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Ahmad N, Sharma P, Sharma S, Singh TP. Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 Å resolution. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:147-157. [PMID: 38456905 DOI: 10.1007/s00249-024-01703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 02/10/2024] [Indexed: 03/09/2024]
Abstract
Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4'-phosphopantetheine (PNS) yielding 3'-dephospho-coenzyme A (dpCoA) and pyrophosphate (PPi). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) was cloned, expressed and purified. It was crystallized using 0.1 M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P41212 with cell dimensions of a = b = 72.82 Å and c = 200.37 Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for Rcryst and Rfree factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of KpPPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a KD value of 3.45 × 10-4 M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.
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Affiliation(s)
- Nabeel Ahmad
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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Liu X, Zhao C, Xu T, Liu W, Chen Q, Li L, Tan Y, Wang X, Dong Y. Pyrite and sulfur-coupled autotrophic denitrification system for efficient nitrate and phosphate removal. BIORESOURCE TECHNOLOGY 2023; 384:129363. [PMID: 37336446 DOI: 10.1016/j.biortech.2023.129363] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
The inefficiency of nitrogen removal in pyrite autotrophic denitrification (PAD) and the low efficiency of PO43--P removal in sulfur autotrophic denitrification (SAD) limit their potential for engineering applications. This study examined the use of pyrite and sulfur coupled autotrophic denitrification (PSAD) in batch and column experiments to remove NO3--N and PO43--P from sewage. The effluent concentration of NO3--N was 0.32 ± 0.11 mg/L, with an average Total nitrogen (TN) removal efficiency of 99.14%. The highest PO43--P removal efficiency was 100% on day 18. There was a significant correlation between pH and the efficiency of PO43--P removal. Thiobacillus, Thiomonas and Thermomonas were found to be dominant at the bacterial genus level in PSAD. Additionally, the abundance of Thermomonas in the PSAD was greater than that observed in the SAD reactor. This result indirectly indicates that the PSAD system has more advantages in reducing N2O.
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Affiliation(s)
- Xuzhen Liu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China
| | - Changsheng Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China.
| | - Tongtong Xu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China
| | - Wei Liu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China
| | - Qingfeng Chen
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Luzhen Li
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China
| | - Yu Tan
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China
| | - Xiaokai Wang
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China
| | - Yanan Dong
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, Shandong 250014, PR China
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Ferreira P, Fernandes P, Ramos M. The archaeal non-heme iron-containing Sulfur Oxygenase Reductase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Molecular Physiology of Anaerobic Phototrophic Purple and Green Sulfur Bacteria. Int J Mol Sci 2021; 22:ijms22126398. [PMID: 34203823 PMCID: PMC8232776 DOI: 10.3390/ijms22126398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/24/2021] [Accepted: 06/11/2021] [Indexed: 12/04/2022] Open
Abstract
There are two main types of bacterial photosynthesis: oxygenic (cyanobacteria) and anoxygenic (sulfur and non-sulfur phototrophs). Molecular mechanisms of photosynthesis in the phototrophic microorganisms can differ and depend on their location and pigments in the cells. This paper describes bacteria capable of molecular oxidizing hydrogen sulfide, specifically the families Chromatiaceae and Chlorobiaceae, also known as purple and green sulfur bacteria in the process of anoxygenic photosynthesis. Further, it analyzes certain important physiological processes, especially those which are characteristic for these bacterial families. Primarily, the molecular metabolism of sulfur, which oxidizes hydrogen sulfide to elementary molecular sulfur, as well as photosynthetic processes taking place inside of cells are presented. Particular attention is paid to the description of the molecular structure of the photosynthetic apparatus in these two families of phototrophs. Moreover, some of their molecular biotechnological perspectives are discussed.
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Molecular and Physiological Adaptations to Low Temperature in Thioalkalivibrio Strains Isolated from Soda Lakes with Different Temperature Regimes. mSystems 2021; 6:6/2/e01202-20. [PMID: 33906913 PMCID: PMC8092127 DOI: 10.1128/msystems.01202-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of two Thioalkalivibrio strains to low (10°C) and high (30°C) temperatures. For this, the strains were grown under controlled conditions in chemostats and analyzed for their gene expression (RNA sequencing [RNA-Seq]), membrane lipid composition, and glycine betaine content. The strain Thioalkalivibrio versutus AL2T originated from a soda lake in southeast Siberia that is exposed to strong seasonal temperature differences, including freezing winters, whereas Thioalkalivibrio nitratis ALJ2 was isolated from an East African Rift Valley soda lake with a constant warm temperature the year round. The strain AL2T grew faster than ALJ2 at 10°C, likely due to its 3-fold-higher concentration of the osmolyte glycine betaine. Moreover, significant changes in the membrane lipid composition were observed for both strains, leading to an increase in their unsaturated fatty acid content via the Fab pathway to avoid membrane stiffness. Genes for the transcriptional and translational machinery, as well as for counteracting cold-induced hampering of nucleotides and proteins, were upregulated. Oxidative stress was reduced by induction of vitamin B12 biosynthesis genes, and growth at 10°C provoked downregulation of genes involved in the second half of the sulfur oxidation pathway. Genes for intracellular signal transduction were differentially expressed, and interestingly, AL2T upregulated flagellin expression, whereas ALJ2 downregulated it. IMPORTANCE In addition to their haloalkaline conditions, soda lakes can also harbor a variety of other extreme parameters, to which their microbial communities need to adapt. However, for most of these supplementary stressors, it is not well known yet how haloalkaliphiles adapt and resist. Here, we studied the strategy for adaptation to low temperature in the haloalkaliphilic genus Thioalkalivibrio by using two strains isolated from soda lakes with different temperature regimes. Even though the strains showed a strong difference in growth rate at 10°C, they exhibited similar molecular and physiological adaptation responses. We hypothesize that they take advantage of resistance mechanisms against other stressors commonly found in soda lakes, which are therefore maintained in the bacteria living in the absence of low-temperature pressure. A major difference, however, was detected for their glycine betaine content at 10°C, highlighting the power of this osmolyte to also act as a key compound in cryoprotection. Author Video: An author video summary of this article is available.
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Cui YX, Biswal BK, Guo G, Deng YF, Huang H, Chen GH, Wu D. Biological nitrogen removal from wastewater using sulphur-driven autotrophic denitrification. Appl Microbiol Biotechnol 2019; 103:6023-6039. [DOI: 10.1007/s00253-019-09935-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/06/2023]
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Berben T, Overmars L, Sorokin DY, Muyzer G. Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria. Front Microbiol 2019; 10:160. [PMID: 30837958 PMCID: PMC6382920 DOI: 10.3389/fmicb.2019.00160] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research.
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Affiliation(s)
- Tom Berben
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lex Overmars
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute for Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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Hou L, Hu BX, He M, Xu X, Zhang W. Effect of intermittent operation model on the function of soil infiltration system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:9615-9625. [PMID: 29363031 DOI: 10.1007/s11356-018-1238-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
To enhance denitrification in a process of solute infiltration through a soil, a two-section mixed-medium soil infiltration system (TMSIS) for urban non-point pollution was developed. The artificial aerobic respiration and nitrification took place in the upper aerobic section (AES), while grass powders and sawdust were mixed in the bottom anaerobic section (ANS) to supply organic carbon source for denitrification bacteria, and the reduction was increased by iron addition in the ANS. Measured resident concentrations from the bottom of each ANS column were assumed to represent mean values averaged over the column cross-sectional area. The TMSIS with hydraulic loading rates (HLR) of 0.32, 0.24, and 0.16 m3 m-2 day-1 and with wetting-drying ratio (RWD) of 1.0 showed remarkable removal efficiencies for chemical oxygen demand (COD), NH4+-N, and TP, respectively. The hydraulic loading rate of 0.32 m3 m-2 day-1 was selected as the optimal HLR due to the high contaminated runoff treatment efficiency. When RWD was 1.0, 0.5, or 0.2 with hydraulic loading rate of 0.32 m3 m-2 day-1, the TMSIS could treat synthetic urban runoff contaminants very well. The corresponding effluent water met the China's national quality standard for class V surface water. The wetting-drying ratio of 0.5 with hydraulic loading of 0.32 m3 m-2 day-1 was selected as the optimal operation conditions for the TMSIS. Aerobic respiration and nitrification mainly took place in the upper AES, in which most of the COD and the NH4+-N were removed. Mixed sawdust and grass powders used as a carbon source and heterotrophic denitrification were put at the bottom of the ANS. The developed TMSIS has the potential to be applied for urban non-point pollution removal.
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Affiliation(s)
- Lizhu Hou
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- MOE Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Bill X Hu
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
- MOE Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
- Institute of Groundwater and Earth Science, Jinan University, 601 W. Huangpu Ave, Guangzhou, Guangdong, 510632, China.
| | - Mengmeng He
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Xue Xu
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Wenjing Zhang
- Water Authority of Shijingshan District, Beijing, 100043, China
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Urbieta MS, Rascovan N, Vázquez MP, Donati E. Genome analysis of the thermoacidophilic archaeon Acidianus copahuensis focusing on the metabolisms associated to biomining activities. BMC Genomics 2017; 18:445. [PMID: 28587624 PMCID: PMC5461723 DOI: 10.1186/s12864-017-3828-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/30/2017] [Indexed: 11/21/2022] Open
Abstract
Background Several archaeal species from the order Sulfolobales are interesting from the biotechnological point of view due to their biomining capacities. Within this group, the genus Acidianus contains four biomining species (from ten known Acidianus species), but none of these have their genome sequenced. To get insights into the genetic potential and metabolic pathways involved in the biomining activity of this group, we sequenced the genome of Acidianus copahuensis ALE1 strain, a novel thermoacidophilic crenarchaeon (optimum growth: 75 °C, pH 3) isolated from the volcanic geothermal area of Copahue at Neuquén province in Argentina. Previous experimental characterization of A. copahuensis revealed a high biomining potential, exhibited as high oxidation activity of sulfur and sulfur compounds, ferrous iron and sulfide minerals (e.g.: pyrite). This strain is also autotrophic and tolerant to heavy metals, thus, it can grow under adverse conditions for most forms of life with a low nutrient demand, conditions that are commonly found in mining environments. Results In this work we analyzed the genome of Acidianus copahuensis and describe the genetic pathways involved in biomining processes. We identified the enzymes that are most likely involved in growth on sulfur and ferrous iron oxidation as well as those involved in autotrophic carbon fixation. We also found that A. copahuensis genome gathers different features that are only present in particular lineages or species from the order Sulfolobales, some of which are involved in biomining. We found that although most of its genes (81%) were found in at least one other Sulfolobales species, it is not specifically closer to any particular species (60–70% of proteins shared with each of them). Although almost one fifth of A. copahuensis proteins are not found in any other Sulfolobales species, most of them corresponded to hypothetical proteins from uncharacterized metabolisms. Conclusion In this work we identified the genes responsible for the biomining metabolisms that we have previously observed experimentally. We provide a landscape of the metabolic potentials of this strain in the context of Sulfolobales and propose various pathways and cellular processes not yet fully understood that can use A. copahuensis as an experimental model to further understand the fascinating biology of thermoacidophilic biomining archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3828-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María Sofía Urbieta
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina. .,, Calle 50, entre 115 y 116, N° 227, La Plata, Buenos Aires, Argentina.
| | - Nicolás Rascovan
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, Predio CCT, Rosario, Argentina
| | - Martín P Vázquez
- Instituto de Agrobiotecnología de Rosario (INDEAR), CONICET, Predio CCT, Rosario, Argentina
| | - Edgardo Donati
- CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina
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Kong Z, Li L, Feng C, Dong S, Chen N. Comparative investigation on integrated vertical-flow biofilters applying sulfur-based and pyrite-based autotrophic denitrification for domestic wastewater treatment. BIORESOURCE TECHNOLOGY 2016; 211:125-135. [PMID: 27015019 DOI: 10.1016/j.biortech.2016.03.083] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/13/2016] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
Two parallel biofilters applying sulfur/pyrite-based autotrophic denitrification were investigated for removing COD, TP and TN by a coordinated process. Results demonstrated good performance by removing 86.32% vs 87.14% COD and 92.56% vs 89.65% NH4(+)-N. Biofilter with sulfur (BS) was superior on nitrate (89.74% vs 80.72%) and TN removal (83.18% vs 70.42%) while biofilter with pyrite (BP) was better on TP removal (82.58% vs 77.40%) and maintaining sulfate (27.56mgL(-1) vs 41.55mgL(-1)) and pH (7.13 vs 6.31). Water-permeable adsorbents lowered clogging risk and buffered loading. Clone library revealed reasons of diversities, pH variation and sulfate accumulation of both biofilters. Sulfur was efficient on denitrification but whose byproducts were troublesome, pyrite produced less byproduct but which was sensitive to organics. This research was the first attempt to systematically compare two promising alternatives and their merits/demerits for rural wastewater on-site treatment.
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Affiliation(s)
- Zhe Kong
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Lu Li
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Chuanping Feng
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Shanshan Dong
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Nan Chen
- Key Laboratory of Groundwater and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
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Kong Z, Li L, Feng C, Chen N, Dong S, Hu W. Soil infiltration bioreactor incorporated with pyrite-based (mixotrophic) denitrification for domestic wastewater treatment. BIORESOURCE TECHNOLOGY 2015; 187:14-22. [PMID: 25827248 DOI: 10.1016/j.biortech.2015.03.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
In this study, an integrated two-stage soil infiltration bioreactor incorporated with pyrite-based (mixotrophic) denitrification (SIBPD) was designed for domestic wastewater treatment. Benefited from excellent adsorption ability and water-permeability, soil infiltration could avoid clogging, shorten operating time and lower maintenance cost. Respiration and nitrification were mostly engaged in aerobic stage (AES), while nitrate was majorly removed by pyrite-based mixotrophic denitrification mainly occurred in anaerobic stage (ANS). Fed with synthetic and real wastewater for 120days at 1.5h HRT, SIBPD demonstrated good removal performance showing 87.14% for COD, 92.84% for NH4(+)-N and 82.58% for TP along with 80.72% of nitrate removed by ANS. TN removal efficiency was 83.74% when conducting real wastewater. Compared with sulfur-based process, the effluent pH of SIBPD was maintained at 6.99-7.34 and the highest SO4(2-) concentration was only 64.63mgL(-1). This study revealed a promising and feasible application prospect for on-site domestic wastewater treatment.
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Affiliation(s)
- Zhe Kong
- Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences, Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Lu Li
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Chuanping Feng
- Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences, Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Nan Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shanshan Dong
- Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences, Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Weiwu Hu
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
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Desta AF, Assefa F, Leta S, Stomeo F, Wamalwa M, Njahira M, Appolinaire D. Microbial community structure and diversity in an integrated system of anaerobic-aerobic reactors and a constructed wetland for the treatment of tannery wastewater in Modjo, Ethiopia. PLoS One 2014; 9:e115576. [PMID: 25541981 PMCID: PMC4277355 DOI: 10.1371/journal.pone.0115576] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 11/29/2014] [Indexed: 11/18/2022] Open
Abstract
A culture-independent approach was used to elucidate the microbial diversity and structure in the anaerobic-aerobic reactors integrated with a constructed wetland for the treatment of tannery wastewater in Modjo town, Ethiopia. The system has been running with removal efficiencies ranging from 94%-96% for COD, 91%-100% for SO4(2-) and S(2-), 92%-94% for BOD, 56%-82% for total Nitrogen and 2%-90% for NH3-N. 16S rRNA gene clone libraries were constructed and microbial community assemblies were determined by analysis of a total of 801 unique clone sequences from all the sites. Operational Taxonomic Unit (OTU)--based analysis of the sequences revealed highly diverse communities in each of the reactors and the constructed wetland. A total of 32 phylotypes were identified with the dominant members affiliated to Clostridia (33%), Betaproteobacteria (10%), Bacteroidia (10%), Deltaproteobacteria (9%) and Gammaproteobacteria (6%). Sequences affiliated to the class Clostridia were the most abundant across all sites. The 801 sequences were assigned to 255 OTUs, of which 3 OTUs were shared among the clone libraries from all sites. The shared OTUs comprised 80 sequences belonging to Clostridiales Family XIII Incertae Sedis, Bacteroidetes and unclassified bacterial group. Significantly different communities were harbored by the anaerobic, aerobic and rhizosphere sites of the constructed wetland. Numerous representative genera of the dominant bacterial classes obtained from the different sample sites of the integrated system have been implicated in the removal of various carbon- containing pollutants of natural and synthetic origins. To our knowledge, this is the first report of microbial community structure in tannery wastewater treatment plant from Ethiopia.
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Affiliation(s)
- Adey Feleke Desta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fassil Assefa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Seyoum Leta
- Centre for Environmental Science, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Francesca Stomeo
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Mark Wamalwa
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Moses Njahira
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Djikeng Appolinaire
- Biosciences eastern and central Africa- International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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13
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Kong Z, Feng C, Chen N, Tong S, Zhang B, Hao C, Chen K. A soil infiltration system incorporated with sulfur-utilizing autotrophic denitrification (SISSAD) for domestic wastewater treatment. BIORESOURCE TECHNOLOGY 2014; 159:272-279. [PMID: 24657758 DOI: 10.1016/j.biortech.2014.02.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/16/2014] [Accepted: 02/22/2014] [Indexed: 06/03/2023]
Abstract
To enhance the denitrification performance of soil infiltration, a soil infiltration system incorporated with sulfur-utilizing autotrophic denitrification (SISSAD) for domestic wastewater treatment was developed, and the SISSAD performance was evaluated using synthetic domestic wastewater in this study. The aerobic respiration and nitrification were mainly taken place in the upper aerobic stage (AES), removed 88.44% COD and 89.99% NH4(+)-N. Moreover, autotrophic denitrification occurred in the bottom anaerobic stage (ANS), using the CO2 produced from AES as inorganic carbon source. Results demonstrated that the SISSAD showed a remarkable performance on COD removal efficiency of 95.09%, 84.86% for NO3(-)-N, 95.25% for NH4(+)-N and 93.15% for TP. This research revealed the developed system exhibits a promising application prospect for domestic wastewater in the future.
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Affiliation(s)
- Zhe Kong
- Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Chuanping Feng
- Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Nan Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shuang Tong
- Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences (Beijing), Ministry of Education, No. 29 Xueyuan Road, Haidian District, Beijing 100083, China; School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Chunbo Hao
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Kun Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, Beijing 100083, China
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14
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Abstract
Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.
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Affiliation(s)
- Jörg Simon
- Department of Biology, Microbial Energy Conversion and Biotechnology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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15
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The effect of energy substrates on PHB accumulation of Acidiphilium cryptum DX1-1. Curr Microbiol 2013; 67:379-87. [PMID: 23657849 DOI: 10.1007/s00284-013-0373-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
Abstract
The effect of glucose and elemental sulfur on the growth and PHB accumulation of Acidiphilium cryptum DX1-1 was investigated. Meanwhile, the differential expressions of 19 genes related with PHB accumulation, sulfur metabolism and carbon fixed in heterotrophy, phytotrophy and mixotrophy were studied by RT-qPCR. The results showed that strain DX1-1 could accumulate PHB with sulfur as the energy substance and atmospheric CO2 as carbon resource. Glucose could improve the growth of strain DX1-1 cultured in medium with sulfur as the energy substance, and almost all the key enzyme-encoding genes related with PHB, sulfur metabolism and carbon fixed were basically up-regulated. PHB polymerase (Arcy_3030), ribulose-bisphosphate carboxylase (Acry_0825), ribulose-phosphate-epimerase (Acry_0022), and cysteine synthase A (Acry_2560) played important role in PHB accumulation, the modified expression of which could influence the PHB yield. With CO2 as carbon resource, the main initial substance of PHB accumulation for strain DX1-1 was acetyl-CoA, instead of acetate with the glucose as the carbon resource. Because of accumulating PHB by fixed atmospheric CO2 while independent of light, A. cryptum DX1-1 may have specifically potential in production of PHB.
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16
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Dual activity of certain HIT-proteins: A. thaliana Hint4 and C. elegans DcpS act on adenosine 5'-phosphosulfate as hydrolases (forming AMP) and as phosphorylases (forming ADP). FEBS Lett 2010; 584:93-8. [PMID: 19896942 DOI: 10.1016/j.febslet.2009.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 10/28/2009] [Accepted: 11/01/2009] [Indexed: 11/20/2022]
Abstract
Histidine triad (HIT)-family proteins interact with different mono- and dinucleotides and catalyze their hydrolysis. During a study of the substrate specificity of seven HIT-family proteins, we have shown that each can act as a sulfohydrolase, catalyzing the liberation of AMP from adenosine 5'-phosphosulfate (APS or SO(4)-pA). However, in the presence of orthophosphate, Arabidopsis thaliana Hint4 and Caenorhabditis elegans DcpS also behaved as APS phosphorylases, forming ADP. Low pH promoted the phosphorolytic and high pH the hydrolytic activities. These proteins, and in particular Hint4, also catalyzed hydrolysis or phosphorolysis of some other adenylyl-derivatives but at lower rates than those for APS cleavage. A mechanism for these activities is proposed and the possible role of some HIT-proteins in APS metabolism is discussed.
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17
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Gay SC, Fribourgh JL, Donohoue PD, Segel IH, Fisher AJ. Kinetic properties of ATP sulfurylase and APS kinase from Thiobacillus denitrificans. Arch Biochem Biophys 2009; 489:110-7. [DOI: 10.1016/j.abb.2009.07.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 07/26/2009] [Indexed: 11/28/2022]
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18
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Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev 2009; 33:999-1043. [PMID: 19645821 DOI: 10.1111/j.1574-6976.2009.00187.x] [Citation(s) in RCA: 289] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.
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Affiliation(s)
- Wriddhiman Ghosh
- Department of Microbiology, University of Burdwan, West Bengal, India.
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19
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20
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Abstract
Phototrophic sulfur bacteria are characterized by oxidizing various inorganic sulfur compounds for use as electron donors in carbon dioxide fixation during anoxygenic photosynthetic growth. These bacteria are divided into the purple sulfur bacteria (PSB) and the green sulfur bacteria (GSB). They utilize various combinations of sulfide, elemental sulfur, and thiosulfate and sometimes also ferrous iron and hydrogen as electron donors. This review focuses on the dissimilatory and assimilatory metabolism of inorganic sulfur compounds in these bacteria and also briefly discusses these metabolisms in other types of anoxygenic phototrophic bacteria. The biochemistry and genetics of sulfur compound oxidation in PSB and GSB are described in detail. A variety of enzymes catalyzing sulfur oxidation reactions have been isolated from GSB and PSB (especially Allochromatium vinosum, a representative of the Chromatiaceae), and many are well characterized also on a molecular genetic level. Complete genome sequence data are currently available for 10 strains of GSB and for one strain of PSB. We present here a genome-based survey of the distribution and phylogenies of genes involved in oxidation of sulfur compounds in these strains. It is evident from biochemical and genetic analyses that the dissimilatory sulfur metabolism of these organisms is very complex and incompletely understood. This metabolism is modular in the sense that individual steps in the metabolism may be performed by different enzymes in different organisms. Despite the distant evolutionary relationship between GSB and PSB, their photosynthetic nature and their dependency on oxidation of sulfur compounds resulted in similar ecological roles in the sulfur cycle as important anaerobic oxidizers of sulfur compounds.
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21
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Dahl C. Inorganic Sulfur Compounds as Electron Donors in Purple Sulfur Bacteria. SULFUR METABOLISM IN PHOTOTROPHIC ORGANISMS 2008. [DOI: 10.1007/978-1-4020-6863-8_15] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Di Salle A, D'Errico G, La Cara F, Cannio R, Rossi M. A novel thermostable sulfite oxidase from Thermus thermophilus: characterization of the enzyme, gene cloning and expression in Escherichia coli. Extremophiles 2006; 10:587-98. [PMID: 16830073 DOI: 10.1007/s00792-006-0534-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 04/25/2006] [Indexed: 11/28/2022]
Abstract
A novel sulfite oxidase has been identified from Thermus thermophilus AT62. Despite this enzyme showing significant amino-acid sequence homology to several bacterial and eukaryal putative and identified sulfite oxidases, the kinetic analysis, performed following the oxidation of sulfite and with ferricyanide as the electron acceptor, already pointed out major differences from representatives of bacterial and eukaryal sources. Sulfite oxidase from T. thermophilus, purified to homogeneity, is a monomeric enzyme with an apparent molecular mass of 39.1 kDa and is almost exclusively located in the periplasm fraction. The enzyme showed sulfite oxidase activity only when ferricyanide was used as electron acceptor, which is different from most of sulfite-oxidizing enzymes from several sources that use cytochrome c as co-substrate. Spectroscopic studies demonstrated that the purified sulfite oxidase has no cytochrome like domain, normally present in homologous enzymes from eukaryotic and prokaryotic sources, and for this particular feature it is similar to homologous enzyme from Arabidopsis thaliana. The identified gene was PCR amplified on T. thermophilus AT62 genome, expressed in Escherichia coli and the recombinant protein identified and characterized.
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Affiliation(s)
- Anna Di Salle
- Istituto di Biochimica delle Proteine, CNR, Napoli, Italy
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23
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McCoy JG, Arabshahi A, Bitto E, Bingman CA, Ruzicka FJ, Frey PA, Phillips GN. Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana. Biochemistry 2006; 45:3154-62. [PMID: 16519510 PMCID: PMC2532824 DOI: 10.1021/bi052232m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The X-ray crystal structure of the At5g18200.1 protein has been determined to a nominal resolution of 2.30 A. The structure has a histidine triad (HIT)-like fold containing two distinct HIT-like motifs. The sequence of At5g18200.1 indicates a distant family relationship to the Escherichia coli galactose-1-P uridylyltransferase (GalT): the determined structure of the At5g18200.1 protein confirms this relationship. The At5g18200.1 protein does not demonstrate GalT activity but instead catalyzes adenylyl transfer in the reaction of ADP-glucose with various phosphates. The best acceptor among those evaluated is phosphate itself; thus, the At5g18200.1 enzyme appears to be an ADP-glucose phosphorylase. The enzyme catalyzes the exchange of (14)C between ADP-[(14)C]glucose and glucose-1-P in the absence of phosphate. The steady state kinetics of exchange follows the ping-pong bi-bi kinetic mechanism, with a k(cat) of 4.1 s(-)(1) and K(m) values of 1.4 and 83 microM for ADP-[(14)C]glucose and glucose-1-P, respectively, at pH 8.5 and 25 degrees C. The overall reaction of ADP-glucose with phosphate to produce ADP and glucose-1-P follows ping-pong bi-bi steady state kinetics, with a k(cat) of 2.7 s(-)(1) and K(m) values of 6.9 and 90 microM for ADP-glucose and phosphate, respectively, at pH 8.5 and 25 degrees C. The kinetics are consistent with a double-displacement mechanism that involves a covalent adenylyl-enzyme intermediate. The X-ray crystal structure of this intermediate was determined to 1.83 A resolution and shows the AMP group bonded to His(186). The value of K(eq) in the direction of ADP and glucose-1-P formation is 5.0 at pH 7.0 and 25 degrees C in the absence of a divalent metal ion, and it is 40 in the presence of 1 mM MgCl(2).
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Affiliation(s)
- Jason G. McCoy
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706
| | - Abolfazl Arabshahi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Eduard Bitto
- University of Wisconsin Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706
| | - Craig A. Bingman
- University of Wisconsin Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706
| | - Frank J. Ruzicka
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- University of Wisconsin Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706
- Corresponding author: George N. Phillips Jr., Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706-1544, Tel (608)263-6142, EM
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24
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Beller HR, Chain PSG, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 2006; 188:1473-88. [PMID: 16452431 PMCID: PMC1367237 DOI: 10.1128/jb.188.4.1473-1488.2006] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 11/30/2005] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by beta-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.
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Affiliation(s)
- Harry R Beller
- Lawrence Livermore National Laboratory, P.O. Box 808, L-542, Livermore, California 94551-0808, USA.
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25
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Kletzin A, Urich T, Müller F, Bandeiras TM, Gomes CM. Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea. J Bioenerg Biomembr 2004; 36:77-91. [PMID: 15168612 DOI: 10.1023/b:jobb.0000019600.36757.8c] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The oxidation and reduction of elemental sulfur and reduced inorganic sulfur species are some of the most important energy-yielding reactions for microorganisms living in volcanic hot springs, solfataras, and submarine hydrothermal vents, including both heterotrophic, mixotrophic, and chemolithoautotrophic, carbon dioxide-fixing species. Elemental sulfur is the electron donor in aerobic archaea like Acidianus and Sulfolobus. It is oxidized via sulfite and thiosulfate in a pathway involving both soluble and membrane-bound enzymes. This pathway was recently found to be coupled to the aerobic respiratory chain, eliciting a link between sulfur oxidation and oxygen reduction at the level of the respiratory heme copper oxidase. In contrast, elemental sulfur is the electron acceptor in a short electron transport chain consisting of a membrane-bound hydrogenase and a sulfur reductase in (facultatively) anaerobic chemolithotrophic archaea Acidianus and Pyrodictium species. It is also the electron acceptor in organoheterotrophic anaerobic species like Pyrococcus and Thermococcus, however, an electron transport chain has not been described as yet. The current knowledge on the composition and properties of the aerobic and anaerobic pathways of dissimilatory elemental sulfur metabolism in thermophilic archaea is summarized in this contribution.
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Affiliation(s)
- Arnulf Kletzin
- Institute of Microbiology and Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany.
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26
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Izard T. A novel adenylate binding site confers phosphopantetheine adenylyltransferase interactions with coenzyme A. J Bacteriol 2003; 185:4074-80. [PMID: 12837781 PMCID: PMC164871 DOI: 10.1128/jb.185.14.4074-4080.2003] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphopantetheine adenylyltransferase (PPAT) regulates the key penultimate step in the essential coenzyme A (CoA) biosynthetic pathway. PPAT catalyzes the reversible transfer of an adenylyl group from Mg(2+):ATP to 4'-phosphopantetheine to form 3'-dephospho-CoA (dPCoA) and pyrophosphate. The high-resolution crystal structure of PPAT complexed with CoA has been determined. Remarkably, CoA and the product dPCoA bind to the active site in distinct ways. Although the phosphate moiety within the phosphopantetheine arm overlaps, the pantetheine arm binds to the same pocket in two distinct conformations, and the adenylyl moieties of these two ligands have distinct binding sites. Moreover, the PPAT:CoA crystal structure confirms the asymmetry of binding to the two trimers within the hexameric enzyme. Specifically, the pantetheine arm of CoA bound to one protomer within the asymmetric unit displays the dPCoA-like conformation with the adenylyl moiety disordered, whereas CoA binds the twofold-related protomer in an ordered and unique fashion.
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Affiliation(s)
- Tina Izard
- Department of Hematology-Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA.
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27
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Hanna E, MacRae IJ, Medina DC, Fisher AJ, Segel IH. ATP sulfurylase from the hyperthermophilic chemolithotroph Aquifex aeolicus. Arch Biochem Biophys 2002; 406:275-88. [PMID: 12361716 DOI: 10.1016/s0003-9861(02)00428-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ATP sulfurylase from the hyperthermophilic chemolithotroph Aquifex aeolicus is a bacterial ortholog of the enzyme from filamentous fungi. (The subunit contains an adenosine 5'-phosphosulfate (APS) kinase-like, C-terminal domain.) The enzyme is highly heat stable with a half-life >1h at 90 degrees C. Steady-state kinetics are consistent with a random A-B, ordered P-Q mechanism where A=MgATP, B=SO4(2-), P=PP(i), and Q=APS. The kinetic constants suggest that the enzyme is optimized to act in the direction of ATP+sulfate formation. Chlorate is competitive with sulfate and with APS. In sulfur chemolithotrophs, ATP sulfurylase provides an efficient route for recycling PP(i) produced by biosynthetic reactions. However, the protein possesses low APS kinase activity. Consequently, it may also function to produce PAPS for sulfate ester formation or sulfate assimilation when hydrogen serves as the energy source and a reduced inorganic sulfur source is unavailable.
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Affiliation(s)
- Eissa Hanna
- Section of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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28
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Brenner C. Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases. Biochemistry 2002; 41:9003-14. [PMID: 12119013 PMCID: PMC2571077 DOI: 10.1021/bi025942q] [Citation(s) in RCA: 226] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIT (histidine triad) proteins, named for a motif related to the sequence HphiHphiHphiphi (phi, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides, and contain a approximately 30 kDa domain that is typically either a homodimer of approximately 15 kDa polypeptides with two active-sites or an internally, imperfectly repeated polypeptide that retains a single HIT active site. On the basis of sequence, substrate specificity, structure, evolution, and mechanism, HIT proteins can be classified into the Hint branch, which consists of adenosine 5'-monophosphoramide hydrolases, the Fhit branch, which consists of diadenosine polyphosphate hydrolases, and the GalT branch, which consists of specific nucleoside monophosphate transferases, including galactose-1-phosphate uridylyltransferase, diadenosine tetraphosphate phosphorylase, and adenylyl sulfate:phosphate adenylytransferase. At least one human representative of each branch is lost in human diseases. Aprataxin, a Hint branch hydrolase, is mutated in ataxia-oculomotor apraxia syndrome. Fhit is lost early in the development of many epithelially derived tumors. GalT is deficient in galactosemia. Additionally, ASW is an avian Hint family member that has evolved to have unusual gene expression properties and the complete loss of its nucleotide binding site. The potential roles of ASW and Hint in avian sexual development are discussed elsewhere. Here we review what is known about biological activities of HIT proteins, the structural and biochemical bases for their functions, and propose a new enzyme mechanism for Hint and Fhit that may account for the differences between HIT hydrolases and transferases.
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Affiliation(s)
- Charles Brenner
- Structural Biology and Bioinformatics Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.
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29
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Bieganowski P, Garrison PN, Hodawadekar SC, Faye G, Barnes LD, Brenner C. Adenosine monophosphoramidase activity of Hint and Hnt1 supports function of Kin28, Ccl1, and Tfb3. J Biol Chem 2002; 277:10852-60. [PMID: 11805111 PMCID: PMC2556056 DOI: 10.1074/jbc.m111480200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The histidine triad superfamily of nucleotide hydrolases and nucleotide transferases consists of a branch of proteins related to Hint and Aprataxin, a branch of Fhit-related hydrolases, and a branch of galactose-1-phosphate uridylyltransferase (GalT)-related transferases. Although substrates of Fhit and GalT are known and consequences of mutations in Aprataxin, Fhit, and GalT are known, good substrates had not been reported for any member of the Hint branch, and mutational consequences were unknown for Hint orthologs, which are the most ancient and widespread proteins in the Hint branch and in the histidine triad superfamily. Here we show that rabbit and yeast Hint hydrolyze the natural product adenosine-5'-monophosphoramidate (AMPNH(2)) in an active-site-dependent manner at second order rates exceeding 1,000,000 m(-1) s(-1). Yeast strains constructed with specific loss of the Hnt1 active site fail to grow on galactose at elevated temperatures. Loss of Hnt1 enzyme activity also leads to hypersensitivity to mutations in Ccl1, Tfb3, and Kin28, which constitute the TFIIK kinase subcomplex of general transcription factor TFIIH and to mutations in Cak1, which phosphorylates Kin28. The target of Hnt1 regulation in this pathway was shown to be downstream of Cak1 and not to affect stability of Kin28 monomers. Functional complementation of all Hnt1 phenotypes was provided by rabbit Hint, which is only 22% identical to yeast Hnt1 but has very similar adenosine monophosphoramidase activity.
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Affiliation(s)
- Pawel Bieganowski
- Structural Biology and Bioinformatics Program, Kimmel Cancer Center, Philadelphia, Pennsylvania 19107, USA
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30
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Garavaglia S, D'Angelo I, Emanuelli M, Carnevali F, Pierella F, Magni G, Rizzi M. Structure of human NMN adenylyltransferase. A key nuclear enzyme for NAD homeostasis. J Biol Chem 2002; 277:8524-30. [PMID: 11751893 DOI: 10.1074/jbc.m111589200] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nicotinamide mononucleotide adenylyltransferase (NMNAT), a member of the nucleotidyltransferase alpha/beta-phosphodiesterases superfamily, catalyzes a universal step (NMN + ATP = NAD + PP(i)) in NAD biosynthesis. Localized within the nucleus, the activity of the human enzyme is greatly altered in tumor cells, rendering it a promising target for cancer chemotherapy. By using a combination of single isomorphous replacement and density modification techniques, the human NMNAT structure was solved by x-ray crystallography to a 2.5-A resolution, revealing a hexamer that is composed of alpha/beta-topology subunits. The active site topology of the enzyme, analyzed through homology modeling and structural comparison with other NMNATs, yielded convincing evidence for a substrate-induced conformational change. We also observed remarkable structural conservation in the ATP-recognition motifs GXXXPX(T/H)XXH and SXTXXR, which we take to be the universal signature for NMNATs. Structural comparison of human and prokaryotic NMNATs may also lead to the rational design of highly selective antimicrobial drugs.
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Affiliation(s)
- Silvia Garavaglia
- Department of Genetics and Microbiology A. Buzzati Traverso, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
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Izard T. The crystal structures of phosphopantetheine adenylyltransferase with bound substrates reveal the enzyme's catalytic mechanism. J Mol Biol 2002; 315:487-95. [PMID: 11812124 DOI: 10.1006/jmbi.2001.5272] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in the coenzyme A pathway that catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) in the presence of magnesium. To investigate the reaction mechanism, the high-resolution crystal structures of the Escherichia coli PPAT have been determined in the presence of either ATP or Ppant. Structural details of the catalytic center revealed specific roles for individual amino acid residues involved in substrate binding and catalysis. The side-chain of His18 stabilizes the expected pentacovalent intermediate, whereas the side-chains of Thr10 and Lys42 orient the nucleophile for an in-line displacement mechanism. The binding site for the manganese ion that interacts with the phosphate groups of the nucleotide has also been identified. Within the PPAT hexamer, one trimer is in its substrate-free state, whereas the other is in a substrate-bound state.
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Affiliation(s)
- Tina Izard
- Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, TN 38105-2794, USA.
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Beynon JD, MacRae IJ, Huston SL, Nelson DC, Segel IH, Fisher AJ. Crystal structure of ATP sulfurylase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila. Biochemistry 2001; 40:14509-17. [PMID: 11724564 DOI: 10.1021/bi015643l] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In sulfur chemolithotrophic bacteria, the enzyme ATP sulfurylase functions to produce ATP and inorganic sulfate from APS and inorganic pyrophosphate, which is the final step in the biological oxidation of hydrogen sulfide to sulfate. The giant tubeworm, Riftia pachyptila, which lives near hydrothermal vents on the ocean floor, harbors a sulfur chemolithotroph as an endosymbiont in its trophosome tissue. This yet-to-be-named bacterium was found to contain high levels of ATP sulfurylase that may provide a substantial fraction of the organisms ATP. We present here, the crystal structure of ATP sulfurylase from this bacterium at 1.7 A resolution. As predicted from sequence homology, the enzyme folds into distinct N-terminal and catalytic domains, but lacks the APS kinase-like C-terminal domain that is present in fungal ATP sulfurylase. The enzyme crystallizes as a dimer with one subunit in the crystallographic asymmetric unit. Many buried solvent molecules mediate subunit contacts at the interface. Despite the high concentration of sulfate needed for crystallization, no ordered sulfate was observed in the sulfate-binding pocket. The structure reveals a mobile loop positioned over the active site. This loop is in a "closed" or "down" position in the reported crystal structures of fungal ATP sulfurylases, which contained bound substrates, but it is in an "open" or "up" position in the ligand-free Riftia symbiont enzyme. Thus, closure of the loop correlates with occupancy of the active site, although the loop itself does not interact directly with bound ligands. Rather, it appears to assist in the orientation of residues that do interact with active-site ligands. Amino acid differences between the mobile loops of the enzymes from sulfate assimilators and sulfur chemolithotrophs may account for the significant kinetic differences between the two classes of ATP sulfurylase.
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Affiliation(s)
- J D Beynon
- Department of Chemistry, Section of Molecular and Cellular Biology, Davis, California 95616, USA
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Abstract
Despite its toxicity, sulfite plays a key role in oxidative sulfur metabolism and there are even some microorganisms which can use it as sole electron source. Sulfite is the main intermediate in the oxidation of sulfur compounds to sulfate, the major product of most dissimilatory sulfur-oxidizing prokaryotes. Two pathways of sulfite oxidation are known: (1) direct oxidation to sulfate catalyzed by a sulfite:acceptor oxidoreductase, which is thought to be a molybdenum-containing enzyme; (2) indirect oxidation under the involvement of the enzymes adenylylsulfate (APS) reductase and ATP sulfurylase and/or adenylylsulfate:phosphate adenylyltransferase with APS as an intermediate. The latter pathway allows substrate phosphorylation and occurs in the bacterial cytoplasm. Direct oxidation appears to have a wider distribution; however, a redundancy of pathways has been described for diverse photo- or chemotrophic, sulfite-oxidizing prokaryotes. In many pro- and also eukaryotes sulfite is formed as a degradative product from molecules containing sulfur as a heteroatom. In these organisms detoxification of sulfite is generally achieved by direct oxidation to sulfate.
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Affiliation(s)
- U Kappler
- School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia, Qld. 4072, Australia.
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D'Angelo I, Raffaelli N, Dabusti V, Lorenzi T, Magni G, Rizzi M. Structure of nicotinamide mononucleotide adenylyltransferase: a key enzyme in NAD(+) biosynthesis. Structure 2000; 8:993-1004. [PMID: 10986466 DOI: 10.1016/s0969-2126(00)00190-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Nicotinamide adenine dinucleotide (NAD(+)) is an essential cofactor involved in fundamental processes in cell metabolism. The enzyme nicotinamide mononucleotide adenylyltransferase (NMN AT) plays a key role in NAD(+) biosynthesis, catalysing the condensation of nicotinamide mononucleotide and ATP, and yielding NAD(+) and pyrophosphate. Given its vital role in cell life, the enzyme represents a possible target for the development of new antibacterial agents. RESULTS The structure of NMN AT from Methanococcus jannaschii in complex with ATP has been solved by X-ray crystallography at 2.0 A resolution, using a combination of single isomorphous replacement and density modification techniques. The structure reveals a hexamer with 32 point group symmetry composed of alpha/beta topology subunits. The catalytic site is located in a deep cleft on the surface of each subunit, where one ATP molecule and one Mg(2+) are observed. A strictly conserved HXGH motif (in single-letter amino acid code) is involved in ATP binding and recognition. CONCLUSIONS The structure of NMN AT closely resembles that of phosphopantetheine adenylyltransferase. Remarkably, in spite of the fact that the two enzymes share the same fold and hexameric assembly, a striking difference in their quaternary structure is observed. Moreover, on the basis of structural similarity including the HXGH motif, we identify NMN AT as a novel member of the newly proposed superfamily of nucleotidyltransferase alpha/beta phosphodiesterases. Our structural data suggest that the catalytic mechanism does not rely on the direct involvement of any protein residues and is likely to be carried out through optimal positioning of substrates and transition-state stabilisation, as is proposed for other members of the nucleotidyltransferase alpha/beta phosphodiesterase superfamily.
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Affiliation(s)
- I D'Angelo
- Department of Genetics and Microbiology 'A. Buzzati Traverso', University of Pavia, via Ferrata 1, 27100, Pavia, Italy
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