robinia pseudoacacia bark (RPB) as raw material, biogas and bio-oil produced by pyrolysis of RPB were detected and analyzed by TG-DTG, TG-FTIR and PY-GC-MS under the action of nanocatalysis. TG results showed that CH4 and CO flammable gases were produced by pyrolysis. PY-GC-MS results showed that RPB was rapidly pyrolyzed to obtain alcohols, ketones, aldehydes and acids bio-oil. The content of phenolic substances was the highest, accounting for 32.18% of all substances.Nanocatalysis has a certain effect on RPB, accelerating the precipitation of pyrolysis products and improving the over-oxidation of bio-oil. In addition, the extracts of RPB were identified and analyzed by FTIR, NMR, GC-MS and LC-Q-TOF-MS, and more than 100 active ingredients, such as Betaine, Epicathin and β-sitosterol, were detected. Their applications as additive energy in other fields were explored. Therefore, Robinia pseudoacacia bark constitutes a fine biofeedstock for biofuels and biochemicals.
Collapse
|
15
|
Mao SH, Zhang HH, Zhuang GC, Li XJ, Liu Q, Zhou Z, Wang WL, Li CY, Lu KY, Liu XT, Montgomery A, Joye SB, Zhang YZ, Yang GP. Aerobic oxidation of methane significantly reduces global diffusive methane emissions from shallow marine waters. Nat Commun 2022; 13:7309. [PMID: 36437260 PMCID: PMC9701681 DOI: 10.1038/s41467-022-35082-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/18/2022] [Indexed: 11/28/2022] Open
Abstract
Methane is supersaturated in surface seawater and shallow coastal waters dominate global ocean methane emissions to the atmosphere. Aerobic methane oxidation (MOx) can reduce atmospheric evasion, but the magnitude and control of MOx remain poorly understood. Here we investigate methane sources and fates in the East China Sea and map global MOx rates in shallow waters by training machine-learning models. We show methane is produced during methylphosphonate decomposition under phosphate-limiting conditions and sedimentary release is also source of methane. High MOx rates observed in these productive coastal waters are correlated with methanotrophic activity and biomass. By merging the measured MOx rates with methane concentrations and other variables from a global database, we predict MOx rates and estimate that half of methane, amounting to 1.8 ± 2.7 Tg, is consumed annually in near-shore waters (<50 m), suggesting that aerobic methanotrophy is an important sink that significantly constrains global methane emissions.
Collapse
Affiliation(s)
- Shi-Hai Mao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Hong-Hai Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Guang-Chao Zhuang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Xiao-Jun Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Qiao Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Zhen Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Wei-Lei Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Chun-Yang Li
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China
| | - Ke-Yu Lu
- Department of Earth Sciences, University College London, London, WC1E 6BS, UK
| | - Xi-Ting Liu
- College of Marine Geosciences, Ocean University of China, Qingdao, 266100, China
| | - Andrew Montgomery
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Gui-Peng Yang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China.
| |
Collapse
|
16
|
Qiu L, Cooks RG. Simultaneous and Spontaneous Oxidation and Reduction in Microdroplets by the Water Radical Cation/Anion Pair. Angew Chem Int Ed Engl 2022; 61:e202210765. [PMID: 35994573 PMCID: PMC9825976 DOI: 10.1002/anie.202210765] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Indexed: 01/11/2023]
Abstract
Microdroplets show unique chemistry, especially in their intrinsic redox properties, and to this we here add a case of simultaneous and spontaneous oxidation and reduction. We report the concurrent conversions of several phosphonates to phosphonic acids by reduction (R-P → H-P) and to pentavalent phosphoric acids by oxidation. The experimental results suggest that the active reagent is the water radical cation/anion pair. The water radical cation is observed directly as the ionized water dimer while the water radical anion is only seen indirectly though the spontaneous reduction of carbon dioxide to formate. The coexistence of oxidative and reductive species in turn supports the proposal of a double-layer structure at the microdroplet surface, where the water radical cation and radical anion are separated and accumulated.
Collapse
Affiliation(s)
- Lingqi Qiu
- Department of ChemistryPurdue University560 Oval. Dr.West LafayetteIN 47907USA
| | - R. Graham Cooks
- Department of ChemistryPurdue University560 Oval. Dr.West LafayetteIN 47907USA
| |
Collapse
|
17
|
Lockwood S, Greening C, Baltar F, Morales SE. Global and seasonal variation of marine phosphonate metabolism. THE ISME JOURNAL 2022; 16:2198-2212. [PMID: 35739297 PMCID: PMC9381506 DOI: 10.1038/s41396-022-01266-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/17/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022]
Abstract
Marine microbial communities rely on dissolved organic phosphorus (DOP) remineralisation to meet phosphorus (P) requirements. We extensively surveyed the genomic and metagenomic distribution of genes directing phosphonate biosynthesis, substrate-specific catabolism of 2-aminoethylphosphonate (2-AEP, the most abundant phosphonate in the marine environment), and broad-specificity catabolism of phosphonates by the C-P lyase (including methylphosphonate, a major source of methane). We developed comprehensive enzyme databases by curating publicly available sequences and then screened metagenomes from TARA Oceans and Munida Microbial Observatory Time Series (MOTS) to assess spatial and seasonal variation in phosphonate metabolism pathways. Phosphonate cycling genes were encoded in diverse gene clusters by 35 marine bacterial and archaeal classes. More than 65% of marine phosphonate cycling genes mapped to Proteobacteria with production demonstrating wider taxonomic diversity than catabolism. Hydrolysis of 2-AEP was the dominant phosphonate catabolism strategy, enabling microbes to assimilate carbon and nitrogen alongside P. Genes for broad-specificity catabolism by the C-P lyase were far less widespread, though enriched in the extremely P-deplete environment of the Mediterranean Sea. Phosphonate cycling genes were abundant in marine metagenomes, particularly from the mesopelagic zone and winter sampling dates. Disparity between prevalence of substrate-specific and broad-specificity catabolism may be due to higher resource expenditure from the cell to build and retain the C-P lyase. This study is the most comprehensive metagenomic survey of marine microbial phosphonate cycling to date and provides curated databases for 14 genes involved in phosphonate cycling.
Collapse
Affiliation(s)
- Scott Lockwood
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Federico Baltar
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
| |
Collapse
|
18
|
Qiu L, Cooks RG. Simultaneous and Spontaneous Oxidation and Reduction in Microdroplets by the Water Radical Cation/Anion Pair. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lingqi Qiu
- Purdue University Chemistry UNITED STATES
| | - R Graham Cooks
- Purdue University Chemistry 560 Oval Drive 47907 West Lafayette UNITED STATES
| |
Collapse
|
19
|
Clark KA, Bushin LB, Seyedsayamdost MR. RaS-RiPPs in Streptococci and the Human Microbiome. ACS BIO & MED CHEM AU 2022; 2:328-339. [PMID: 35996476 PMCID: PMC9389541 DOI: 10.1021/acsbiomedchemau.2c00004] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Radical S-adenosylmethionine (RaS) enzymes have
quickly advanced to one of the most abundant and versatile enzyme
superfamilies known. Their chemistry is predicated upon reductive
homolytic cleavage of a carbon–sulfur bond in cofactor S-adenosylmethionine forming an oxidizing carbon-based radical,
which can initiate myriad radical transformations. An emerging role
for RaS enzymes is their involvement in the biosynthesis of ribosomally
synthesized and post-translationally modified peptides (RiPPs), a
natural product family that has become known as RaS-RiPPs. These metabolites
are especially prevalent in human and mammalian microbiomes because
the complex chemistry of RaS enzymes gives rise to correspondingly
complex natural products with minimal cellular energy and genomic
fingerprint, a feature that is advantageous in microbes with small,
host-adapted genomes in competitive environments. Herein, we review
the discovery and characterization of RaS-RiPPs from the human microbiome
with a focus on streptococcal bacteria. We discuss the varied chemical
modifications that RaS enzymes introduce onto their peptide substrates
and the diverse natural products that they give rise to. The majority
of RaS-RiPPs remain to be discovered, providing an intriguing avenue
for future investigations at the intersection of metalloenzymology,
chemical ecology, and the human microbiome.
Collapse
Affiliation(s)
- Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
20
|
Zhao L, Lin LZ, Chen MY, Teng WK, Zheng LL, Peng L, Lv J, Brand JJ, Hu CX, Han BP, Song LR, Shu WS. The widespread capability of methylphosphonate utilization in filamentous cyanobacteria and its ecological significance. WATER RESEARCH 2022; 217:118385. [PMID: 35405550 DOI: 10.1016/j.watres.2022.118385] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Aquatic ecosystems comprise almost half of total global methane emissions. Recent evidence indicates that a few strains of cyanobacteria, the predominant primary producers in bodies of water, can produce methane under oxic conditions with methylphosphonate serving as substrate. In this work, we have screened the published 2 568 cyanobacterial genomes for genetic elements encoding phosphonate-metabolizing enzymes. We show that phosphonate degradation (phn) gene clusters are widely distributed in filamentous cyanobacteria, including several bloom-forming genera. Algal growth experiments revealed that methylphosphonate is an alternative phosphorous source for four of five tested strains carrying phn clusters, and can sustain cellular metabolic homeostasis of strains under phosphorus stress. Liberation of methane by cyanobacteria in the presence of methylphosphonate occurred mostly during the light period of a 12 h/12 h diurnal cycle and was suppressed in the presence of orthophosphate, features that are consistent with observations in natural aquatic systems under oxic conditions. The results presented here demonstrate a genetic basis for ubiquitous methane emission via cyanobacterial methylphosphonate mineralization, while contributing to the phosphorus redox cycle.
Collapse
Affiliation(s)
- Liang Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, China
| | - Li-Zhou Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Meng-Yun Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wen-Kai Teng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ling-Ling Zheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, China
| | - Liang Peng
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Jin Lv
- Analysis and Testing Center, South China Normal University, Guangzhou 510631, China
| | - Jerry J Brand
- Department of Molecular Biosciences and the Culture Collection of Algae, University of Texas at Austin, Austin TX 78712, United States
| | - Chun-Xiang Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China.
| | - Li-Rong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan 430072, China.
| | - Wen-Sheng Shu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| |
Collapse
|
21
|
Abstract
Nematode predation plays an essential role in determining changes in the rhizosphere microbiome. These changes affect the local nutrient balance and cycling of essential nutrients by selectively structuring interactions across functional taxa in the system. Currently, it is largely unknown to what extent nematode predation induces shifts in the microbiome associated with different rates of soil phosphorous (P) mineralization. Here, we performed an 7-year field experiment to investigate the importance of nematode predation influencing P availability and cycling. These were tracked via the changes in the alkaline phosphomonoesterase (ALP)-producing bacterial community and ALP activity in the rhizosphere of rapeseed. Here, we found that the nematode addition led to high predation pressure and thereby caused shifts in the abundance and composition of the ALP-producing bacterial community. Further analyses based on cooccurrence networks and metabolomics consistently showed that nematode addition induced competitive interactions between potentially keystone ALP-producing bacteria and other members within the community. Structural equation modeling revealed that the outcome of this competition induced by stronger predation pressure of nematodes was significantly associated with higher diversity of ALP-producing bacteria, thereby enhancing ALP activity and P availability. Taken together, our results provide evidence for the importance of predator-prey and competitive interactions in soil biology and their direct influences on nutrient cycling dynamics.
Collapse
|
22
|
Liu LY, Xie GJ, Ding J, Liu BF, Xing DF, Ren NQ, Wang Q. Microbial methane emissions from the non-methanogenesis processes: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151362. [PMID: 34740653 DOI: 10.1016/j.scitotenv.2021.151362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Methane, a potent greenhouse gas of global importance, has traditionally been considered as an end product of microbial methanogenesis of organic matter. Paradoxically, growing evidence has shown that some microbes, such as cyanobacteria, algae, fungi, purple non-sulfur bacteria, and cryptogamic covers, produce methane in oxygen-saturated aquatic and terrestrial ecosystems. The non-methanogenesis process could be an important potential contributor to methane emissions. This systematic review summarizes the knowledge of microorganisms involved in the non-methanogenesis process and the possible mechanisms of methane formation. Cyanobacteria-derived methane production may be attributed to either demethylation of methyl phosphonates or linked to light-driven primary productivity, while algae produce methane by utilizing methylated sulfur compounds as possible carbon precursors. In addition, fungi produce methane by utilizing methionine as a possible carbon precursor, and purple non-sulfur bacteria reduce carbon dioxide to methane by nitrogenase. The microbial methane distribution from the non-methanogenesis processes in aquatic and terrestrial environments and its environmental significance to global methane emissions, possible mechanisms of methane production in each open water, water-to-air methane fluxes, and the impact of climate change on microorganisms are also discussed. Finally, future perspectives are highlighted, such as establishing more in-situ experiments, quantifying methane flux through optimizing empirical models, distinguishing individual methane sources, and investigating nitrogenase-like enzyme systems to improve our understanding of microbial methane emission from the non-methanogenesis process.
Collapse
Affiliation(s)
- Lu-Yao Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| |
Collapse
|
23
|
Han C, Ren J, Wang B, Wang Z, Yin H, Ke F, Xu D, Zhang L, Si X, Shen Q. Ignored effects of phosphite (P +III) on the growth responses of three typical algae species. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118672. [PMID: 34896401 DOI: 10.1016/j.envpol.2021.118672] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/14/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Nowadays, the ubiquitous distribution and increasing abundance of P+III in waterbodies have caused serious concerns regarding its bioavailability and potential toxicity. However, our knowledge on these issues is relatively limited. We addressed previously unknown effects of P+III on three dominate algae species i.e. Microcystic aeruginosa (M. aeruginosa), Chlorella pyrenoidesa (C. pyrenoidesa) and Cyclotella. sp in eutrophic waterbodies in China. Remarkable declines in biomass, specific growth rate and Chl-a of algae cells treated with 0.01-0.7 mg/L P+III as sole or an alternative P source were observed, indicating P+III had an inhibitory effect on the algal growth. Besides, the intracellular enzyme activities e.g superoxide dismutase (SOD) and malondialdehyde (MDA) were significantly increased with P+III stress. M. aeruginosa and Cyclotella. sp cells seemed to be more sensitive to P+III toxicity than C. pyrenoidesa since cell membrane suffered more serious stress and destruction. These findings combined, it confirmed P+III could not be utilized as bioavailable P, but had certain toxicity to the tested algae. It indicated that the increased P+III abundance in eutrophic waterbodies would accelerate the algal cell death, which could have a positive effect against algal blooms. Our results provide new insights into assessing the ecological risks of P+III in aquatic environments.
Collapse
Affiliation(s)
- Chao Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Jinghua Ren
- Technology Innovation Center for Ecological Monitoring & Restoration Project on Land (arable), Ministry of Natural Resources, Geological Survey of Jiangsu Province, Nanjing, 210018, China
| | - Baoying Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China
| | - Zhaode Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Hongbin Yin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fan Ke
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Di Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Lei Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiaoxia Si
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China
| | - Qiushi Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, PR China
| |
Collapse
|
24
|
Bueno de Mesquita CP, Zhou J, Theroux S, Tringe SG. Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns. Genes (Basel) 2022; 13:genes13010148. [PMID: 35052488 PMCID: PMC8774927 DOI: 10.3390/genes13010148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/30/2022] Open
Abstract
Aerobic bacteria that degrade methylphosphonates and produce methane as a byproduct have emerged as key players in marine carbon and phosphorus cycles. Here, we present two new draft genome sequences of the genus Marivita that were assembled from metagenomes from hypersaline former industrial salterns and compare them to five other Marivita reference genomes. Phylogenetic analyses suggest that both of these metagenome-assembled genomes (MAGs) represent new species in the genus. Average nucleotide identities to the closest taxon were <85%. The MAGs were assembled with SPAdes, binned with MetaBAT, and curated with scaffold extension and reassembly. Both genomes contained the phnCDEGHIJLMP suite of genes encoding the full C-P lyase pathway of methylphosphonate degradation and were significantly more abundant in two former industrial salterns than in nearby reference and restored wetlands, which have lower salinity levels and lower methane emissions than the salterns. These organisms contain a variety of compatible solute biosynthesis and transporter genes to cope with high salinity levels but harbor only slightly acidic proteomes (mean isoelectric point of 6.48).
Collapse
Affiliation(s)
- Clifton P. Bueno de Mesquita
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
| | - Jinglie Zhou
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
| | - Susanna Theroux
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA;
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence:
| |
Collapse
|
25
|
He R, Ding C, Luo Y, Guo G, Tang J, Shen H, Wang Q, Zhang X. Congener-Induced Sulfur-Related Metabolism Interference Therapy Promoted by Photothermal Sensitization for Combating Bacteria. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2104410. [PMID: 34486185 DOI: 10.1002/adma.202104410] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Metabolic homeostasis is vital for individual cells to keep alive. Stronger metabolic homeostasis allows bacteria to survive in vivo and do persistent harm to hosts, which is especially typical in implant-associated infection (IAI) with biofilm intervention. Herein, based on the competitive role of selenium (Se) and sulfur (S) in bacteria metabolism as congeners, a congener-induced sulfur-related metabolism interference therapy (SMIT) eradicating IAI is proposed by specific destruction of bacteria metabolic homeostasis. The original nanodrug manganese diselenide (MnSe2 ) is devised to generate permeable H2 Se in bacteria, triggered by the acidic microenvironment. H2 Se, the congener substitution of H2 S, as a bacteria-specific intermediate metabolite, can embed itself into the H2 S-utilization pathway and further alternatively disrupt the downstream sulfur-related metabolism state inside bacteria. A proteomic study indicates ribosome-related proteins are heavily downregulated and the basic metabolic pathways are mainly disordered after SMIT, revealing the destruction of bacteria metabolic homeostasis. The efficiency of SMIT is significantly promoted with the mild temperature sensitization provided by the photothermal treatment (PTT) of MnSe2 nanoparticles, verified by the proteomic study and the anti-IAI effect in vitro and in vivo. With the intelligent nanodrug, a PTT-promoted SMIT strategy against IAI is provided and a new insight into the interference design toward metabolic homeostasis with biochemical similarity is demonstrated.
Collapse
Affiliation(s)
- Renke He
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Cheng Ding
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Yao Luo
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Geyong Guo
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Jin Tang
- Department of Clinical Laboratory, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Hao Shen
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Qiaojie Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Xianlong Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| |
Collapse
|
26
|
McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
Collapse
Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| |
Collapse
|
27
|
Wang X, Guo X, Wang J, Li H, He F, Xu S, Chen K, Ouyang P. Ameliorating end-product inhibition to improve cadaverine production in engineered Escherichia coli and its application in the synthesis of bio-based diisocyanates. Synth Syst Biotechnol 2021; 6:243-253. [PMID: 34584992 PMCID: PMC8446744 DOI: 10.1016/j.synbio.2021.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Cadaverine is an important C5 platform chemical with a wide range of industrial applications. However, the cadaverine inhibition on the fermenting strain limited its industrial efficiency of the strain. In this study, we report an engineered Escherichia coli strain with high cadaverine productivity that was generated by developing a robust host coupled with metabolic engineering to mitigate cadaverine inhibition. First, a lysine producing E. coli was treated with a combination of radiation (ultraviolet and visible spectrum) and ARTP (atmospheric and room temperature plasma) mutagenesis to obtain a robust host with high cadaverine tolerance. Three mutant targets including HokD, PhnI and PuuR are identified for improved cadaverine tolerance. Further transcriptome analysis suggested that cadaverine suppressed the synthesis of ATP and lysine precursor. Accordingly, the related genes involved in glycolysis and lysine precursor, as well as cadaverine exporter was engineered to release the cadaverine inhibition. The final engineered strain was fed-batch cultured and a titer of 58.7 g/L cadaverine was achieved with a yield of 0.396 g/g, both of which were the highest level reported to date in E. coli. The bio-based cadaverine was purified to >99.6% purity, and successfully used for the synthesis of polyurethane precursor 1,5-pentamethylene diisocyanate (PDI) through the approach of carbamate decomposition.
Collapse
Affiliation(s)
- Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| | - Xing Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| | - Jing Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| | - Hui Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| | - Feng He
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China Bbitechnology and Bioengineering
| |
Collapse
|
28
|
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
|
29
|
Hertel R, Gibhardt J, Martienssen M, Kuhn R, Commichau FM. Molecular mechanisms underlying glyphosate resistance in bacteria. Environ Microbiol 2021; 23:2891-2905. [PMID: 33876549 DOI: 10.1111/1462-2920.15534] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 11/29/2022]
Abstract
Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.
Collapse
Affiliation(s)
- Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Johannes Gibhardt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Marion Martienssen
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Ramona Kuhn
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| |
Collapse
|
30
|
Huang B, Yan D, Wang Q, Fang W, Song Z, Cheng H, Li Y, Ouyang C, Han Q, Jin X, Cao A. Effects of Dazomet Fumigation on Soil Phosphorus and the Composition of phoD-Harboring Microbial Communities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5049-5058. [PMID: 32134657 DOI: 10.1021/acs.jafc.9b08033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The soil phosphorus (P) cycle and P transformation are largely driven by the soil bacterial microbial community. However, little is known about the effects of dazomet (DZ) soil fumigation on soil P and soil microbial communities associated with P transformation. This research investigated P released from three farm soils as a result of DZ fumigation and changes in enzyme activity, gene abundance, and the encoding alkaline phosphatase PhoD microbial community. After DZ fumigation, we observed a briefly significant increase in the available P and the active P fractionation. The soil ALP activity, 16s rRNA abundance, and the phoD gene decreased significantly after DZ fumigation. The abundance and diversity of phoD-harboring microbes also decreased shortly after fumigation, increased significantly 14-28 days later, and then decreased again toward the end of the experimental period of 86 days. The shared OTUs between treatments became fewer with increasing time after fumigation. The changes in available P and the active P fractionation after DZ fumigation were significantly correlated with the abundance of the dominant phoD-harboring microbes. DZ fumigation promoted P mineralization in these farm soils and changed the composition of phoD-harboring microbial communities, which will benefit crops able to absorb and use P.
Collapse
Affiliation(s)
- Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhaoxin Song
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qingli Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Xi Jin
- IPPCAAS-BU Joint Research Centre for Soil Remediation, Baoding University, Hebei 071000, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| |
Collapse
|
31
|
Rees-Garbutt J, Chalkley O, Landon S, Purcell O, Marucci L, Grierson C. Designing minimal genomes using whole-cell models. Nat Commun 2020; 11:836. [PMID: 32047145 PMCID: PMC7012841 DOI: 10.1038/s41467-020-14545-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 12/17/2019] [Indexed: 11/29/2022] Open
Abstract
In the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay whether the cell replicates or not. We used the first (and currently only published) whole-cell model for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in silico minimal genomes which, if biologically correct, predict in vivo genomes smaller than JCVI-Syn3.0; a bacterium with, currently, the smallest genome that can be grown in pure culture. In the process, we identified 10 low essential genes and produced evidence for at least two Mycoplasma genitalium in silico minimal genomes. This work brings combined computational and laboratory genome engineering a step closer. Genome engineering will one day benefit from computational tools that can design genomes with desired functions. Here the authors develop computational design-simulate-test algorithms to design minimal genomes based on the whole-cell model of Mycoplasma genitalium.
Collapse
Affiliation(s)
- Joshua Rees-Garbutt
- BrisSynBio, University of Bristol, Bristol, BS8 1TQ, UK.,School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Oliver Chalkley
- BrisSynBio, University of Bristol, Bristol, BS8 1TQ, UK.,Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK.,Bristol Centre for Complexity Science, Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK
| | - Sophie Landon
- BrisSynBio, University of Bristol, Bristol, BS8 1TQ, UK.,Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK
| | - Oliver Purcell
- Engine Biosciences, MBC Biolabs, 733 Industrial Road, San Carlos, CA, 94070, USA
| | - Lucia Marucci
- BrisSynBio, University of Bristol, Bristol, BS8 1TQ, UK. .,Department of Engineering Mathematics, University of Bristol, Bristol, BS8 1UB, UK. .,School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1UB, UK.
| | - Claire Grierson
- BrisSynBio, University of Bristol, Bristol, BS8 1TQ, UK. .,School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| |
Collapse
|
32
|
Yan J, Chen S. How To Produce Methane Precursor in the Upper Ocean by An Untypical Non‐Heme Fe‐Dependent Methylphosphonate Synthase? Chemphyschem 2020; 21:385-396. [DOI: 10.1002/cphc.202000025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ji‐Fan Yan
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Shi‐Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| |
Collapse
|
33
|
Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19 T. Int J Genomics 2019; 2019:7586430. [PMID: 31583244 PMCID: PMC6754898 DOI: 10.1155/2019/7586430] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022] Open
Abstract
Strain E19T described as Hartmannibacter diazotrophicus gen. nov. sp. nov. was isolated from the rhizosphere of Plantago winteri from a natural salt meadow in a nature protection area. Strain E19T is a plant growth-promoting rhizobacterium able to colonize the rhizosphere of barley and to promote its growth only under salt stress conditions. To gain insights into the genetic bases of plant growth promotion and its lifestyle at the rhizosphere under salty conditions, we determined the complete genome sequence using two complementary sequencing platforms (Ilumina MiSeq and PacBio RSII). The E19T genome comprises one circular chromosome and one plasmid containing several genes involved in salt adaptation and genes related to plant growth-promoting traits under salt stress. Based on previous experiments, ACC deaminase activity was identified as a main mechanism of E19T to promote plant growth under salt stress. Interestingly, no genes classically reported to encode for ACC deaminase activity are present. In general, the E19T genome provides information to confirm, discover, and better understand many of its previously evaluated traits involved in plant growth promotion under salt stress. Furthermore, the complete E19T genome sequence helps to define its previously reported unclear 16S rRNA gene-based phylogenetic affiliation. Hartmannibacter forms a distinct subcluster with genera Methylobrevis, Pleomorphomonas, Oharaeibacter, and Mongoliimonas subclustered with genera belonging to Rhizobiales.
Collapse
|
34
|
Wang F, Kertesz MA, Feng G. Phosphorus forms affect the hyphosphere bacterial community involved in soil organic phosphorus turnover. MYCORRHIZA 2019; 29:351-362. [PMID: 31044298 DOI: 10.1007/s00572-019-00896-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Interactions between bacteria and arbuscular mycorrhizal (AM) fungi play a significant role in mediating organic phosphorus (P) transformations and turnover in soil. The bacterial community in soil is largely responsible for mobilization of the soil organic P pool, and the released P is taken up by extraradical AM hyphae, which mediate its use for plant growth. However, the functional microbiome involved in organic P mineralization in the hyphosphere remains poorly understood. The aim of this study was to determine how AM hyphae-associated bacterial communities related to P turnover in the hyphosphere of leek (Allium porrum) respond to different forms of soil P. Using a compartmented microcosm, leek was grown with the AM fungus Funneliformis mosseae, and the extraradical mycelium of F. mosseae was allowed to grow into a separate hyphal compartment containing either no added P, or P as KH2PO4 or phytin. High-throughput sequencing showed that the alkaline phosphatase (ALP)-harboring bacterial community associated with the AM hyphae was dominated by Sinorhizobium, Bradyrhizobium, Pseudomonas, and Ralstonia and was significantly changed in response to different P treatments, with Pseudomonas showing higher relative abundance in organic P treatments than in control and inorganic P treatments. Pseudomonas was also the major genus harboring the β-propeller phytase (BPP) gene in the hyphosphere, but the BPP-harboring community structure was not affected by the presence of different P forms. These results demonstrate the profound differences in ALP- and BPP-harboring bacterial communities in the hyphosphere at bacterial genus level, providing new insights to link bacteria and biogeochemical P cycling driven in association with mycorrhizal hyphae.
Collapse
Affiliation(s)
- Fei Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
- School of Resource and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Michael A Kertesz
- Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Gu Feng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.
| |
Collapse
|
35
|
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol 2019; 35:904-908. [PMID: 29020004 DOI: 10.1038/nbt.3956] [Citation(s) in RCA: 311] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Colton J Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Elizabeth Brunk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Nathan Mih
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Anand Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Zachary King
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Rikiya Takeuchi
- Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma, Nara, Japan
| | - Wataru Nomura
- Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma, Nara, Japan
| | - Zhen Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Hirotada Mori
- Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma, Nara, Japan
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,The NNF Center for Biosustainability, The Technical University of Denmark, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,The NNF Center for Biosustainability, The Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
36
|
Gama SR, Vogt M, Kalina T, Hupp K, Hammerschmidt F, Pallitsch K, Zechel DL. An Oxidative Pathway for Microbial Utilization of Methylphosphonic Acid as a Phosphate Source. ACS Chem Biol 2019; 14:735-741. [PMID: 30810303 DOI: 10.1021/acschembio.9b00024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Methylphosphonic acid is synthesized by marine bacteria and is a prominent component of dissolved organic phosphorus. Consequently, methylphosphonic acid also serves as a source of inorganic phosphate (Pi) for marine bacteria that are starved of this nutrient. Conversion of methylphosphonic acid into Pi is currently only known to occur through the carbon-phosphorus lyase pathway, yielding methane as a byproduct. In this work, we describe an oxidative pathway for the catabolism of methylphosphonic acid in Gimesia maris DSM8797. G. maris can use methylphosphonic acid as Pi sources despite lacking a phn operon encoding a carbon-phosphorus lyase pathway. Instead, the genome contains a locus encoding homologues of the non-heme Fe(II) dependent oxygenases HF130PhnY* and HF130PhnZ, which were previously shown to convert 2-aminoethylphosphonic acid into glycine and Pi. GmPhnY* and GmPhnZ1 were produced in E. coli and purified for characterization in vitro. The substrate specificities of the enzymes were evaluated with a panel of synthetic phosphonates. Via 31P NMR spectroscopy, it is demonstrated that the GmPhnY* converts methylphosphonic acid to hydroxymethylphosphonic acid, which in turn is oxidized by GmPhnZ1 to produce formic acid and Pi. In contrast, 2-aminoethylphosphonic acid is not a substrate for GmPhnY* and is therefore not a substrate for this pathway. These results thus reveal a new metabolic fate for methylphosphonic acid.
Collapse
Affiliation(s)
- Simanga R. Gama
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada
| | - Margret Vogt
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Thomas Kalina
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Kendall Hupp
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada
| | | | | | - David L. Zechel
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada
| |
Collapse
|
37
|
Hong H, Zhang L, Xie F, Zhuang R, Jiang D, Liu H, Li J, Yang H, Zhang X, Nie L, Li Z. Rapid one-step 18F-radiolabeling of biomolecules in aqueous media by organophosphine fluoride acceptors. Nat Commun 2019; 10:989. [PMID: 30824691 PMCID: PMC6397219 DOI: 10.1038/s41467-019-08953-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/07/2019] [Indexed: 11/19/2022] Open
Abstract
Currently, only a few 18F-radiolabeling methods were conducted in aqueous media, with non-macroelement fluoride acceptors and stringent conditions required. Herein, we describe a one-step non-solvent-biased, room-temperature-driven 18F-radiolabeling methodology based on organophosphine fluoride acceptors. The high water tolerance for this isotope-exchange-based 18F-labeling method is attributed to the kinetic and thermodynamic preference of F/F over the OH/F substitution based on computational calculations and experimental validation. Compact [18/19F]di-tert-butyl-organofluorophosphine and its derivatives used as 18F-labeling synthons exhibit excellent stability in vivo. The synthons are further conjugated to several biomolecular ligands such as c(RGDyk) and human serum albumin. The one-step labeled biomolecular tracers demonstrate intrinsic target imaging ability and negligible defluorination in vivo. The current method thus offers a facile and efficient 18F-radiolabeling pathway, enabling further widespread application of 18F. The synthesis of 18F-labeled positron emission tomography (PET) tracers is difficult and typically requires anhydrous conditions. Here, the authors developed organophosphine precursors that allow for quick, high-yield synthesis of 18F-labeled probes in either organic solvents or aqueous media.
Collapse
Affiliation(s)
- Huawei Hong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China
| | - Lei Zhang
- Tianjin Engineering Technology Center of Chemical Wastewater Source Reduction and Recycling, School of Science, Tianjin Chengjian University, 300384, Tianjin, China
| | - Fang Xie
- PET center, Huashan Hospital, Fudan University, 200235, Shanghai, China
| | - Rongqiang Zhuang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China
| | - Donglang Jiang
- PET center, Huashan Hospital, Fudan University, 200235, Shanghai, China
| | - Huanhuan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China
| | - Jindian Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China
| | - Hongzhang Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China
| | - Xianzhong Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China
| | - Liming Nie
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Zijing Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China.
| |
Collapse
|
38
|
The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
Collapse
|
39
|
LeBrun ES, King RS, Back JA, Kang S. A Metagenome-Based Investigation of Gene Relationships for Non-Substrate-Associated Microbial Phosphorus Cycling in the Water Column of Streams and Rivers. MICROBIAL ECOLOGY 2018; 76:856-865. [PMID: 29569048 DOI: 10.1007/s00248-018-1178-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
Phosphorus (P) is a nutrient of primary importance in all living systems, and it is especially important in streams and rivers which are sensitive to anthropogenic P inputs and eutrophication. Microbes are accepted as the primary mineralizers and solubilizers of P improving bioavailability for organisms at all trophic levels. Here, we use a genomics approach with metagenome sequencing of 24 temperate streams and rivers representing a total P (TP) gradient to identify relationships between functional genes, functional gene groupings, P, and organisms within the P biogeochemical cycle. Combining information from network analyses, functional groupings, and system P levels, we have constructed a System Relational Overview of Gene Groupings (SROGG) which is a cohesive system level representation of P cycle gene and nutrient relationships. Using SROGG analysis in concert with other statistical approaches, we found that the compositional makeup of P cycle genes is strongly correlated to environmental P whereas absolute abundance of P genes shows no significant correlation to environmental P. We also found orthophosphate (PO43-) to be the dominant factor correlating with system P cycle gene composition with little evidence of a strong organic phosphorous correlation present even in more oligotrophic streams.
Collapse
Affiliation(s)
- Erick S LeBrun
- Center for Reservoir and Aquatic Systems Research, Department of Biology, Baylor University, One Bear Place 97388, Waco, TX, 76798-7388, USA
| | - Ryan S King
- Center for Reservoir and Aquatic Systems Research, Department of Biology, Baylor University, One Bear Place 97388, Waco, TX, 76798-7388, USA
| | - Jeffrey A Back
- Center for Reservoir and Aquatic Systems Research, Department of Biology, Baylor University, One Bear Place 97388, Waco, TX, 76798-7388, USA
| | - Sanghoon Kang
- Center for Reservoir and Aquatic Systems Research, Department of Biology, Baylor University, One Bear Place 97388, Waco, TX, 76798-7388, USA.
| |
Collapse
|
40
|
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
|
41
|
Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol 2018; 606:1-71. [PMID: 30097089 DOI: 10.1016/bs.mie.2018.06.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
Collapse
Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States.
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Elaine C Meng
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, United States
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Sara Calhoun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Graduate Program in Biophysics, University of California, San Francisco, CA, United States
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
| |
Collapse
|
42
|
Ghodge SV, Raushel FM. Structure, Mechanism, and Substrate Profiles of the Trinuclear Metallophosphatases from the Amidohydrolase Superfamily. Methods Enzymol 2018; 607:187-216. [PMID: 30149858 DOI: 10.1016/bs.mie.2018.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The rate of reliable protein function annotation has not kept pace with the rapid advances in genome sequencing technology. This has created a gap between the number of available protein sequences, and an accurate determination of the respective physiological functions. This investigation has attempted to bridge the gap within the confines of members of the polymerase and histidinol phosphatase family of proteins in cog1387 and cog0613, which is related to the amidohydrolase superfamily. The adopted approach relies on using the mechanistic knowledge of a known enzymatic reaction, and discovering functions of closely related homologs using various tools including bioinformatics and rational library screening. The initial enzymatic reaction was that of L-histidinol phosphate phosphatase. Extensive structural, biochemical, and bioinformatic analysis of enzymes capable of hydrolyzing L-histidinol phosphate provided useful insights in predicting substrates and mechanistic studies of related enzymes. This led to the discovery of unprecedented catalytic functions such as a cyclic phosphate dihydrolase that specifically hydrolyzed a cyclic phosphodiester to inorganic phosphate and a vicinal diol; a phosphoesterase that hydrolyzes the 3'-phosphate of 3',5'-adenosine bisphosphate and similar nucleotides; and the first reported 5'-3' exonuclease for 5'-phosphorylated oligonucleotides from Escherichia coli and related organisms. This work provides a template for developing sequence-structure-function correlations within a family of enzymes that helps expedite new enzyme function discovery and more accurate annotations in protein databases.
Collapse
Affiliation(s)
- Swapnil V Ghodge
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank M Raushel
- Department of Chemistry, Texas A & M University, College Station, TX, United States.
| |
Collapse
|
43
|
Teikari JE, Fewer DP, Shrestha R, Hou S, Leikoski N, Mäkelä M, Simojoki A, Hess WR, Sivonen K. Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane. THE ISME JOURNAL 2018; 12:1619-1630. [PMID: 29445131 PMCID: PMC5955973 DOI: 10.1038/s41396-018-0056-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 11/10/2022]
Abstract
Nodularia spumigena is a nitrogen-fixing cyanobacterium that forms toxic blooms in the Baltic Sea each summer and the availability of phosphorous is an important factor limiting the formation of these blooms. Bioinformatic analysis identified a phosphonate degrading (phn) gene cluster in the genome of N. spumigena suggesting that this bacterium may use phosphonates as a phosphorus source. Our results show that strains of N. spumigena could grow in medium containing methylphosphonic acid (MPn) as the sole source of phosphorous and released methane when growing in medium containing MPn. We analyzed the total transcriptomes of N. spumigena UHCC 0039 grown using MPn and compared them with cultures growing in Pi-replete medium. The phnJ, phosphonate lyase gene, was upregulated when MPn was the sole source of phosphorus, suggesting that the expression of this gene could be used to indicate the presence of bioavailable phosphonates. Otherwise, growth on MPn resulted in only a minor reconstruction of the transcriptome and enabled good growth. However, N. spumigena strains were not able to utilize any of the anthropogenic phosphonates tested. The phosphonate utilizing pathway may offer N. spumigena a competitive advantage in the Pi-limited cyanobacterial blooms of the Baltic Sea.
Collapse
Affiliation(s)
- Jonna E Teikari
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Rashmi Shrestha
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Institute of Biology III, University Freiburg, Schänzlestraße 1, Freiburg, D-79104, Germany
| | - Niina Leikoski
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Minna Mäkelä
- Department of Agricultural Sciences, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Asko Simojoki
- Department of Agricultural Sciences, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University Freiburg, Schänzlestraße 1, Freiburg, D-79104, Germany
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland.
| |
Collapse
|
44
|
Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng 2018; 48:82-93. [PMID: 29842925 DOI: 10.1016/j.ymben.2018.05.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/03/2018] [Accepted: 05/23/2018] [Indexed: 11/21/2022]
Abstract
Methylglyoxal is a highly toxic metabolite that can be produced in all living organisms. Methylglyoxal was artificially elevated by removal of the tpiA gene from a growth optimized Escherichia coli strain. The initial response to elevated methylglyoxal and its toxicity was characterized, and detoxification mechanisms were studied using adaptive laboratory evolution. We found that: 1) Multi-omics analysis revealed biological consequences of methylglyoxal toxicity, which included attack on macromolecules including DNA and RNA and perturbation of nucleotide levels; 2) Counter-intuitive cross-talk between carbon starvation and inorganic phosphate signalling was revealed in the tpiA deletion strain that required mutations in inorganic phosphate signalling mechanisms to alleviate; and 3) The split flux through lower glycolysis depleted glycolytic intermediates requiring a host of synchronized and coordinated mutations in non-intuitive network locations in order to re-adjust the metabolic flux map to achieve optimal growth. Such mutations included a systematic inactivation of the Phosphotransferase System (PTS) and alterations in cell wall biosynthesis enzyme activity. This study demonstrated that deletion of major metabolic genes followed by ALE was a productive approach to gain novel insight into the systems biology underlying optimal phenotypic states.
Collapse
|
45
|
Archean phosphorus liberation induced by iron redox geochemistry. Nat Commun 2018; 9:1346. [PMID: 29632373 PMCID: PMC5890264 DOI: 10.1038/s41467-018-03835-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 03/15/2018] [Indexed: 11/23/2022] Open
Abstract
The element phosphorus (P) is central to ecosystem growth and is proposed to be a limiting nutrient for life. The Archean ocean may have been strongly phosphorus-limited due to the selective binding of phosphate to iron oxyhydroxide. Here we report a new route to solubilizing phosphorus in the ancient oceans: reduction of phosphate to phosphite by iron(II) at low (<200 °C) diagenetic temperatures. Reduction of phosphate to phosphite was likely widespread in the Archean, as the reaction occurs rapidly and is demonstrated from thermochemical modeling, experimental analogs, and detection of phosphite in early Archean rocks. We further demonstrate that the higher solubility of phosphite compared to phosphate results in the liberation of phosphorus from ferruginous sediments. This phosphite is relatively stable after its formation, allowing its accumulation in the early oceans. As such, phosphorus, not as phosphate but as phosphite, could have been a major nutrient in early pre-oxygenated oceans. Phosphorus is presumed to have been a limiting nutrient in the Archean ocean due to binding to iron oxides. Here, the authors show the heating of iron with phosphate results in the reduction of phosphate to the ion phosphite, which is solubilized and ameliorates the issue of a low Archean phosphorus supply.
Collapse
|
46
|
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]
|
47
|
Wendels S, Chavez T, Bonnet M, Salmeia KA, Gaan S. Recent Developments in Organophosphorus Flame Retardants Containing P-C Bond and Their Applications. MATERIALS (BASEL, SWITZERLAND) 2017; 10:E784. [PMID: 28773147 PMCID: PMC5551827 DOI: 10.3390/ma10070784] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/17/2017] [Accepted: 07/04/2017] [Indexed: 01/05/2023]
Abstract
Organophosphorus compounds containing P-C bonds are increasingly developed as flame retardant additives due to their excellent thermal and hydrolytic stability and ease of synthesis. The latest development (since 2010) in organophosphorus flame retardants containing P-C bonds summarized in this review. In this review, we have broadly classified such phosphorus compounds based on the carbon unit linked to the phosphorus atom i.e., could be a part of either an aliphatic or an aromatic unit. We have only considered those published literature where a P-C bond was created as a part of synthetic strategy to make either an intermediate or a final organophosphorus compound with an aim to use it as a flame retardant. General synthetic strategies to create P-C bonds are briefly discussed. Most popular synthetic strategies used for developing P-C containing phosphorus based flame retardants include Michael addition, Michaelis-Arbuzov, Friedels-Crafts and Grignard reactions. In general, most flame retardant derivatives discussed in this review have been prepared via a one- to two-step synthetic strategy with relatively high yields greater than 80%. Specific examples of P-C containing flame retardants synthesized via suitable synthetic strategy and their applications on various polymer systems are described in detail. Aliphatic phosphorus compounds being liquids or low melting solids are generally applied in polymers via coatings (cellulose) or are incorporated in the bulk of the polymers (epoxy, polyurethanes) during their polymerization as reactive or non-reactive additives. Substituents on the P atoms and the chemistry of the polymer matrix greatly influence the flame retardant behavior of these compounds (condensed phase vs. the gas phase). Recently, aromatic DOPO based phosphinate flame retardants have been developed with relatively higher thermal stabilities (>250 °C). Such compounds have potential as flame retardants for high temperature processable polymers such as polyesters and polyamides. A vast variety of P-C bond containing efficient flame retardants are being developed; however, further work in terms of their economical synthetic methods, detailed impact on mechanical properties and processability, long term durability and their toxicity and environmental impact is much needed for their potential commercial exploitations.
Collapse
Affiliation(s)
- Sophie Wendels
- Additives and Chemistry Group, Advanced Fibers, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland.
| | - Thiebault Chavez
- Additives and Chemistry Group, Advanced Fibers, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland.
| | - Martin Bonnet
- Additives and Chemistry Group, Advanced Fibers, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland.
| | - Khalifah A Salmeia
- Additives and Chemistry Group, Advanced Fibers, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland.
| | - Sabyasachi Gaan
- Additives and Chemistry Group, Advanced Fibers, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland.
| |
Collapse
|
48
|
Effects upon metabolic pathways and energy production by Sb(III) and As(III)/Sb(III)-oxidase gene aioA in Agrobacterium tumefaciens GW4. PLoS One 2017; 12:e0172823. [PMID: 28241045 PMCID: PMC5328403 DOI: 10.1371/journal.pone.0172823] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/11/2017] [Indexed: 12/23/2022] Open
Abstract
Agrobacterium tumefaciens GW4 is a heterotrophic arsenite [As(III)]/antimonite [Sb(III)]-oxidizing strain. The As(III) oxidase AioAB is responsible for As(III) oxidation in the periplasm and it is also involved in Sb(III) oxidation in Agrobacterium tumefaciens 5A. In addition, Sb(III) oxidase AnoA and cellular H2O2 are also responsible for Sb(III) oxidation in strain GW4. However, the deletion of aioA increased the Sb(III) oxidation efficiency in strain GW4. In the present study, we found that the cell mobility to Sb(III), ATP and NADH contents and heat release were also increased by Sb(III) and more significantly in the aioA mutant. Proteomics and transcriptional analyses showed that proteins/genes involved in Sb(III) oxidation and resistance, stress responses, carbon metabolism, cell mobility, phosphonate and phosphinate metabolism, and amino acid and nucleotide metabolism were induced by Sb(III) and were more significantly induced in the aioA mutant. The results suggested that Sb(III) oxidation may produce energy. In addition, without periplasmic AioAB, more Sb(III) would enter bacterial cells, however, the cytoplasmic AnoA and the oxidative stress response proteins were significantly up-regulated, which may contribute to the increased Sb(III) oxidation efficiency. Moreover, the carbon metabolism was also activated to generate more energy against Sb(III) stress. The generated energy may be used in Sb transportation, DNA repair, amino acid synthesis, and cell mobility, and may be released in the form of heat.
Collapse
|
49
|
Artiukhov AV, Graf AV, Bunik VI. Directed regulation of multienzyme complexes of 2-oxo acid dehydrogenases using phosphonate and phosphinate analogs of 2-oxo acids. BIOCHEMISTRY (MOSCOW) 2016; 81:1498-1521. [DOI: 10.1134/s0006297916120129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
50
|
Drzyzga D, Forlani G, Vermander J, Kafarski P, Lipok J. Biodegradation of the aminopolyphosphonate DTPMP by the cyanobacterium Anabaena variabilis proceeds via a C-P lyase-independent pathway. Environ Microbiol 2016; 19:1065-1076. [PMID: 27907245 DOI: 10.1111/1462-2920.13616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyanobacteria, the only prokaryotes capable of oxygenic photosynthesis, play a major role in carbon, nitrogen and phosphorus global cycling. Under conditions of increased P availability and nutrient loading, some cyanobacteria are capable of blooming, rapidly multiplying and possibly altering the ecological structure of the ecosystem. Because of their ability of using non-conventional P sources, these microalgae can be used for bioremediation purposes. Under this perspective, the metabolization of the polyphosphonate diethylenetriaminepenta(methylenephosphonic) acid (DTPMP) by the strain CCALA 007 of Anabaena variabilis was investigated using 31 P NMR analysis. Results showed a quantitative breakdown of DTPMP by cell-free extracts from cyanobacterial cells grown in the absence of any phosphonate. The identification of intermediates and products allowed us to propose a unique and new biodegradation pathway in which the formation of (N-acetylaminomethyl)phosphonic acid represents a key step. This hypothesis was strengthened by the results obtained by incubating cell-free extracts with pathway intermediates. When Anabaena cultures were grown in the presence of the phosphonate, or phosphorus-starved before the extraction, significantly higher biodegradation rates were found.
Collapse
Affiliation(s)
- Damian Drzyzga
- Faculty of Chemistry, Opole University, Oleska 48, Opole, 45-052, Poland
| | - Giuseppe Forlani
- Department of Life Science and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, I-44121, Italy
| | - Jochen Vermander
- Odisee Technologiecampus, Gebroeders de Smetstraat 1, Ghent, 9000, Belgium
| | - Paweł Kafarski
- Faculty of Chemistry, Opole University, Oleska 48, Opole, 45-052, Poland.,Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże, Wyspiańskiego 27, 50-370, Wrocław
| | - Jacek Lipok
- Faculty of Chemistry, Opole University, Oleska 48, Opole, 45-052, Poland
| |
Collapse
|