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Frank C, Teleki A, Jendrossek D. Characterization of Agrobacterium tumefaciens PPKs reveals the formation of oligophosphorylated products up to nucleoside nona-phosphates. Appl Microbiol Biotechnol 2020; 104:9683-9692. [PMID: 33025129 PMCID: PMC7595981 DOI: 10.1007/s00253-020-10891-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022]
Abstract
Agrobacterium tumefaciens synthesizes polyphosphate (polyP) in the form of one or two polyP granules per cell during growth. The A. tumefaciens genome codes for two polyphosphate kinase genes, ppk1AT and ppk2AT, of which only ppk1AT is essential for polyP granule formation in vivo. Biochemical characterization of the purified PPK1AT and PPK2AT proteins revealed a higher substrate specificity of PPK1AT (in particular for adenine nucleotides) than for PPK2AT. In contrast, PPK2AT accepted all nucleotides at comparable rates. Most interestingly, PPK2AT catalyzed also the formation of tetra-, penta-, hexa-, hepta-, and octa-phosphorylated nucleosides from guanine, cytosine, desoxy-thymidine, and uridine nucleotides and even nona-phosphorylated adenosine. Our data-in combination with in vivo results-suggest that PPK1AT is important for the formation of polyP whereas PPK2AT has the function to replenish nucleoside triphosphate pools during times of enhanced demand. The potential physiological function(s) of the detected oligophosphorylated nucleotides await clarification. KEY POINTS: •PPK1AT and PPK2AT have different substrate specificities, •PPK2AT is a subgroup 1 member of PPK2s, •PPK2AT catalyzes the formation of polyphosphorylated nucleosides.
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Affiliation(s)
- Celina Frank
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Hildenbrand JC, Teleki A, Jendrossek D. A universal polyphosphate kinase: PPK2c of Ralstonia eutropha accepts purine and pyrimidine nucleotides including uridine diphosphate. Appl Microbiol Biotechnol 2020; 104:6659-6667. [PMID: 32500270 PMCID: PMC7347700 DOI: 10.1007/s00253-020-10706-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 01/15/2023]
Abstract
Polyphosphosphate kinases (PPKs) catalyse the reversible transfer of the γ-phosphate group of a nucleoside-triphosphate to a growing chain of polyphosphate. Most known PPKs are specific for ATP, but some can also use GTP as a phosphate donor. In this study, we describe the properties of a PPK2-type PPK of the β-proteobacterium Ralstonia eutropha. The purified enzyme (PPK2c) is highly unspecific and accepts purine nucleotides as well as the pyridine nucleotides including UTP as substrates. The presence of a polyP primer is not necessary for activity. The corresponding nucleoside diphosphates and microscopically detectable polyphosphate granules were identified as reaction products. PPK2c also catalyses the formation of ATP, GTP, CTP, dTTP and UTP from the corresponding nucleoside diphosphates, if polyP is present as a phosphate donor. Remarkably, the nucleoside-tetraphosphates AT(4)P, GT(4)P, CT(4)P, dTT(4)P and UT(4)P were also detected in substantial amounts. The low nucleotide specificity of PPK2c predestines this enzyme in combination with polyP to become a powerful tool for the regeneration of ATP and other nucleotides in biotechnological applications. As an example, PPK2c and polyP were used to replace ATP and to fuel the hexokinase-catalysed phosphorylation of glucose with only catalytic amounts of ADP. KEY POINTS: • PPK2c of R. eutropha can be used for regeneration of any NTP or dNTP. • PPK2c is highly unspecific and accepts all purine and pyrimidine nucleotides. • PPK2c forms polyphosphate granules in vitro from any NTP.
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Affiliation(s)
- Jennie C Hildenbrand
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Sanhueza D, Chevillon C, Bouzinbi N, Godreuil S, Guégan JF. Chitin Increases Mycobacterium ulcerans Growth in Acidic Environments. Microbes Environ 2018; 33:234-237. [PMID: 29910219 PMCID: PMC6031397 DOI: 10.1264/jsme2.me17160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 04/11/2018] [Indexed: 11/12/2022] Open
Abstract
Species with a chitinous exoskeleton are overrepresented among the aquatic organisms carrying Mycobacterium ulcerans (MU) in nature and laboratory experiments have demonstrated the enhancing effects of chitin on the growth of MU. Field surveys identified pH as one of the key parameters delineating the distribution of MU in tropical regions. The present study investigated the relationship between chitin and pH in MU growth. By focusing on pH variations in the field, our results revealed that chitin enhanced MU growth in acidic environments. The present study provides new information on the ecological conditions favoring the development of this mycobacterium in nature.
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Affiliation(s)
- Daniel Sanhueza
- MIVEGEC, IRD, CNRS, Université de MontpellierMontpellierFrance
| | | | - Nicolas Bouzinbi
- MIVEGEC, IRD, CNRS, Université de MontpellierMontpellierFrance
- Laboratoire de bactériologie, CHU de Montpellier, Université de MontpellierFrance
| | - Sylvain Godreuil
- MIVEGEC, IRD, CNRS, Université de MontpellierMontpellierFrance
- Laboratoire de bactériologie, CHU de Montpellier, Université de MontpellierFrance
| | - Jean-François Guégan
- MIVEGEC, IRD, CNRS, Université de MontpellierMontpellierFrance
- International United Nations Program FutureEarth, OneHealth Core Research ProgramMontrealCanada
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Sumathi M, Vasudevan N. Removal of phosphate by Staphylococcus aureus under aerobic and alternating anaerobic-aerobic conditions. ENVIRONMENTAL TECHNOLOGY 2018; 39:1071-1080. [PMID: 28478737 DOI: 10.1080/09593330.2017.1320432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
Eutrophication of water bodies due to phosphate enrichment is an ecological problem. Phosphate is removed from wastewaters by enhanced biological phosphate removal worldwide by phosphate accumulating organism. In order to understand the process of treatment, the existing microbial community and its metabolism of phosphate removal are studied widely. This study focuses on the isolation of polyphosphate-accumulating bacteria from different environments and studying their phosphate removal capacity with different carbon supplements under varying culture conditions. The total heterotrophic bacterial population from the diverse environments showed the existence of phosphate-accumulating bacteria. Among them, Staphylococcus aureus removed 81% of phosphate in a polyphosphate-accumulating medium with storage of 93 mM polyphosphate internally. Among the different carbon sources provided, glucose induced a net specific growth rate of 0.816/d. S. aureus removed 70% of phosphate with a phosphate uptake rate of 6.29 mg PO4/g cells and a growth yield of 0.2 g cells/g glucose consumed when 1 g/L glucose was provided. Furthermore, when 2 g/L glucose was provided, 78% of phosphate was removed with a phosphate uptake rate of 13.24 mg PO4/g cells and a growth yield of 0.4 g cells/g glucose consumed under aerobic condition. S. aureus showed enhanced phosphate removal under aerobic condition in the presence of glucose.
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Affiliation(s)
- Malairajan Sumathi
- a Centre for Environmental Studies , Anna University , Chennai 600 025 , Tamil Nadu , India
| | - Namasivayam Vasudevan
- a Centre for Environmental Studies , Anna University , Chennai 600 025 , Tamil Nadu , India
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Proteins with CHADs (Conserved Histidine α-Helical Domains) Are Attached to Polyphosphate Granules In Vivo and Constitute a Novel Family of Polyphosphate-Associated Proteins (Phosins). Appl Environ Microbiol 2017; 83:AEM.03399-16. [PMID: 28130300 DOI: 10.1128/aem.03399-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/17/2017] [Indexed: 01/13/2023] Open
Abstract
On the basis of bioinformatic evidence, we suspected that proteins with a CYTH (CyaB thiamine triphosphatase) domain and/or a CHAD (conserved histidine α-helical domain) motif might represent polyphosphate (polyP) granule-associated proteins. We found no evidence of polyP targeting by proteins with CYTH domains. In contrast, two CHAD motif-containing proteins from Ralstonia eutropha H16 (A0104 and B1017) that were expressed as fusions with enhanced yellow fluorescent protein (eYFP) colocalized with polyP granules. While the expression of B1017 was not detectable, the A0104 protein was specifically identified in an isolated polyP granule fraction by proteome analysis. Moreover, eYFP fusions with the CHAD motif-containing proteins MGMSRV2-1987 from Magnetospirillum gryphiswaldense and PP2307 from Pseudomonas putida also colocalized with polyP granules in a transspecies-specific manner. These data indicated that CHAD-containing proteins are generally attached to polyP granules. Together with the findings from four previously polyP-attached proteins (polyP kinases), the results of this study raised the number of polyP-associated proteins in R. eutropha to six. We suggest designating polyP granule-bound proteins with CHAD motifs as phosins (phosphate), analogous to phasins and oleosins that are specifically bound to the surface of polyhydroxyalkanoate (PHA) granules in PHA-accumulating bacteria and to oil droplets in oil seed plants, respectively.IMPORTANCE The importance of polyphosphate (polyP) for life is evident from the ubiquitous presence of polyP in all species on earth. In unicellular eukaryotic microorganisms, polyP is located in specific membrane-enclosed organelles, called acidocalcisomes. However, in most prokaryotes, polyP is present as insoluble granules that have been designated previously as volutin granules. Almost nothing is known regarding the macromolecular composition of polyP granules. Particularly, the absence or presence of cellular compounds on the surface of polyP granules has not yet been investigated. In this study, we identified a novel class of proteins that are attached to the surface of polyP granules in three model species of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria These proteins are characterized by the presence of a CHAD (conserved histidine α-helical domain) motif that functions as a polyP granule-targeting signal. We suggest designating CHAD motif-containing proteins as phosins [analogous to phasins for poly(3-hydroxybutyrate)-associated proteins and to oleosins for oil droplet-associated proteins in oil seed plants]. The expression of phosins in different species confirmed their polyP-targeting function in a transspecies-specific manner. We postulate that polyP granules in prokaryotic species generally have a complex surface structure that consists of one to several polyP kinases and phosin proteins. We suggest differentiating polyP granules from acidocalcisomes by designating them as polyphosphatosomes.
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Sulphide effects on the physiology of Candidatus Accumulibacter phosphatis type I. Appl Microbiol Biotechnol 2016; 101:1661-1672. [DOI: 10.1007/s00253-016-7946-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
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Sunden F, AlSadhan I, Lyubimov AY, Ressl S, Wiersma-Koch H, Borland J, Brown CL, Johnson TA, Singh Z, Herschlag D. Mechanistic and Evolutionary Insights from Comparative Enzymology of Phosphomonoesterases and Phosphodiesterases across the Alkaline Phosphatase Superfamily. J Am Chem Soc 2016; 138:14273-14287. [PMID: 27670607 PMCID: PMC5096464 DOI: 10.1021/jacs.6b06186] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Naively one might have expected an early division between phosphate monoesterases and diesterases of the alkaline phosphatase (AP) superfamily. On the contrary, prior results and our structural and biochemical analyses of phosphate monoesterase PafA, from Chryseobacterium meningosepticum, indicate similarities to a superfamily phosphate diesterase [Xanthomonas citri nucleotide pyrophosphatase/phosphodiesterase (NPP)] and distinct differences from the three metal ion AP superfamily monoesterase, from Escherichia coli AP (EcAP). We carried out a series of experiments to map out and learn from the differences and similarities between these enzymes. First, we asked why there would be independent instances of monoesterases in the AP superfamily? PafA has a much weaker product inhibition and slightly higher activity relative to EcAP, suggesting that different metabolic evolutionary pressures favored distinct active-site architectures. Next, we addressed the preferential phosphate monoester and diester catalysis of PafA and NPP, respectively. We asked whether the >80% sequence differences throughout these scaffolds provide functional specialization for each enzyme's cognate reaction. In contrast to expectations from this model, PafA and NPP mutants with the common subset of active-site groups embedded in each native scaffold had the same monoesterase:diesterase specificities; thus, the >107-fold difference in native specificities appears to arise from distinct interactions at a single phosphoryl substituent. We also uncovered striking mechanistic similarities between the PafA and EcAP monoesterases, including evidence for ground-state destabilization and functional active-site networks that involve different active-site groups but may play analogous catalytic roles. Discovering common network functions may reveal active-site architectural connections that are critical for function, and identifying regions of functional modularity may facilitate the design of new enzymes from existing promiscuous templates. More generally, comparative enzymology and analysis of catalytic promiscuity can provide mechanistic and evolutionary insights.
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Affiliation(s)
- Fanny Sunden
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Ishraq AlSadhan
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Artem Y Lyubimov
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States
| | - Susanne Ressl
- Molecular and Cellular Biochemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Helen Wiersma-Koch
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States.,Department of Biology, Indian River State College , Fort Pierce, Florida 34981, United States
| | - Jamar Borland
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Clayton L Brown
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Tory A Johnson
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Zorawar Singh
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States.,Departments of Chemical Engineering and Chemistry, and Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University , Stanford, California 94305, United States
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Keating C, Chin JP, Hughes D, Manesiotis P, Cysneiros D, Mahony T, Smith CJ, McGrath JW, O'Flaherty V. Biological Phosphorus Removal During High-Rate, Low-Temperature, Anaerobic Digestion of Wastewater. Front Microbiol 2016; 7:226. [PMID: 26973608 PMCID: PMC4776080 DOI: 10.3389/fmicb.2016.00226] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/12/2016] [Indexed: 12/20/2022] Open
Abstract
We report, for the first time, extensive biologically mediated phosphate removal from wastewater during high-rate anaerobic digestion (AD). A hybrid sludge bed/fixed-film (packed pumice stone) reactor was employed for low-temperature (12°C) anaerobic treatment of synthetic sewage wastewater. Successful phosphate removal from the wastewater (up to 78% of influent phosphate) was observed, mediated by biofilms in the reactor. Scanning electron microscopy and energy dispersive X-ray analysis revealed the accumulation of elemental phosphorus (∼2%) within the sludge bed and fixed-film biofilms. 4′, 6-diamidino-2-phenylindole (DAPI) staining indicated phosphorus accumulation was biological in nature and mediated through the formation of intracellular inorganic polyphosphate (polyP) granules within these biofilms. DAPI staining further indicated that polyP accumulation was rarely associated with free cells. Efficient and consistent chemical oxygen demand (COD) removal was recorded, throughout the 732-day trial, at applied organic loading rates between 0.4 and 1.5 kg COD m-3 d-1 and hydraulic retention times of 8–24 h, while phosphate removal efficiency ranged from 28 to 78% on average per phase. Analysis of protein hydrolysis kinetics and the methanogenic activity profiles of the biomass revealed the development, at 12°C, of active hydrolytic and methanogenic populations. Temporal microbial changes were monitored using Illumina MiSeq analysis of bacterial and archaeal 16S rRNA gene sequences. The dominant bacterial phyla present in the biomass at the conclusion of the trial were the Proteobacteria and Firmicutes and the dominant archaeal genus was Methanosaeta. Trichococcus and Flavobacterium populations, previously associated with low temperature protein degradation, developed in the reactor biomass. The presence of previously characterized polyphosphate accumulating organisms (PAOs) such as Rhodocyclus, Chromatiales, Actinobacter, and Acinetobacter was recorded at low numbers. However, it is unknown as yet if these were responsible for the luxury polyP uptake observed in this system. The possibility of efficient phosphate removal and recovery from wastewater during AD would represent a major advance in the scope for widespread application of anaerobic wastewater treatment technologies.
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Affiliation(s)
- Ciara Keating
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Jason P Chin
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast Belfast, UK
| | - Dermot Hughes
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Panagiotis Manesiotis
- School of Chemistry and Chemical Engineering, The Queen's University of Belfast Belfast, UK
| | - Denise Cysneiros
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Therese Mahony
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - Cindy J Smith
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
| | - John W McGrath
- School of Biological Sciences and the Institute for Global Food Security, The Queen's University of Belfast Belfast, UK
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway Ireland
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