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Kaviraj M, Kumar U, Snigdha A, Chatterjee S. Nitrate reduction to ammonium: a phylogenetic, physiological, and genetic aspects in Prokaryotes and eukaryotes. Arch Microbiol 2024; 206:297. [PMID: 38861039 DOI: 10.1007/s00203-024-04009-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024]
Abstract
The microbe-mediated conversion of nitrate (NO3-) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3- reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3- -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3--reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3- assimilation genes in response to NO3- availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.
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Affiliation(s)
- Megha Kaviraj
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
- The University of Burdwan, Burdwan, 713104, West Bengal, India.
| | - Upendra Kumar
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
| | - Alisha Snigdha
- Siksha 'O' Anusandhan University, Bhubaneswar, 751003, Odisha, India
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Thakur P, Gauba P. Expression Analysis of Nitrogen Metabolism Genes in Lelliottia amnigena PTJIIT1005, Comparison with Escherichia coli K12 and Validation of Nitrogen Metabolism Genes. Biochem Genet 2024:10.1007/s10528-024-10677-w. [PMID: 38341394 DOI: 10.1007/s10528-024-10677-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Escherichia coli K12 and Lelliottia amnigena PTJIIT1005 bacteria were isolated from the polluted Yamuna River (Delhi, India) site, which can remediate nitrate from groundwater media under anaerobic conditions. BV-BRC (Bacterial and Viral Bioinformatics Resource Center) information system, RAST, and PGAP servers were used to annotate the nitrogen metabolism genes from the genome sequence of these microbes. Here we compared the strains L. amnigena PTJIIT1005 with E. coli K12 in the context of nitrogen metabolism genes. Sequence alignment, similarity percentage, and phylogenetic analysis were done to find similarities between the genes. Common nitrogen genes of these strains, like respiratory nitrate reductase, nitrite reductase, nitric oxide reductase, glutamine synthetase, and hydroxylamine reductase, have found good sequence similarity (83-94%) with each other. The PATRIC tool identified N-operons, and the nitrate reductase gene clusters were also determined as per literature survey. Protein-protein interaction network was constructed using STRING 12.0 database and Cytoscape v 3.10.0 software plug-in Network analyzer. On the basis of network topological parameters NarG, NarZ, NarY, NarH, NarI, NarV, NirB, NirD, NapA, and NapB are the key genes in network of E. coli K12 strain. Nar, NirB, NirD, NasA, NasB, NasC, NasD, NasE, and GlnA are the key genes in network of L. amnigena PTJIIT1005. Among these, NarG and NirB are the superhub genes because of having highest Betweenness centrality (BC) and node degree. The functional enrichment analysis was determined using PANTHER GENE ONTOLOGY and DAVID software exhibited their role in nitrogen metabolism pathway and nitrate assimilation. Further, SWISS-MODEL was used to predict the 3D protein structure of these enzymes, and after, these structures were validated by Ramachandran plot using the PROCHECK tool. The Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) method was used to determine the N-genes expression level in both strains. This study showed that E. coli K12 and L. amnigena PTJIIT1005 have common nitrogen metabolism genes involved in the same functional role, like the denitrification pathway. Additionally, operon arrangement study and PPI network revealed that E. coli K12 has only a denitrification pathway, while L. amnigena PTJIIT1005 has both an assimilation and denitrification pathway. PCR successfully amplified selected N-metabolizing genes, and the expression level of N-genes was high in strain L. amnigena PTJIIT1005. Our previous experimental study exhibited a better nitrate remediation rate in L. amnigena PTJIIT1005 over E. coli K12. This study confirmed the presence of assimilation and denitrification process through amplified N-metabolizing genes and showed high expression of N-genes in L. amnigena PTJIIT1005, which favor the evidence of better nitrate remediation in L. amnigena PTJIIT1005 over E. coli K12.
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Affiliation(s)
- Preeti Thakur
- Department of Biotechnology, Jaypee Institute of Information & Technology, Noida, 201307, India
| | - Pammi Gauba
- Head of Department, Jaypee Institute of Information & Technology, Noida, Uttar Pradesh, 201307, India.
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Gao Y, Zhu J, Wang K, Ma Y, Fang J, Liu G. Discovery of a heterotrophic aerobic denitrification Pseudomonas sp. G16 and its unconventional nitrogen metabolic pathway. BIORESOURCE TECHNOLOGY 2023; 387:129670. [PMID: 37591467 DOI: 10.1016/j.biortech.2023.129670] [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: 07/01/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023]
Abstract
From the aerobic pond of the farm, the Pseudomonas sp. G16 was screened and isolated, which was confirmed to exhibit heterotrophic nitrification and aerobic denitrification. The removal rates of Ammonia (100 mg/L), nitrate (120 mg/L), and nitrite (100 mg/L) by the strain were 94.13%, 92.62%, and 85.67%, and the nitrogen metabolism pathway of strain G16 was analyzed by whole genome sequencing combined with its nitrification-denitrification intermediate products, it was found that the strain had independent nitrification-denitrification ability and no nitrite accumulation. Under the conditions of carbon source of sodium succinate hexahydrate, C/N ratio of 15, pH of 7.5, temperature of 15 °C, and DO of 210 rpm, strain G16 showed excellent denitrification performance. Strain G16 was prepared into biochar-based immobilized bacterial particles, which successfully improved its nitrogen removal efficiency and stability. Therefore, the application of strain G16 in the field of real wastewater treatment has very necessary research value.
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Affiliation(s)
- Yu Gao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Junwen Zhu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Keyu Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Yong Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China.
| | - Gang Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
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Xie Y, Tian X, Liu Y, Zhao K, Li Y, Luo K, Wang B, Dong S. Nitrogen removal capability and mechanism of a novel heterotrophic nitrifying-aerobic denitrifying strain H1 as a potential candidate in mariculture wastewater treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:106366-106377. [PMID: 37728674 DOI: 10.1007/s11356-023-29666-4] [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: 04/12/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
The nitrogen removal performance and mechanisms of Bacillus subtilis H1 isolated from a mariculture environment were investigated. Strain H1 efficiently removed NH4+-N, NO2--N, and NO3--N in simulated wastewater with removal efficiencies of 85.61%, 90.58%, and 57.82%, respectively. Strain H1 also efficiently degraded mixed nitrogen (NH4+-N mixed with NO2--N and/or NO3--N) and had removal efficiencies ranging from 82.39 to 89.54%. Nitrogen balance analysis revealed that inorganic nitrogen was degraded by heterotrophic nitrification-aerobic denitrification (HN-AD) and assimilation. 15N isotope tracing indicated that N2O was the product of the HN-AD process, while N2 as the final product was only detected during the reduction of 15NO2--N. The nitrogen assimilation and dissimilation pathways by strain H1 were further clarified using complete genome sequencing, nitrification inhibitor addition, and enzymatic activity measurement, and the ammonium oxidation process was speculated as NH4+ → NH2OH → NO → N2O. These results showed the application prospect of B. subtilis H1 in treating mariculture wastewater.
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Affiliation(s)
- Yumeng Xie
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China.
| | - Yang Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kun Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Yongmei Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kai Luo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Bo Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Shuanglin Dong
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China
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Kametani Y, Ikeda K, Yoshizawa K, Shiota Y. Mechanistic Study of Reduction of Nitrite to NO by the Copper(II) Complex: Different Concerted Proton-Electron Transfer Reactivity between Nitrite and Nitro Complexes. Inorg Chem 2023; 62:13765-13774. [PMID: 37590095 DOI: 10.1021/acs.inorgchem.3c01383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The literature contains numerous reports of copper complexes for nitrite (NO2-) reduction. However, details of how protons and electrons arrive and how nitric oxide (NO) is released remain unknown. The influence of the coordination mode of nitrite on reactivity is also under debate. Kundu and co-workers have reported nitrite reduction by a copper(II) complex [J. Am. Chem. Soc. 2020, 142, 1726-1730]. In their report, the copper(II) complex reduced nitrite using a phenol derivative as a reductant, resulting in NO, a hydroxyl copper(II) complex, and the corresponding biphenol. Also, the involvement of proton-coupled electron transfer was proposed by mechanistic studies. Herein, density functional theory calculations were performed to determine a mechanism for reduction of nitrite by a copper(II) complex. As a result of geometry optimization of an initial complex, two possible structures were obtained: Cu-ONO and Cu-NO2. Two possible reaction pathways initiated from Cu-ONO or Cu-NO2 were then considered. The calculation results indicated that the Cu-ONO pathway is energetically favorable. When changes in the electronic structure were considered, both pathways were found to involve concerted proton-electron transfer (CPET). In addition, an intrinsic reaction coordinate analysis revealed that the two pathways were achieved by different types of CPET. Furthermore, an intrinsic bond orbital analysis clearly indicated that, in the Cu-ONO pathway, the chemical events involved proceeded concertedly yet asynchronously.
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Affiliation(s)
- Yohei Kametani
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kei Ikeda
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Harland JB, Samanta S, Lehnert N. Bacterial nitric oxide reductase (NorBC) models employing click chemistry. J Inorg Biochem 2023; 246:112280. [PMID: 37352656 DOI: 10.1016/j.jinorgbio.2023.112280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/15/2023] [Accepted: 05/30/2023] [Indexed: 06/25/2023]
Abstract
Bacterial NO Reductase (NorBC or cNOR) is a membrane-bound enzyme found in denitrifying bacteria that catalyzes the two-electron reduction of NO to N2O and water. The mechanism by which NorBC operates is highly debated, due to the fact that this enzyme is difficult to work with, and no intermediates of the NO reduction reaction could have been identified so far. The unique active site of NorBC consists of a heme b3/non-heme FeB diiron center. Synthetic model complexes provide the opportunity to obtain insight into possible mechanistic alternatives for this enzyme. In this paper, we present three new synthetic model systems for NorBC, consisting of a tetraphenylporphyrin-derivative clicked to modified BMPA-based ligands (BMPA = bis(methylpyridyl)amine) that model the non-heme site in the enzyme. These complexes have been characterized by EPR, IR and UV-Vis spectroscopy. The reactivity with NO was then investigated, and it was found that the complex with the BMPA-carboxylate ligand as the non-heme component has a very low affinity for NO at the non-heme iron site. If the carboxylate functional group is replaced with a phenolate or pyridine group, reactivity is restored and formation of a diiron dinitrosyl complex was observed. Upon one-electron reduction of the nitrosylated complexes, following the semireduced pathway for NO reduction, formation of dinitrosyl iron complexes (DNICs) was observed in all three cases, but no N2O could be detected.
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Affiliation(s)
- Jill B Harland
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Subhra Samanta
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States.
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Wu S, Lv N, Zhou Y, Li X. Simultaneous nitrogen removal via heterotrophic nitrification and aerobic denitrification by a novel Lysinibacillus fusiformis B301. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2023; 95:e10850. [PMID: 36889322 DOI: 10.1002/wer.10850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/16/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
Simultaneous nitrogen removal via heterotrophic nitrification and aerobic denitrification (HN-AD) has received widespread attention in biological treatment of wastewater. This study reported a novel Lysinibacillus fusiformis B301 strain, which effectively removed nitrogenous pollutants via HN-AD in one aerobic reactor with no nitrite accumulated. It exhibited the optimal nitrogen removal efficiency under 30°C, citrate as the carbon source and C/N ratio of 15. The maximum nitrogen removal rates were up to 2.11 mgNH4 + -N/(L·h), 1.62 mgNO3 - -N/(L·h), and 1.41 mgNO2 - -N/(L·h), respectively, when ammonium, nitrate, and nitrite were employed as the only nitrogen source under aerobic conditions. Ammonium nitrogen was preferentially consumed via HN-AD in the coexistence of three nitrogen species, and the removal efficiencies of total nitrogen were up to 94.26%. Nitrogen balance analysis suggested that 83.25% of ammonium was converted to gaseous nitrogen. The HD-AD pathway catalyzed by L. fusiformis B301 followed NH 4 + → N H 2 OH → NO 2 - → NO 3 - → NO 2 - → N 2 , supported by the results of key denitrifying enzymatic activities. PRACTITIONER POINTS: The novel Lysinibacillus fusiformis B301 exhibited the outstanding HN-AD ability. The novel Lysinibacillus fusiformis B301 simultaneously removed multiple nitrogen species. No nitrite accumulated during the HN-AD process. Five key denitrifying enzymes were involved in the HN-AD process. Ammonium nitrogen (83.25%) was converted to gaseous nitrogen by the novel strain.
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Affiliation(s)
- Shiqi Wu
- Laboratory of Environmental Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, China
- Jiangsu Cooperative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
| | - Na Lv
- Laboratory of Environmental Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, China
- Jiangsu Cooperative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
| | - Yu Zhou
- Laboratory of Environmental Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, China
- Jiangsu Cooperative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
| | - Xiufen Li
- Laboratory of Environmental Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, China
- Jiangsu Cooperative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
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Zhou Y, Jiang D, Yao X, Luo Y, Yang Z, Ren M, Zhang G, Yu Y, Lu A, Wang Y. Pan-genome wide association study of Glaesserella parasuis highlights genes associated with virulence and biofilm formation. Front Microbiol 2023; 14:1160433. [PMID: 37138622 PMCID: PMC10149723 DOI: 10.3389/fmicb.2023.1160433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
Glaesserella parasuis is a gram-negative bacterium that causes fibrotic polyserositis and arthritis in pig, significantly affecting the pig industry. The pan-genome of G. parasuis is open. As the number of genes increases, the core and accessory genomes may show more pronounced differences. The genes associated with virulence and biofilm formation are also still unclear due to the diversity of G. parasuis. Therefore, we have applied a pan-genome-wide association study (Pan-GWAS) to 121 strains G. parasuis. Our analysis revealed that the core genome consists of 1,133 genes associated with the cytoskeleton, virulence, and basic biological processes. The accessory genome is highly variable and is a major cause of genetic diversity in G. parasuis. Furthermore, two biologically important traits (virulence, biofilm formation) of G. parasuis were studied via pan-GWAS to search for genes associated with the traits. A total of 142 genes were associated with strong virulence traits. By affecting metabolic pathways and capturing the host nutrients, these genes are involved in signal pathways and virulence factors, which are beneficial for bacterial survival and biofilm formation. This research lays the foundation for further studies on virulence and biofilm formation and provides potential new drug and vaccine targets against G. parasuis.
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Affiliation(s)
- You Zhou
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dike Jiang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xueping Yao
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan Luo
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zexiao Yang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Meishen Ren
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yin Wang,
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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Bernabeu E, Miralles-Robledillo JM, Giani M, Valdés E, Martínez-Espinosa RM, Pire C. In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification. Biomolecules 2021; 11:biom11071043. [PMID: 34356667 PMCID: PMC8301774 DOI: 10.3390/biom11071043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Affiliation(s)
- Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Elena Valdés
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
- Correspondence: ; Tel.: +34-965903400 (ext. 2064)
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11
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Chen H, Zhou W, Zhu S, Liu F, Qin L, Xu C, Wang Z. Biological nitrogen and phosphorus removal by a phosphorus-accumulating bacteria Acinetobacter sp. strain C-13 with the ability of heterotrophic nitrification-aerobic denitrification. BIORESOURCE TECHNOLOGY 2021; 322:124507. [PMID: 33338941 DOI: 10.1016/j.biortech.2020.124507] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/29/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Strain C-13, identified as an Acinetobacter sp. by homology searches, exhibited efficient simultaneous heterotrophic nitrification-aerobic denitrification phosphorus removal (SNDPR) abilities by nitrogen balance analysis and further confirmation of successful amplification of functional genes ppk, napA, and nirS. In addition, strain C-13 could utilize NH4+-N, NO3--N, and NO2--N as nitrogen sources, among which NH4+-N was indicated to be an excellent nitrogen source for assimilation and heterotrophic nitrification. Besides, the optimum conditions for nutrient removal were determined as follows: sodium acetate as the sole carbon source, C/N/P ratio of 100/10/2, pH = 7.5, and temperature of 30 °C. Meanwhile, the strain also showed the traditional features, such as release and the excess uptake of phosphate under anaerobic/aerobic conditions, with the highest phosphorus content of 5.01% after cultivation. Strain C-13 presents promising prospects for application in biologicalnutrient removal in wastewater treatment.
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Affiliation(s)
- Huanjun Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China; University of China Academy of Sciences, Beijing 100049, China
| | - Weizheng Zhou
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China
| | - Shunni Zhu
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China
| | - Fen Liu
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China; University of China Academy of Sciences, Beijing 100049, China
| | - Lei Qin
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China
| | - Chao Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Zhongming Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, China.
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12
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Mycobacterium smegmatis does not display functional redundancy in nitrate reductase enzymes. PLoS One 2021; 16:e0245745. [PMID: 33471823 PMCID: PMC7816997 DOI: 10.1371/journal.pone.0245745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/06/2021] [Indexed: 12/04/2022] Open
Abstract
Reduction of nitrate to nitrite in bacteria is an essential step in the nitrogen cycle, catalysed by a variety of nitrate reductase (NR) enzymes. The soil dweller, Mycobacterium smegmatis is able to assimilate nitrate and herein we set out to confirm the genetic basis for this by probing NR activity in mutants defective for putative nitrate reductase (NR) encoding genes. In addition to the annotated narB and narGHJI, bioinformatics identified three other putative NR-encoding genes: MSMEG_4206, MSMEG_2237 and MSMEG_6816. To assess the relative contribution of each, the corresponding gene loci were deleted using two-step allelic replacement, individually and in combination. The resulting strains were tested for their ability to assimilate nitrate and reduce nitrate under aerobic and anaerobic conditions, using nitrate assimilation and modified Griess assays. We demonstrated that narB, narGHJI, MSMEG_2237 and MSMEG_6816 were individually dispensable for nitrate assimilation and for nitrate reductase activity under aerobic and anaerobic conditions. Only deletion of MSMEG_4206 resulted in significant reduction in nitrate assimilation under aerobic conditions. These data confirm that in M. smegmatis, narB, narGHJI, MSMEG_2237 and MSMEG_6816 are not required for nitrate reduction as MSMEG_4206 serves as the sole assimilatory NR.
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Dissimilatory Nitrate Reduction to Ammonium (DNRA) and Denitrification Pathways Are Leveraged by Cyclic AMP Receptor Protein (CRP) Paralogues Based on Electron Donor/Acceptor Limitation in Shewanella loihica PV-4. Appl Environ Microbiol 2021; 87:AEM.01964-20. [PMID: 33158888 DOI: 10.1128/aem.01964-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Under anoxic conditions, many bacteria, including Shewanella loihica strain PV-4, could use nitrate as an electron acceptor for dissimilatory nitrate reduction to ammonium (DNRA) and/or denitrification. Previous and current studies have shown that DNRA is favored under higher ambient carbon-to-nitrogen (C/N) ratios, whereas denitrification is upregulated under lower C/N ratios, which is consistent with our bioenergetics calculations. Interestingly, computational analyses indicate that the common cyclic AMP receptor protein (designated CRP1) and its paralogue CRP2 might both be involved in the regulation of two competing dissimilatory nitrate reduction pathways, DNRA and denitrification, in S. loihica PV-4 and several other denitrifying Shewanella species. To explore the regulatory mechanism underlying the dissimilatory nitrate reduction (DNR) pathways, nitrate reduction of a series of in-frame deletion mutants was analyzed under different C/N ratios. Deletion of crp1 could accelerate the reduction of nitrite to NO under both low and high C/N ratios. CRP1 is not required for denitrification and actually suppresses production of NO and N2O gases. Deletion of either of the NO-forming nitrite reductase genes nirK or crp2 blocked production of NO gas. Furthermore, real-time PCR and electrophoretic mobility shift assays (EMSAs) demonstrated that the transcription levels of DNRA-relevant genes such as nap-β (napDABGH), nrfA, and cymA were upregulated by CRP1, while nirK transcription was dependent on CRP2. There are tradeoffs between the different physiological roles of nitrate/lactate, as nitrogen nutrient/carbon source and electron acceptor/donor and CRPs may leverage dissimilatory nitrate reduction pathways for maximizing energy yield and bacterial survival under ambient environmental conditions.IMPORTANCE Some microbes utilize different dissimilatory nitrate reduction (DNR) pathways, including DNR to ammonia (DNRA) and denitrification pathways, for anaerobic respiration in response to ambient carbon/nitrogen ratio changes. Large-scale industrial nitrogen fixation and fertilizer application raise the concern of emission of N2O, a stable gas with potent global warming potential, as consequence of microbial respiration, thereby aggravating global warming and climate change. However, little is known about the molecular mechanism underlying the choice of two competing DNR pathways. We demonstrate that the global regulator CRP1, which is widely encoded in bacteria, is required for DNRA in S. loihica PV-4 strain, while the CRP2 paralogue is required for transcription of the nitrite reductase gene nirK for denitrification. Sufficient carbon source lead to the predominance of DNRA, while carbon source/electron donor deficiency may result in an incomplete denitrification process, raising the concern of high levels of N2O emission from nitrate-rich and carbon source-poor waters and soils.
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Benyoucef N, Pauss A, Abdi N, Sarde CO, Grib H, Mameri N. Enhancement of the denitrification performance of an activated sludge using an electromagnetic field in batch mode. CHEMOSPHERE 2021; 262:127698. [PMID: 32791365 DOI: 10.1016/j.chemosphere.2020.127698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/26/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
The influence of electromagnetic fields on bacterial denitrification has been tested on synthetic media with sludges from wastewater treatment stations, in batch mode. The effects of the intensity of the magnetic induction ratio B (mT), reaction volume and initial biomass concentration on the kinetics of the denitrification process were studied. Magnetic field had both an optimal stimulating effect on the activity of the denitrifying flora for B (mT)/mgx values of the order of 0.212, and an inhibitory effect for the values beyond the latter.Sludges underwent multiple exposure cycles to magnetic fields. It was shown that, after three exposure cycles, denitrification kinetics went from 6.5 to 12.7 mg N-NO-3.L-1.h-1 which corresponds to a 2.7 fold improvement. The improved performance persists even after the cessation of the magnetic field. Observation of the sludge by the environmentalelectron microscope shows that the microbial population forming the starting sludge; changed following exposure to the magnetic field. The action of the; electromagnetic field on the microbial populations in denitrification resulted in the modification of the diversity of the flora that is initially present, favoring the development of Proteo bacteria, particularly the Betaproteo bacteria subclass, which results in improved denitrification.
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Affiliation(s)
- Nabil Benyoucef
- Laboratoire BIOGEP, Ecole Nationale Polytechnique, 10 avenue HacenBadi, 16200, Algiers, Algeria
| | - André Pauss
- Université de Technologie de Compiègne, Transformations Intégrées de la Matière Renouvelable (TIMR), EA 4297, France
| | - Nadia Abdi
- Laboratoire BIOGEP, Ecole Nationale Polytechnique, 10 avenue HacenBadi, 16200, Algiers, Algeria
| | - Claude-Olivier Sarde
- Université de Technologie de Compiègne, Transformations Intégrées de la Matière Renouvelable (TIMR), EA 4297, France
| | - Hocine Grib
- Laboratoire BIOGEP, Ecole Nationale Polytechnique, 10 avenue HacenBadi, 16200, Algiers, Algeria
| | - Nabil Mameri
- Laboratoire BIOGEP, Ecole Nationale Polytechnique, 10 avenue HacenBadi, 16200, Algiers, Algeria.
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15
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Nitrate removal performances of a new aerobic denitrifier, Acinetobacter haemolyticus ZYL, isolated from domestic wastewater. Bioprocess Biosyst Eng 2020; 44:391-401. [PMID: 32980939 DOI: 10.1007/s00449-020-02451-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022]
Abstract
A new aerobic denitrifying bacterium ZYL was isolated from domestic wastewater sludge and identified as Acinetobacter haemolyticus (similarity 99%) by the 16S rDNA sequencing analysis. The strain could use nitrate, nitrite and ammonium as the sole N-source for growth with a final product of N2, demonstrating its good abilities for aerobic denitrification and heterotrophic nitrification. Single-factor experiment results showed that the effective removal of nitrate by strain ZYL occurred with carbon source sodium succinate, C/N 16-24, pH 5-9, temperature 20-40 °C, DO ≥ 4.84 mg/L. Ammonium was preferentially used by strain ZYL with nitrate and ammonium as the mixed nitrogen sources. According to nitrogen utilization, nitrogen balance analysis, enzyme assay and denitrifying gene amplification, nitrate was assimilated directly by the isolate for cell synthesis and also converted into N2 through aerobic denitrification. All these make strain ZYL an ideal choice for treating nitrogen-containing wastewater.
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16
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Ramzan S, Rasool T, Bhat RA, Ahmad P, Ashraf I, Rashid N, Ul Shafiq M, Mir IA. Agricultural soils a trigger to nitrous oxide: a persuasive greenhouse gas and its management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:436. [PMID: 32548706 DOI: 10.1007/s10661-020-08410-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Agricultural soils form the backbone of the country's economic development. The increased population has not only reduced this treasure but also has affected the global climate at an alarming rate. Among the GHGs, emission of N2O due to agricultural activities is nowadays a global concern. Agricultural industries have increased N2O and CH4 by 17% in the atmosphere since 1990, with an average emanation rate of around 60 MT CO2 equivalents per year. Crop production accounts for approximately 50% of N2O emissions stemming from the farming community and discharges of fertilizer-induced N2O, for the time being estimated by IPCC at 1.24% of the N used ranging from 0.76% (rice) to 2.77% (maize). The concentration of atmospheric N2O has increased (60 ppb) after the industrial revolution, at the pace of 0.73 ppb year-1. Besides, soil structure, temperature, moisture, denitrifying microbial population, pH, C:N ratio, and relief are the factors which significantly enhance the N2O levels into the atmosphere. N2O as a GHG has more potential towards global warming than CO2 and has a very long residence period (115 years) in the atmosphere. N2O emission is nowadays a core issue which needs to be mitigated so as to decline the levels of its production in agricultural soils. However, priority should be given to the organic farming, management of soil chemistry, and phytoremediation to reduce the addition of N2O into the ambient air. Furthermore, deployment of N2O reductase in agricultural soils increases the efficiency of converting N2O to inert N2 which is a valuable strategy to reduce N2O production.
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Affiliation(s)
- Shazia Ramzan
- SMS, Soil science, KVK Anantnag, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Tabasum Rasool
- Department of Civil Engineering, National Institute of Technology Srinagar Campus, Srinagar, India
| | - Rouf Ahmad Bhat
- Division of Environmental Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir Shalimar Campus, Srinagar, Jammu and Kashmir, India.
| | - Pervez Ahmad
- Department of Geography and Regional Development, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ifra Ashraf
- College of Agricultural Engineering and Technology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir Shalimar Campus, Srinagar, Jammu and Kashmir, India
| | - Nowsheeba Rashid
- Amity Institute of Food Technology, Amity University Noida, Noida, Uttar Pradesh, India
| | - Mifta Ul Shafiq
- Department of Geography and Regional, Development Climate and Cryosphere Group, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ikhlaq A Mir
- Division of Environmental Science Centre for climate Change, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir Shalimar Campus, Srinagar, Jammu and Kashmir, India
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17
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Astorga-Eló M, Zhang Q, Larama G, Stoll A, Sadowsky MJ, Jorquera MA. Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile. Front Microbiol 2020; 11:571. [PMID: 32322245 PMCID: PMC7156552 DOI: 10.3389/fmicb.2020.00571] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 03/16/2020] [Indexed: 12/22/2022] Open
Abstract
Flowering desert (FD) events consist of the rapid flowering of a wide variety of native plants in the Atacama Desert of Chile, which is categorized as the driest desert in the world. While ephemeral plants are an integral part of the desert ecosystem, there is little knowledge on plant-microbe interactions that occur during FD events. Consequently, the overall goals of this present study were to investigate changes in the composition and potential functions of rhizobacterial community of Cistanthe longiscapa (Montiaceae) during the 2014 and 2015 FD events and determine the composition, potential functions, and co-occurrence networks of rhizobacterial community associated with the root zone of C. longiscapa during pre- (PF) and full-flowering (FF) phenological stages. Results of this study showed that the Proteobacteria and Actinobacteria were the dominant taxa in rhizosphere soils during the three FD events (2014, 2015, and 2017) examined. In general, greater microbial richness and diversity were observed in rhizosphere soils during the 2015-, compared with the 2014-FD event. Similarly, predicted functional analyses indicated that a larger number of sequences were assigned to information processing (e.g., ion channel, transporters and ribosome) and metabolism (e.g., lipids, nitrogen, and sulfur) during 2015 compared with 2014. Despite the lack of significant differences in diversity among PF and FF stages, the combined analysis of rhizobacterial community data, along with data concerning rhizosphere soil properties, evidenced differences among both phenological stages and suggested that sodium is a relevant abiotic factor shaping the rhizosphere. In general, no significant differences in predicted functions (most of them assigned to chemoheterotrophy, magnesium metabolisms, and fermentation) were observed among PF and FF. Co-occurrence analysis revealed the complex rhizobacterial interactions that occur in C. longiscapa during FD, highlighting to Kouleothrixaceae family as keystone taxa. Taken together this study shows that the composition and function of rhizobacteria vary among and during FD events, where some bacterial groups and their activity may influence the growth and flowering of native plants, and therefore, the ecology and trophic webs in Atacama Desert.
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Affiliation(s)
- Marcia Astorga-Eló
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Giovanni Larama
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States.,Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,The Network for Extreme Environment Research (NEXER), Scientific and Biotechnological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
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Genomic Analysis of Bacillus megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil. Int J Genomics 2020; 2020:4109186. [PMID: 32190639 PMCID: PMC7066406 DOI: 10.1155/2020/4109186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/01/2020] [Accepted: 02/08/2020] [Indexed: 12/17/2022] Open
Abstract
Bacillus megaterium NCT-2 is a nitrate-uptake bacterial, which shows high bioremediation capacity in secondary salinization soil, including nitrate-reducing capacity, phosphate solubilization, and salinity adaptation. To gain insights into the bioremediation capacity at the genetic level, the complete genome sequence was obtained by using a multiplatform strategy involving HiSeq and PacBio sequencing. The NCT-2 genome consists of a circular chromosome of 5.19 Mbp and ten indigenous plasmids, totaling 5.88 Mbp with an average GC content of 37.87%. The chromosome encodes 5,606 genes, 142 tRNAs, and 53 rRNAs. Genes involved in the features of the bioremediation in secondary salinization soil and plant growth promotion were identified in the genome, such as nitrogen metabolism, phosphate uptake, the synthesis of organic acids and phosphatase for phosphate-solubilizing ability, and Trp-dependent IAA synthetic system. Furthermore, strain NCT-2 has great ability of adaption to environments due to the genes involved in cation transporters, osmotic stress, and oxidative stress. This study sheds light on understanding the molecular basis of using B. megaterium NCT-2 in bioremediation of the secondary salinization soils.
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Ammonium-Nitrogen (NH4+-N) Removal from Groundwater by a Dropping Nitrification Reactor: Characterization of NH4+-N Transformation and Bacterial Community in the Reactor. WATER 2020. [DOI: 10.3390/w12020599] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A dropping nitrification reactor was proposed as a low-cost and energy-saving option for the removal of NH4+-N from contaminated groundwater. The objectives of this study were to investigate NH4+-N removal performance and the nitrogen removal pathway and to characterize the microbial communities in the reactor. Polyolefin sponge cubes (10 mm × 10 mm × 10 mm) were connected diagonally in a nylon thread to produce 1 m long dropping nitrification units. Synthetic groundwater containing 50 mg L−1 NH4+-N was added from the top of the hanging units at a flow rate of 4.32 L day−1 for 56 days. Nitrogen-oxidizing microorganisms in the reactor removed 50.8–68.7% of the NH4+-N in the groundwater, which was aerated with atmospheric oxygen as it flowed downwards through the sponge units. Nitrogen transformation and the functional bacteria contributing to it were stratified in the sponge units. Nitrosomonadales-like AOB predominated and transformed NH4+-N to NO2−-N in the upper part of the reactor. Nitrospirales-like NOB predominated and transformed NO2−-N to NO3−-N in the lower part of the reactor. The dropping nitrification reactor could be a promising technology for oxidizing NH4+-N in groundwater and other similar contaminated wastewaters.
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20
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Theoretical basis of nitrosomyoglobin formation in a dry sausage model by coagulase-negative staphylococci: Behavior and expression of nitric oxide synthase. Meat Sci 2019; 161:108022. [PMID: 31838366 DOI: 10.1016/j.meatsci.2019.108022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/22/2019] [Accepted: 11/25/2019] [Indexed: 01/04/2023]
Abstract
Three coagulase-negative staphylococci (CNS) species were investigated for gene expression of nitric oxide synthase (NOS) and the ability of nitrosomyoglobin (NO-Mb) formation in a dry sausage model without nitrite addition. The expression of nos gene was systematically proven from DNA to RNA to protein, and nitric oxide (NO) generation was also directly detected. In the dry sausage model system, the redness (a*-values) of samples inoculated with the three CNS species were higher than those inoculated with Pediococcus pentosaceus and the control (P < 0.05). The results from UV-vis and electron spin resonance spectroscopies revealed that pentacoordinate NO-Mb was formed in the sausages with either CNS or nitrite added. The sausage inoculated with Staphylococcus vitulinus had the highest NO-Mb content among the CNS-treated sausages. Dimer interface residues and phosphorylation sites of NOS in . itulinus differ from the other two CNS species as revealed by amino acid sequences, which may be responsible for the different catalytic activities.
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Suga M, Shimada A, Akita F, Shen JR, Tosha T, Sugimoto H. Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Biochim Biophys Acta Gen Subj 2019; 1864:129466. [PMID: 31678142 DOI: 10.1016/j.bbagen.2019.129466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach. SCOPE OF REVIEW Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described. MAJOR CONCLUSIONS XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data. GENERAL SIGNIFICANCE XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.
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Affiliation(s)
- Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan..
| | - Atsuhiro Shimada
- Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan..
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Takehiko Tosha
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Sugimoto
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan..
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22
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Margalef-Marti R, Carrey R, Viladés M, Jubany I, Vilanova E, Grau R, Soler A, Otero N. Use of nitrogen and oxygen isotopes of dissolved nitrate to trace field-scale induced denitrification efficiency throughout an in-situ groundwater remediation strategy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 686:709-718. [PMID: 31195279 DOI: 10.1016/j.scitotenv.2019.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 06/09/2023]
Abstract
In the framework of the Life+ InSiTrate project, a pilot-plant was established to demonstrate the viability of inducing in-situ heterotrophic denitrification to remediate nitrate (NO3-)-polluted groundwater. Two injection wells supplied acetic acid by pulses to an alluvial aquifer for 22months. The monitoring was performed by regular sampling at three piezometers and two wells located downstream. In the present work, the pilot-plant monitoring samples were used to test the usefulness of the isotopic tools to evaluate the efficiency of the treatment. The laboratory microcosm experiments determined an isotopic fractionation (ε) for N-NO3- of -12.6‰ and for O-NO3- of -13.3‰. These ε15NNO3/N2 and ε18ONO3/N2 values were modelled by using a Rayleigh distillation equation to estimate the percentage of the induced denitrification at the pilot-plant while avoiding a possible interference from dilution due to non-polluted water inputs. In some of the field samples, the induced NO3- reduction was higher than 50% with respect to the background concentration. The field samples showed a reduced slope between δ18O-NO3- and δ15N-NO3- (0.7) compared to the laboratory experiments (1.1). This finding was attributed to the reoxidation of NO2- to NO3- during the treatment. The NO3- isotopic characterization also permitted the recognition of a mixture between the denitrified and partially or non-denitrified groundwater in one of the sampling points. Therefore, the isotopic tools demonstrated usefulness in assessing the implementation of the field-scale induced denitrification strategy.
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Affiliation(s)
- Rosanna Margalef-Marti
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Barcelona, Spain.
| | - Raúl Carrey
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Viladés
- Sustainability Department, Fundació CTM Centre Tecnològic, Spain
| | - Irene Jubany
- Sustainability Area, Eurecat, Centre Tecnològic de Catalunya, Spain
| | | | | | - Albert Soler
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Barcelona, Spain
| | - Neus Otero
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Barcelona, Spain; Serra Húnter Fellow, Generalitat de Catalunya, Spain
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23
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Wan R, Wang L, Chen Y, Zheng X, Chew J, Huang H. Tetrabromobisphenol A (TBBPA) inhibits denitrification via regulating carbon metabolism to decrease electron donation and bacterial population. WATER RESEARCH 2019; 162:190-199. [PMID: 31272044 DOI: 10.1016/j.watres.2019.06.046] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
The potential risks of brominated flame retardants (BFRs) like tetrabromobisphenol A (TBBPA) have attracted much attention. However, the influence of TBBPA on functional microbes remains poorly understood, especially with regards to denitrification, which is closely related with the carbon and nitrogen cycles, eutrophication and greenhouse gas emission. Herein, we found that 1.0 mg/L of TBBPA significantly decreased the total nitrogen removal efficiency by 81.7%, but increased the accumulation of NO2--N (by 81.5%) and N2O (by 172-fold). This was found to be underlie by the significant decrease in both the denitrifying capability of denitrifiers and total bacterial population. Further investigation revealed that TBBPA inhibited the pathways of glucolysis and pentose phosphate, and promoted glyoxylate bypass via regulating genes expressions of key enzymes (such as glucose-6-phosphate isomerase, pyruvate dehydrogenase, isocitrate lyase, etc.), then decreased the generation of NADH serving as electron donor for denitrification, and inhibited the denitrifying capability of denitrifiers. Moreover, insufficient NADH stimulated the accumulation of denitrifying intermediates (NO2--N and N2O), which induced the increase of reactive nitrogen species (RNS), whose accumulation decreased proliferation and increased apoptosis of denitrifying bacteria. Finally, the decrease in the denitrifying capability of denitrifier and bacterial population resulted in negative denitrifying performance.
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Affiliation(s)
- Rui Wan
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, School of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui, 241002, China; School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore.
| | - Lei Wang
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, School of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui, 241002, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Jiawei Chew
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
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24
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Lehnert N, Fujisawa K, Camarena S, Dong HT, White CJ. Activation of Non-Heme Iron-Nitrosyl Complexes: Turning Up the Heat. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03219] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kiyoshi Fujisawa
- Department of Chemistry, Ibaraki University, Mito 310-8512, Japan
| | - Stephanie Camarena
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Hai T. Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Corey J. White
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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25
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Hwang S, Chavarria NE, Hackley RK, Schmid AK, Maupin-Furlow JA. Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. Int J Mol Sci 2019; 20:ijms20194784. [PMID: 31561502 PMCID: PMC6801745 DOI: 10.3390/ijms20194784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H. volcanii grown on ammonium as an abundant source of fixed nitrogen compared to l-alanine, the latter of which exemplifies an intermediate source of nitrogen that can be obtained from dead cells in natural habitats. By comparing the two growth conditions, 30 genes were found to be differentially expressed, including 16 genes associated with amino acid metabolism and transport. The gene expression profiles contributed to mapping ammonium and l-alanine usage with respect to transporters and metabolic pathways. In addition, conserved DNA motifs were identified in the putative promoter regions and transcription factors were found to be in synteny with the differentially expressed genes, leading us to propose regulons of transcriptionally co-regulated operons. This study provides insight to how H. volcanii responds to and utilizes intermediate vs. abundant sources of fixed nitrogen for growth, with implications for conserved functions in related halophilic archaea.
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Affiliation(s)
- Sungmin Hwang
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | - Nikita E Chavarria
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
- Center for Genomics and Computational Biology, Duke University, Duke University, Durham, NC 27708, USA.
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
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26
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Qu X, Zhang M, Yang Y, Xie Y, Ren Z, Peng W, Du X. Taxonomic structure and potential nitrogen metabolism of microbial assemblage in a large hypereutrophic steppe lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:21151-21160. [PMID: 31119540 DOI: 10.1007/s11356-019-05411-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
Recent studies have expanded the interests about microbial community and function following the rapid development of high-throughput sequencing techniques in the freshwater ecosystem. In this study, we aimed to attain a deep understanding of microbial community structure and potential nitrogen metabolism in Hulun Lake, a shallow hypereutrophic steppe lake in the Mongolian Plateau in China. The result demonstrated that cyanobacteria were the most dominant phylum. Network analysis showed both intra- and inter-phylum co-occurrence were pervasive, and there were modular structures in the microbial assemblages. The cluster dominated by proteobacteria was mainly negatively connected to the cluster dominated by both proteobacteria and actinobacteria. Cyanobacteria were tightly clustered together and positively connected to these two clusters. The major nitrogen metabolism pathways were glutamine synthetase-glutamate synthase and assimilatory nitrate reduction, indicating the nitrogen was mainly retained in the lake by microbial uptake. Cyanobacteria contributed 43.25% gene reads involved in the overall nitrogen metabolism but mainly contributed to assimilatory nitrate reduction and nitrogen fixation, aggravating the lake eutrophication. This study adds to our knowledge of microbial assemblages and nitrogen metabolism in the shallow hypereutrophic lake and provided an insight understanding for the purposes of lake ecosystem's protection and efficient management in the Mongolian Plateau.
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Affiliation(s)
- Xiaodong Qu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Department of Water Environment, China Institute of Water Resources and Hydropower Research, Fuxing Road, Jia No.1, Haidian District, Beijing, 100038, China
| | - Min Zhang
- Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Yu Yang
- Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Ying Xie
- Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Ze Ren
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA.
| | - Wenqi Peng
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Department of Water Environment, China Institute of Water Resources and Hydropower Research, Fuxing Road, Jia No.1, Haidian District, Beijing, 100038, China.
| | - Xia Du
- Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
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27
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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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28
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Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary. PLoS One 2019; 14:e0217431. [PMID: 31170168 PMCID: PMC6553723 DOI: 10.1371/journal.pone.0217431] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterioplankton play a key role in the global cycling of elements. To characterize the effects of hypoxia on bacterioplankton, bacterial community structure and function were investigated in the Changjiang Estuary. Water samples were collected from three layers (surface, middle, and bottom) at ten sampling sites in the Changjiang Estuary hypoxic and non-hypoxic zones. The community structure was analyzed using high-throughput sequencing of 16S rDNA genes, and the predictive metagenomic approach was used to investigate the functions of the bacterial community. Co-occurrence networks are constructed to investigate the relationship between different bacterioplankton. The results showed that community composition in hypoxic and non-hypoxic zones were markedly different. The diversity and richness of bacterial communities in the bottom layer (hypoxic zone) were remarkably higher than that of the surface layer (non-hypoxic). In the non-hypoxic zone, it was found that Proteobacteria, Bacteroidetes, and Flavobacteriia were the dominant groups while Alphaproteobacteria, SAR406 and Deltaproteobacteria were the dominant groups in the hypoxic zone. From the RDA analysis, it was shown that dissolved oxygen (DO) explained most of the bacterial community variation in the redundancy analysis targeting only hypoxia zones, whereas nutrients and salinity explained most of the variation across all samples in the Changjiang Estuary. To understand the genes involved in nitrogen metabolism, an analysis of the oxidation state of nitrogen was performed. The results showed that the bacterial community in the surface layer (non-hypoxic) had more genes involved in dissimilatory nitrate reduction, assimilatory nitrate reduction, denitrification, and anammox, while that in the middle and bottom layers (hypoxic zone) had more abundant genes associated with nitrogen fixation and nitrification. Co-occurrence networks revealed that microbial assemblages in the middle and bottom layers shared more niche spaces than in the surface layer (non-hypoxic zone). The environmental heterogeneity in the hypoxic and non-hypoxic zones might be important environmental factors that determine the bacterial composition in these two zones.
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29
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Campos PC, Gomes MTR, Marinho FAV, Guimarães ES, de Moura Lodi Cruz MGF, Oliveira SC. Brucella abortus nitric oxide metabolite regulates inflammasome activation and IL-1β secretion in murine macrophages. Eur J Immunol 2019; 49:1023-1037. [PMID: 30919410 DOI: 10.1002/eji.201848016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/20/2019] [Accepted: 03/25/2019] [Indexed: 11/07/2022]
Abstract
NLRP3 inflammasome is a protein complex crucial to caspase-1 activation and IL-1β and IL-18 maturation. This receptor participates in innate immune responses to different pathogens, including the bacteria of genus Brucella. Our group recently demonstrated that Brucella abortus-induced IL-1β secretion involves NLRP3 inflammasome and it is partially dependent on mitochondrial ROS production. However, other factors could be involved, such as P2X7-dependent potassium efflux, membrane destabilization, and cathepsin release. Moreover, there is increasing evidence that nitric oxide acts as a modulator of NLRP3 inflammasome. The aim of this study was to unravel the mechanism of NLRP3 inflammasome activation induced by B. abortus, as well as the involvement of bacterial nitric oxide (NO) as a modulator of this inflammasome pathway. We demonstrated that NO produced by B. abortus can be used by the bacteria to modulate IL-1β secretion in infected murine macrophages. Additionally, our results suggest that B. abortus-induced IL-1β secretion depends on a P2X7-independent potassium efflux, lysosomal acidification, cathepsin release, mechanisms clearly associated to NLRP3 inflammasome. In summary, our results help to elucidate the molecular mechanisms of NLRP3 activation and regulation during an intracellular bacterial infection.
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Affiliation(s)
- Priscila Carneiro Campos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marco Túlio Ribeiro Gomes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fábio Antônio Vitarelli Marinho
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Erika Sousa Guimarães
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Sergio Costa Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Ministério de Ciência, Tecnologia e Inovação, Salvador, Bahia, Brazil
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30
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Huang X, Xu Y, He T, Jia H, Feng M, Xiang S, Wang S, Ni J, Xie D, Li Z. Ammonium transformed into nitrous oxide via nitric oxide by Pseudomonas putida Y-9 under aerobic conditions without hydroxylamine as intermediate. BIORESOURCE TECHNOLOGY 2019; 277:87-93. [PMID: 30660065 DOI: 10.1016/j.biortech.2019.01.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Previous studies have reported that hydroxylamine (NH2OH) is an inevitable intermediate of the ammonium (NH4+) oxidation pathway under aerobic conditions. In this study, Pseudomonas putida Y-9 was found to oxidize ammonium into N2O via NO without the accumulation of NH2OH and NO2- under aerobic conditions. NH2OH was nearly completely transformed into NO2- whether NH4+ was present in the medium, and NH4+ could accelerate the transformation of NH2OH to NO2- by promoting Y-9 growth. NH4+ was oxidized rapidly by Y-9 with or without the presence of NH2OH in the medium, and the decrease of total nitrogen reached 30.65 mg/L and 39.38 mg/L, respectively, which indicates that NH2OH inhibits the transformation efficiency of NH4+ to N2O. Gene amplification and enzyme assays demonstrated that ammonia monooxygenase doesn't exist in Y-9. All results show that NH4+ can be transformed into N2O via NO by Y-9 under aerobic conditions without NH2OH as intermediate.
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Affiliation(s)
- Xuejiao Huang
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Yi Xu
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Tengxia He
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Hongjie Jia
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Mi Feng
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Shudi Xiang
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Shutong Wang
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Jiupai Ni
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Deti Xie
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China.
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China.
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31
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Yang JR, Wang Y, Chen H, Lyu YK. Ammonium removal characteristics of an acid-resistant bacterium Acinetobacter sp. JR1 from pharmaceutical wastewater capable of heterotrophic nitrification-aerobic denitrification. BIORESOURCE TECHNOLOGY 2019; 274:56-64. [PMID: 30500764 DOI: 10.1016/j.biortech.2018.10.052] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 06/09/2023]
Abstract
A new acid-resistant bacterium Acinetobacter sp. JR1 was isolated, and its feasibility in nitrogen removal was investigated under acidic condition. Results show that JR1 indicated excellent ammonium and nitrate removal abilities with no accumulation of intermediates, and the maximum ammonium and nitrate removal efficiencies were 98.5% and 91.1%, respectively. Further experiments demonstrated that JR1 preferred to use ammonium with ammonium and nitrate as the mixed N-sources. For JR1, ammonium was assimilated directly as nutrients into cells and also converted into N2 through heterotrophic nitrification-aerobic denitrification. Under acidic condition, JR1 performed comparable nitrogen removal abilities to other strains under neutral or weak alkaline environment, and the efficient removal of ammonium occurred at pH 4.5-10, C/N 12-24, 20-40 °C, DO ≥4.72 mg/L, 0-1.5% of salinity, 10 mg/L Zn2+ or 20 mg/L Mn2+. All these make JR1 a promising candidate for treating acidic wastewater containing nitrogen.
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Affiliation(s)
- Jing-Rui Yang
- Key Laboratory of Coal Science and Technology, Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Ying Wang
- Key Laboratory of Coal Science and Technology, Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Hu Chen
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Yong-Kang Lyu
- Key Laboratory of Coal Science and Technology, Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China.
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32
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Ascenzi P, De Simone G, Ciaccio C, Santucci R, Coletta M. Hydroxylamine-induced oxidation of ferrous CO-bound carboxymethylated-cytochrome c. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424618501055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The hexa-coordinated metal center of horse heart cyt[Formula: see text] (cyt[Formula: see text] is at the root of its low reactivity. In contrast, carboxymethylated cyt[Formula: see text] (CM-cyt[Formula: see text] displays myoglobin-like properties. Herein, kinetics of CO binding to ferrous CM-cyt[Formula: see text] (CM-cyt[Formula: see text](II)) and of the irreversible oxidation of ferrous carbonylated CM-cyt[Formula: see text] (CM-cyt[Formula: see text](II)-CO) by hydroxylamine (HA), at pH 5.8 and 20.0 [Formula: see text]C, are reported. HA irreversibly oxidizes CM-cyt[Formula: see text](II)-CO with the 1:2 stoichiometry leading to the formation of the ferric species (CM-cyt[Formula: see text](III)) without the observation of intermediates. Present data indicate that: (i) the rate of CO dissociation from CM-cyt[Formula: see text](II)-CO represents the rate-limiting step of HA-mediated oxidation of the carbonylated metal center, (ii) the fast oxidation of CM-cyt[Formula: see text](II)-CO from HA reflects the penta-coordination of the transient CM-cyt[Formula: see text](II) species, (iii) the HA-catalyzed conversion of CM-cyt[Formula: see text](II)-CO to CM-cyt[Formula: see text](III) could proceed via the geminate mechanism, (iv) values of the second-order rate constants for the carbonylation and the HA-mediated oxidation of ferrous heme-proteins are linearly correlated reflecting the penta- or hexa-coordination of the metal center, the free energy for the in-plane positioning of the heme-Fe atom in the unliganded species, and the arrangement of the distal portion of the heme pocket that affects ligand and/or electron transfer.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, I-00146 Roma, Italy
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, I-00133 Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, I-70126 Bari, Italy
| | - Roberto Santucci
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, I-00133 Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, I-00133 Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, I-70126 Bari, Italy
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33
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Isolation and Nitrogen Removal Characteristics of an Aerobic Heterotrophic Nitrifying-Denitrifying Bacterium, Klebsiella sp. TN-10. Appl Biochem Biotechnol 2018; 188:540-554. [PMID: 30542795 DOI: 10.1007/s12010-018-02932-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
Abstract
Nitrogen removal by microorganisms has attracted increasing attention in wastewater treatment. In the present study, a heterotrophic nitrification bacterium was isolated from tannery wastewater and identified as Klebsiella sp. TN-10 based on phenotypic and phylogenetic characteristics. The optimal conditions for cell growth and nitrogen removal were investigated, and the results showed that the greatest ammonium removal rate and maximum biomass were achieved by using sodium pyruvate (7 g/L) as carbon source, C/N 12, pH 7, and temperature 30 °C. Under optimal conditions, the removal rate of ammonia nitrogen reached 96%. Besides, the growth characteristic and the ability of utilizing nitrate and nitrite were investigated. The results demonstrated that strain TN-10 exhibited excellent characteristics to remove both nitrate and nitrite, with the removal rate of 95.44% and 99.87%, respectively. In addition, the nitrite reductase (NiR) and nitrate reductase (NR) involved in denitrification were both active, with the activities of 0.0815 and 0.0283 U/mg proteins, respectively. Furthermore, the aggregation ability, auto-aggregation kinetics, and the relationship between zeta potentials and flocculating efficiency were determined. These results indicated that the strain Klebsiella sp. TN-10, with efficient heterotrophic nitrification-aerobic denitrification ability, has potential application in wastewater treatment.
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Chahlafi Z, Alvarez L, Cava F, Berenguer J. The role of conserved proteins DrpA and DrpB in nitrate respiration of Thermus thermophilus. Environ Microbiol 2018; 20:3851-3861. [PMID: 30187633 PMCID: PMC6282519 DOI: 10.1111/1462-2920.14400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/03/2018] [Accepted: 08/27/2018] [Indexed: 12/26/2022]
Abstract
In many Thermus thermophilus strains, nitrate respiration is encoded in mobile genetic regions, along with regulatory circuits that modulate its expression based on anoxia and nitrate presence. The oxygen-responsive system has been identified as the product of the dnrST (dnr) operon located immediately upstream of the nar operon (narCGHJIKT), which encodes the nitrate reductase (NR) and nitrate/nitrite transporters. In contrast, the nature of the nitrate sensory system is not known. Here, we analyse the putative nitrate-sensing role of the bicistronic drp operon (drpAB) present downstream of the nar operon in most denitrifying Thermus spp. Expression of drp was found to depend on the master regulator DnrT, whereas the absence of DrpA or DrpB increased the expression of both DnrS and DnrT and, concomitantly, of the NR. Absence of both proteins made expression from the dnr and nar operons independent of nitrate. Polyclonal antisera allowed us to identify DrpA as a periplasmic protein and DrpB as a membrane protein, with capacity to bind to the cytoplasmic membrane. Here, we propose a role for DrpA/DrpB as nitrate sensors during denitrification.
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Affiliation(s)
- Zahra Chahlafi
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
| | - Laura Alvarez
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, 28049, Spain
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Mitra S, Das A, Sen S, Mahanty B. Potential of metabolic engineering in bacterial nanosilver synthesis. World J Microbiol Biotechnol 2018; 34:138. [DOI: 10.1007/s11274-018-2522-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
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Heme redox potentials hold the key to reactivity differences between nitric oxide reductase and heme-copper oxidase. Proc Natl Acad Sci U S A 2018; 115:6195-6200. [PMID: 29802230 DOI: 10.1073/pnas.1720298115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite high structural homology between NO reductases (NORs) and heme-copper oxidases (HCOs), factors governing their reaction specificity remain to be understood. Using a myoglobin-based model of NOR (FeBMb) and tuning its heme redox potentials (E°') to cover the native NOR range, through manipulating hydrogen bonding to the proximal histidine ligand and replacing heme b with monoformyl (MF-) or diformyl (DF-) hemes, we herein demonstrate that the E°' holds the key to reactivity differences between NOR and HCO. Detailed electrochemical, kinetic, and vibrational spectroscopic studies, in tandem with density functional theory calculations, demonstrate a strong influence of heme E°' on NO reduction. Decreasing E°' from +148 to -130 mV significantly impacts electronic properties of the NOR mimics, resulting in 180- and 633-fold enhancements in NO association and heme-nitrosyl decay rates, respectively. Our results indicate that NORs exhibit finely tuned E°' that maximizes their enzymatic efficiency and helps achieve a balance between opposite factors: fast NO binding and decay of dinitrosyl species facilitated by low E°' and fast electron transfer facilitated by high E°'. Only when E°' is optimally tuned in FeBMb(MF-heme) for NO binding, heme-nitrosyl decay, and electron transfer does the protein achieve multiple (>35) turnovers, previously not achieved by synthetic or enzyme-based NOR models. This also explains a long-standing question in bioenergetics of selective cross-reactivity in HCOs. Only HCOs with heme E°' in a similar range as NORs (between -59 and 200 mV) exhibit NOR reactivity. Thus, our work demonstrates efficient tuning of E°' in various metalloproteins for their optimal functionality.
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Van Stappen C, Lehnert N. Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases. Inorg Chem 2018; 57:4252-4269. [DOI: 10.1021/acs.inorgchem.7b02333] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Casey Van Stappen
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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Zhao L, Meng Q, Li Y, Wu H, Huo Y, Zhang X, Zhou Z. Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate-adapted steers. BMC Microbiol 2018; 18:21. [PMID: 29554875 PMCID: PMC5859718 DOI: 10.1186/s12866-018-1164-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 03/15/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either 0% (0NR), 1% (1NR), or 2% (2NR) nitrate (dry matter basis) regimens in succession. Rumen fluid was taken after two-week adaptation for evaluation of in vitro methane production, methanogen abundance, and composition measurements. RESULTS Results showed that nitrate significantly decreased in vitro ruminal methane production at 6 h, 12 h, and 24 h (P < 0.01; P < 0.01; P = 0.01). The 1NR and 2NR regimens numerically reduced the methanogen population by 4.47% and 25.82% respectively. However, there was no significant difference observed between treatments. The alpha and beta diversity of the methanogen community was not significantly changed by nitrate either. However, the relative abundance of the methanogen genera was greatly changed. Methanosphaera (PL = 0.0033) and Methanimicrococcus (PL = 0.0113) abundance increased linearly commensurate with increasing nitration levels, while Methanoplanus abundance was significantly decreased (PL = 0.0013). The population of Methanoculleus, the least frequently identified genus in this study, exhibited quadratic growth from 0% to 2% when nitrate was added (PQ = 0.0140). CONCLUSIONS Correlation analysis found that methane reduction was significantly related to Methanobrevibacter and Methanoplanus abundance, and negatively correlated with Methanosphaera and Methanimicrococcus abundance.
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Affiliation(s)
- Liping Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yan Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunlong Huo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xinzhuang Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhenming Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Wang X, An Q, Zhao B, Guo JS, Huang YS, Tian M. Auto-aggregation properties of a novel aerobic denitrifier Enterobacter sp. strain FL. Appl Microbiol Biotechnol 2018; 102:2019-2030. [DOI: 10.1007/s00253-017-8720-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 10/18/2022]
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Torregrosa-Crespo J, Bergaust L, Pire C, Martínez-Espinosa RM. Denitrifying haloarchaea: sources and sinks of nitrogenous gases. FEMS Microbiol Lett 2017; 365:4718458. [DOI: 10.1093/femsle/fnx270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/08/2017] [Indexed: 11/14/2022] Open
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Torregrosa-Crespo J, González-Torres P, Bautista V, Esclapez JM, Pire C, Camacho M, Bonete MJ, Richardson DJ, Watmough NJ, Martínez-Espinosa RM. Analysis of multiple haloarchaeal genomes suggests that the quinone-dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:788-796. [PMID: 28925557 DOI: 10.1111/1758-2229.12596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. While the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors). The study revealed that the only nor gene found in haloarchaea is one that encodes a single subunit quinone dependent Nor homologous to the qNor found in bacteria. This surprising discovery is considered in terms of our emerging understanding of haloarchaeal bioenergetics and NO management.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Pedro González-Torres
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain
| | - Vanesa Bautista
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Julia M Esclapez
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Mónica Camacho
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - María José Bonete
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - David J Richardson
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Nicholas J Watmough
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Rosa María Martínez-Espinosa
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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Influences of anthropogenic land use on microbial community structure and functional potentials of stream benthic biofilms. Sci Rep 2017; 7:15117. [PMID: 29118402 PMCID: PMC5678132 DOI: 10.1038/s41598-017-15624-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022] Open
Abstract
Stream ecosystems are the primary receivers of nutrient and organic carbon exported from terrestrial ecosystems and are profoundly influenced by the land use of the surrounding landscape. The aquatic impacts of anthropogenic land use are often first observed in stream benthic biofilms. We studied the benthic biofilms in streams flowing through forest (upstream) and anthropogenic land use (downstream) areas in southwestern China. The results showed that anthropogenic land use increased nutrient and organic carbon in both stream water and benthic biofilms, which are closely related to the differences in the microbial communities. The taxonomic dissimilarity of the communities was significantly correlated with the functional gene dissimilarity, and the upstream sites had more distinct functional genes. Network analysis showed that upstream sites had more highly connected microbial networks. Furthermore, downstream sites had higher relative abundances of anammox and denitrification suggesting stronger nitrogen removal than upstream sites. Increased nutrients in both the stream water and biofilms caused by anthropogenic land use had severe impacts on the nitrogen cycle in stream ecosystems. Downstream sites also had stronger carbon metabolism than upstream sites. This study provides insights into the influences of anthropogenic land use on microbial community structure and functions of stream benthic biofilms.
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Ren Z, Gao H, Elser JJ, Zhao Q. Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams. Sci Rep 2017; 7:12668. [PMID: 28978929 PMCID: PMC5627277 DOI: 10.1038/s41598-017-13086-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/18/2017] [Indexed: 11/09/2022] Open
Abstract
Benthic biofilms in glacier-fed streams harbor diverse microorganisms driving biogeochemical cycles and, consequently, influencing ecosystem-level processes. Benthic biofilms are vulnerable to glacial retreat induced by climate change. To investigate microbial functions of benthic biofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRUSt and identified functional genes associated with nitrogen and sulfur metabolisms based on KEGG database and explored the relationships between metabolic pathways and abiotic factors in glacier-fed streams in the Tianshan Mountains in Central Asia. Results showed that the distribution of functional genes was mainly associated with glacier area proportion, glacier source proportion, total nitrogen, dissolved organic carbon, and pH. For nitrogen metabolism, the relative abundance of functional genes associated with dissimilatory pathways was higher than those for assimilatory pathways. The relative abundance of functional genes associated with assimilatory sulfate reduction was higher than those involved with the sulfur oxidation system and dissimilatory sulfate reduction. Hydrological factors had more significant correlations with nitrogen metabolism than physicochemical factors and anammox was the most sensitive nitrogen cycling pathway responding to variation of the abiotic environment in these glacial-fed streams. In contrast, sulfur metabolism pathways were not sensitive to variations of abiotic factors in these systems.
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Affiliation(s)
- Ze Ren
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Hongkai Gao
- State Key Laboratory of Cryosheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China. .,School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA. .,School of Geography and Planing, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - James J Elser
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Qiudong Zhao
- State Key Laboratory of Cryosheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
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McQuarters AB, Kampf JW, Alp EE, Hu M, Zhao J, Lehnert N. Ferric Heme-Nitrosyl Complexes: Kinetically Robust or Unstable Intermediates? Inorg Chem 2017; 56:10513-10528. [PMID: 28825299 DOI: 10.1021/acs.inorgchem.7b01493] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We have determined a convenient method for the bulk synthesis of high-purity ferric heme-nitrosyl complexes ({FeNO}6 in the Enemark-Feltham notation); this method is based on the chemical or electrochemical oxidation of corresponding {FeNO}7 precursors. We used this method to obtain the five- and six-coordinate complexes [Fe(TPP)(NO)]+ (TPP2- = tetraphenylporphyrin dianion) and [Fe(TPP)(NO)(MI)]+ (MI = 1-methylimidazole) and demonstrate that these complexes are stable in solution in the absence of excess NO gas. This is in stark contrast to the often-cited instability of such {FeNO}6 model complexes in the literature, which is likely due to the common presence of halide impurities (although other impurities could certainly also play a role). This is avoided in our approach for the synthesis of {FeNO}6 complexes via oxidation of pure {FeNO}7 precursors. On the basis of these results, {FeNO}6 complexes in proteins do not show an increased stability toward NO loss compared to model complexes. We also prepared the halide-coordinated complexes [Fe(TPP)(NO)(X)] (X = Cl-, Br-), which correspond to the elusive, key reactive intermediate in the so-called autoreduction reaction, which is frequently used to prepare {FeNO}7 complexes from ferric precursors. All of the complexes were characterized using X-ray crystallography, UV-vis, IR, and nuclear resonance vibrational spectroscopy (NRVS). On the basis of the vibrational data, further insight into the electronic structure of these {FeNO}6 complexes, in particular with respect to the role of the axial ligand trans to NO, is obtained.
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Affiliation(s)
- Ashley B McQuarters
- Department of Chemistry and Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jeff W Kampf
- Department of Chemistry and Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Michael Hu
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
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Habib U, Hoffman M. Effect of molybdenum and tungsten on the reduction of nitrate in nitrate reductase, a DFT study. Chem Cent J 2017; 11:35. [PMID: 29086812 PMCID: PMC5405038 DOI: 10.1186/s13065-017-0263-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/11/2017] [Indexed: 12/03/2022] Open
Abstract
The molybdenum and tungsten active site model complexes, derived from the protein X-ray crystal structure of the first W-containing nitrate reductase isolated from Pyrobaculum aerophilum, were computed for nitrate reduction at the COSMO-B3LYP/SDDp//B3LYP/Lanl2DZ(p) energy level of density functional theory. The molybdenum containing active site model complex (Mo–Nar) has the largest activation energy (34.4 kcal/mol) for the oxygen atom transfer from the nitrate to the metal center as compared to the tungsten containing active site model complex (W–Nar) (12.0 kcal/mol). Oxidation of the educt complex is close to thermoneutral (−1.9 kcal/mol) for the Mo active site model complex but strongly exothermic (−34.7 kcal/mol) for the W containing active site model complex, however, the MVI to MIV reduction requires equal amount of reductive power for both metal complexes, Mo–Nar or W–Nar.
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Affiliation(s)
- Uzma Habib
- Research Center for Modeling and Simulation (RCMS), National University of Science and Technology (NUST), H-12, Islamabad, Pakistan.
| | - Matthias Hoffman
- Institute of Inorganic Chemistry, Heidelberg University, Heidelberg, Germany
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Nitrate reduction in Haloferax alexandrinus: the case of assimilatory nitrate reductase. Extremophiles 2017; 21:551-561. [DOI: 10.1007/s00792-017-0924-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/27/2017] [Indexed: 11/25/2022]
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Bhagi-Damodaran A, Petrik I, Lu Y. Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities. Isr J Chem 2016; 56:773-790. [PMID: 27994254 PMCID: PMC5161413 DOI: 10.1002/ijch.201600033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In biology, a heme-Cu center in heme-copper oxidases (HCOs) is used to catalyze the four-electron reduction of oxygen to water, while a heme-nonheme diiron center in nitric oxide reductases (NORs) is employed to catalyze the two-electron reduction of nitric oxide to nitrous oxide. Although much progress has been made in biochemical and biophysical studies of HCOs and NORs, structural features responsible for similarities and differences within the two enzymatic systems remain to be understood. Here, we discuss the progress made in the design and characterization of myoglobin-based enzyme models of HCOs and NORs. In particular, we focus on use of these models to understand the structure-function relations between HCOs and NORs, including the role of nonheme metals, conserved amino acids in the active site, heme types and hydrogen-bonding network in tuning enzymatic activities and total turnovers. Insights gained from these studies are summarized and future directions are proposed.
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Affiliation(s)
| | - Igor Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL. 61801
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Bhagi-Damodaran A, Hosseinzadeh P, Mirts E, Reed J, Petrik ID, Lu Y. Design of Heteronuclear Metalloenzymes. Methods Enzymol 2016; 580:501-37. [PMID: 27586347 PMCID: PMC5156654 DOI: 10.1016/bs.mie.2016.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Heteronuclear metalloenzymes catalyze some of the most fundamentally interesting and practically useful reactions in nature. However, the presence of two or more metal ions in close proximity in these enzymes makes them more difficult to prepare and study than homonuclear metalloenzymes. To meet these challenges, heteronuclear metal centers have been designed into small and stable proteins with rigid scaffolds to understand how these heteronuclear centers are constructed and the mechanism of their function. This chapter describes methods for designing heterobinuclear metal centers in a protein scaffold by giving specific examples of a few heme-nonheme bimetallic centers engineered in myoglobin and cytochrome c peroxidase. We provide step-by-step procedures on how to choose the protein scaffold, design a heterobinuclear metal center in the protein scaffold computationally, incorporate metal ions into the protein, and characterize the resulting metalloproteins, both structurally and functionally. Finally, we discuss how an initial design can be further improved by rationally tuning its secondary coordination sphere, electron/proton transfer rates, and the substrate affinity.
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Affiliation(s)
- A Bhagi-Damodaran
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Hosseinzadeh
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Mirts
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J Reed
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - I D Petrik
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Lu
- University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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