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Chen K, Xue W, Di X, Sun T, Gao W, Sun Y. Effects of nitrogen forms on Cd uptake and tolerance in wheat seedlings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 936:173451. [PMID: 38782266 DOI: 10.1016/j.scitotenv.2024.173451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/25/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Hydroponic experiment was conducted to explore the effects of two nitrogen (N) levels with five nitrate nitrogen (NO3--N) and ammonium nitrogen (NH4+-N) ratios on the growth status and Cd migration patterns of wheat seedlings under Cd5 and Cd30 level. Results showed that higher Cd were detrimental to the growth, absorption of K and Ca, expression of genes mediating NO3--N and NH4+-N transport, which also increased the content of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in shoots and roots of wheat seedlings. Higher N treatment alleviated the inhibitory effects of Cd stress on the biomass, root development, photosynthesis and increased the tolerance index of wheat seedlings. The ratio of NO3--N and NH4+-N was the main factor driving Cd accumulation in wheat seedlings, the combined application of NH4+-N and NO3--N was more conducive for the growth, nitrogen assimilation and Cd tolerance to the Cd stressed wheat seedlings. Increased NO3--N application rates significantly up-regulated the expression levels of TaNPF2.12, TaNRT2.2, increased NH4+-N application rates significantly up-regulated the expression levels of TaAMT1.1. The high proportion of NO3--N promoted the absorption of K, Ca and Cd in the shoots and roots of wheat seedlings, while NH4+-N was the opposite. Under low Cd conditions, the NO3--N to NH4+-N ratio of 1:1 was more conducive to the growth of wheat seedlings, under high Cd stress, the optimal of NO3--N to NH4+-N was 1:2 for inhibiting the accumulation of Cd in wheat seedlings. The results indicated that increasing NH4+-N ratio appropriately could inhibit wheat Cd uptake by increasing NH4+, K+ and Ca2+ for K and Ca channels, and promote wheat growth by promoting N assimilation process.
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Affiliation(s)
- Kexin Chen
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, P.R. China, Tianjin 300191, China
| | - Weijie Xue
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, P.R. China, Tianjin 300191, China.
| | - Xuerong Di
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, P.R. China, Tianjin 300191, China
| | - Tao Sun
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, P.R. China, Tianjin 300191, China
| | - Wei Gao
- College of Resources and Environment, Henan Agricultural University, No.218 Ping'an Avenue, Zhengzhou 450046, Henan, China; Henan Key Lab of Soil Pollution Control & Remediation, Henan Agricultural University, No.218 Ping'an Avenue, Zhengzhou 450046, Henan, China.
| | - Yuebing Sun
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, P.R. China, Tianjin 300191, China.
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Ribeiro IDA, Paes JA, Wendisch VF, Ferreira HB, Passaglia LMP. Proteome profiling of Paenibacillus sonchi genomovar Riograndensis SBR5 T under conventional and alternative nitrogen fixation. J Proteomics 2024; 294:105061. [PMID: 38154550 DOI: 10.1016/j.jprot.2023.105061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023]
Abstract
Paenibacillus sonchi SBR5T is a Gram-positive, endospore-forming facultative aerobic diazotrophic bacterium that can fix nitrogen via an alternative Fe-only nitrogenase (AnfHDGK). In several bacteria, this alternative system is expressed under molybdenum (Mo)-limiting conditions when the conventional Mo-dependent nitrogenase (NifHDK) production is impaired. The regulatory mechanisms, metabolic processes, and cellular functions of N2 fixation by alternative and/or conventional systems are poorly understood in the Paenibacillus genus. We conducted a comparative proteomic profiling study of P. sonchi SBR5T grown under N2-fixing conditions with and without Mo supply through an LC-MS/MS and label-free quantification analysis to address this gap. Protein abundances revealed overrepresented processes related to anaerobiosis growth adaption, Fe-S cluster biosynthesis, ammonia assimilation, electron transfer, and sporulation under N2-fixing conditions compared to non-fixing control. Under Mo limitation, the Fe-only nitrogenase components were overrepresented together with the Mo-transporter system, while the dinitrogenase component (NifDK) of Mo‑nitrogenase was underrepresented. The dinitrogenase reductase component (NifH) and accessory proteins encoded by the nif operon had no significant differential expression, suggesting post-transcriptional regulation of nif gene products in this strain. Overall, this was the first comprehensive proteomic analysis of a diazotrophic strain from the Paenibacillaceae family, and it provided insights related to alternative N2-fixation by Fe-only nitrogenase. SIGNIFICANCE: In this work, we try to understand how the alternative nitrogen fixation system, presented by some diazotrophic bacteria, works. For this, we used the SBR5 lineage of P. sonchi, which presents the alternative system in which the nitrogenase cofactor is composed only of iron. In addition, we tried to unravel the proteome of this strain in different situations of nitrogen fixation, since, for Gram-positive bacteria, these systems are little known. The results achieved, through LC-MS/MS and label-free quantitative analysis, showed an overrepresentation of proteins related to different processes involved with growth under stressful conditions in situations of nitrogen deficiency, in addition to suggesting that some encoded proteins by the nif operon may be regulated at post-transcriptional levels. Our findings represent important steps toward the elucidation of nitrogen fixation systems in Gram-positive diazotrophic bacteria.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil
| | - Jéssica Andrade Paes
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Volker F Wendisch
- Institute for Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves, 9500 Porto Alegre, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43312, Porto Alegre, RS, Brazil.
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3
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Müller MC, Lemaire ON, Kurth JM, Welte CU, Wagner T. Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Commun Biol 2024; 7:111. [PMID: 38243071 PMCID: PMC10799026 DOI: 10.1038/s42003-023-05726-w] [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: 06/28/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024] Open
Abstract
Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.
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Affiliation(s)
- Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Olivier N Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Microcosm Earth Center, Philipps-University Marburg and Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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4
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Klem H, Alegre-Requena JV, Paton RS. Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase. ACS Catal 2023; 13:16249-16257. [PMID: 38125975 PMCID: PMC10729027 DOI: 10.1021/acscatal.3c04176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Imidazole glycerol phosphate synthase (IGPS) is a class-I glutamine amidotransferase (GAT) that hydrolyzes glutamine. Ammonia is produced and transferred to a second active site, where it reacts with N1-(5'-phosphoribosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) to form precursors to purine and histidine biosynthesis. Binding of PrFAR over 25 Å away from the active site increases glutaminase efficiency by ∼4500-fold, primarily altering the glutamine turnover number. IGPS has been the focus of many studies on allosteric communication; however, atomic details for how the glutamine hydrolysis rate increases in the presence of PrFAR are lacking. We present a density functional theory study on 237-atom active site cluster models of IGPS based on crystallized structures representing the inactive and allosterically active conformations and investigate the multistep reaction leading to thioester formation and ammonia production. The proposed mechanism is supported by similar, well-studied enzyme mechanisms, and the corresponding energy profile is consistent with steady-state kinetic studies of PrFAR + IGPS. Additional active site models are constructed to examine the relationship between active site structural change and transition-state stabilization via energy decomposition schemes. The results reveal that the inactive IGPS conformation does not provide an adequately formed oxyanion hole structure and that repositioning of the oxyanion strand relative to the substrate is vital for a catalysis-competent oxyanion hole, with or without the hVal51 dihedral flip. These findings are valuable for future endeavors in modeling the IGPS allosteric mechanism by providing insight into the atomistic changes required for rate enhancement that can inform suitable reaction coordinates for subsequent investigations.
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Affiliation(s)
- Heidi Klem
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Juan V Alegre-Requena
- Dpto.de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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Eungrasamee K, Lindblad P, Jantaro S. Improved lipid production and component of mycosporine-like amino acids by co-overexpression of amt1 and aroB genes in Synechocystis sp. PCC6803. Sci Rep 2023; 13:19439. [PMID: 37945676 PMCID: PMC10636201 DOI: 10.1038/s41598-023-46290-x] [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: 07/09/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Implementing homologous overexpression of the amt1 (A) and aroB (B) genes involved in ammonium transporter and the synthesis of mycosporine-like amino acids (MAAs) and aromatic amino acids, respectively, we created three engineered Synechocystis sp. PCC6803 strains, including Ox-A, Ox-B, and Ox-AB, to study the utilization of carbon and nitrogen in cyanobacteria for the production of valuable products. With respect to amt1 overexpression, the Ox-A and Ox-AB strains had a greater growth rate under (NH4)2SO4 supplemented condition. Both the higher level of intracellular accumulation of lipids in Ox-A and Ox-AB as well as the increased secretion of free fatty acids from the Ox-A strain were impacted by the late-log phase of cell growth. It is noteworthy that among all strains, the Ox-B strain undoubtedly spotted a substantial accumulation of glycogen as a consequence of aroB overexpression. Additionally, the ammonium condition drove the potent antioxidant activity in Ox strains with a late-log phase, particularly in the Ox-B and Ox-AB strains. This was probably related to the altered MAA component inside the cells. The higher proportion of P4-fraction was induced by the ammonium condition in both Ox-B and Ox-AB, while the noted increase of the P1 component was found in the Ox-A strain.
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Affiliation(s)
- Kamonchanock Eungrasamee
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Box 523, 75120, Uppsala, Sweden
| | - Saowarath Jantaro
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Zhu L, Huang C, Li W, Wu W, Tang Z, Tian Y, Xi B. Ammonia assimilation is key for the preservation of nitrogen during industrial-scale composting of chicken manure. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 170:50-61. [PMID: 37544234 DOI: 10.1016/j.wasman.2023.07.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/16/2023] [Accepted: 07/23/2023] [Indexed: 08/08/2023]
Abstract
Nitrogen loss from compost is a serious concern, causing severe environmental pollution. The NH4+-N content reflects the release of NH3. However, the nitrogen conversion pathway that has the greatest impact on NH4+-N content is still unclear. This study attempted to explore the key pathways, core functional microorganisms, and mechanisms involved in the transformation of ammonia nitrogen during composting. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathways revealed that ammonia assimilation was dominated by the glutamate dehydrogenase (GDH) pathway (53.4%), which is crucial for nitrogen preservation. The combined analysis of KEGG, NR species annotation, and co-occurrence network identified 20 easy-to-regulate obligate core nitrogen-transforming functional microorganisms, including 18 ammonia-assimilating bacteria. Furthermore, the effects of environmental parameters on the obligate core functional microorganisms were investigated. The present study results provided a theoretical basis for the utilization of ten ammonia-assimilating bacteria, such as Paenibacillus, Erysipelatoclostridium, and Defluviimonas to improve the quality of compost.
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Affiliation(s)
- Lin Zhu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Caihong Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Wei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Weixia Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541006, China
| | - Zhurui Tang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yu Tian
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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Couto-Rodríguez RL, Koh J, Chen S, Maupin-Furlow JA. Insights into the Lysine Acetylome of the Haloarchaeon Haloferax volcanii during Oxidative Stress by Quantitative SILAC-Based Proteomics. Antioxidants (Basel) 2023; 12:1203. [PMID: 37371933 PMCID: PMC10294847 DOI: 10.3390/antiox12061203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Oxidative stress adaptation strategies are important to cell function and are linked to cardiac, neurodegenerative disease, and cancer. Representatives of the Archaea domain are used as model organisms based on their extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. A study of the halophilic archaeon Haloferax volcanii reveals lysine acetylation to be associated with oxidative stress responses. The strong oxidant hypochlorite: (i) stimulates an increase in lysine acetyltransferase HvPat2 to HvPat1 abundance ratios and (ii) selects for lysine deacetylase sir2 mutants. Here we report the dynamic occupancy of the lysine acetylome of glycerol-grown H. volcanii as it shifts in profile in response to hypochlorite. These findings are revealed by the: (1) quantitative multiplex proteomics of the SILAC-compatible parent and Δsir2 mutant strains and (2) label-free proteomics of H26 'wild type' cells. The results show that lysine acetylation is associated with key biological processes including DNA topology, central metabolism, cobalamin biosynthesis, and translation. Lysine acetylation targets are found conserved across species. Moreover, lysine residues modified by acetylation and ubiquitin-like sampylation are identified suggesting post-translational modification (PTM) crosstalk. Overall, the results of this study expand the current knowledge of lysine acetylation in Archaea, with the long-term goal to provide a balanced evolutionary perspective of PTM systems in living organisms.
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Affiliation(s)
- Ricardo L. Couto-Rodríguez
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA; (J.K.); (S.C.)
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA; (J.K.); (S.C.)
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, The University of Mississippi, Oxford, MS 38677, 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 32610, USA
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8
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Lu ZB, Li YD, Jiang SG, Yang QB, Jiang S, Huang JH, Yang LS, Chen X, Zhou FL. Transcriptome analysis of hepatopancreas in penaeus monodon under acute low pH stress. FISH & SHELLFISH IMMUNOLOGY 2022; 131:1166-1172. [PMID: 36410647 DOI: 10.1016/j.fsi.2022.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
The decrease of seawater pH can affect the metabolism, acid-base balance, immune response and immunoprotease activity of aquatic animals, leading to aquatic animal stress, impairing the immune system of aquatic animals and weakening disease resistance, etc. In this study, we performed high-throughput sequencing analysis of the hepatopancreas transcriptome library of low pH stress penaeus monodon, and after sequencing quality control, a total of 43488612-56271828 Clean Reads were obtained, and GO annotation and KEGG pathway enrichment analysis were performed on the obtained Clean Reads, and a total of 395 DEGs were identified. we mined 10 differentially expressed and found that they were significantly enriched in the Metabolic pathways (ko01100), Biosynthesis of secondary metabolites (ko01110), Nitrogen metabolism (ko00910) pathways, such as PIGA, DGAT1, DGAT2, UBE2E on Metabolic pathways; UGT, GLT1, TIM genes on Biosynthesis of secondary metabolites; CA, CA2, CA4 genes on Nitrogen metabolism, are involved in lipid metabolism, induction of oxidative stress and inflammation in the muscular body of spot prawns. These genes play an important role in lipid metabolism, induction of oxidative stress and inflammatory response in the muscle of the shrimp. In summary, these genes provide valuable reference information for future breeding of low pH-tolerant shrimp.
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Affiliation(s)
- Zhi-Bin Lu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yun-Dong Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China; Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Shi-Gui Jiang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, 572018, China
| | - Qi-Bin Yang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China
| | - Song Jiang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China
| | - Jian-Hua Huang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China
| | - Li-Shi Yang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China
| | - Xu Chen
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, 572018, China
| | - Fa-Lin Zhou
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, 510300, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, 572018, China.
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9
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Jingjing E, Jingya Z, Rongze M, Zichao C, Caiqing Y, Ruixue W, Qiaoling Z, Ying Y, Jing L, Junguo W. Study of the internal mechanism of L-glutamate for improving the survival rate of Lactiplantibacillus plantarum LIP-1 after freeze-drying. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2022.103253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis. INORGANICS 2022. [DOI: 10.3390/inorganics10100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.
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A Reduced F 420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon. J Bacteriol 2022; 204:e0007822. [PMID: 35695516 PMCID: PMC9295563 DOI: 10.1128/jb.00078-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F420-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F420 (F420H2), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F420H2. Instead, it acted as an F420H2-dependent nitrite reductase (FNiR) with physiologically relevant Km values (nitrite, 5 μM; F420H2, 14 μM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F420H2-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E0' [standard potential], +440 mV) but not sulfite (E0', -116 mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies. IMPORTANCE Coenzyme F420-dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade. We show that a member of this clade from ANME-2c functions as F420-dependent nitrite reductase (FNiR) and lacks Fsr activity. This specialization arose from a distinct feature of the reductant processing system and not the substrate recognition element. We hypothesize FNiR may protect ANME Mcr from inactivation by nitrite. This is an example of functional specialization within a protein family that is induced by changes in electron transfer modules to fit an ecological need.
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Han Z, Wu F, Yu P, Mao L. Computer-Aided Rational Construction of Mediated Bioelectrocatalysis with π-Conjugated (Hetero)cyclic Molecules: Toward Promoted Distant Electron Tunneling and Improved Biosensing. Anal Chem 2022; 94:8033-8040. [PMID: 35604848 DOI: 10.1021/acs.analchem.2c01289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Highly π-conjugated (hetero)cyclic molecules having delocalized orbitals and tunable charge mobilities are attractive redox relays for mediated bioelectrocatalysis in manifold applications. As rigid molecules, their dynamics within the soft but confined intraprotein space becomes the crucial determinant of the enzyme-mediator electron-tunneling efficiency. However, it is rarely investigated in designing the mediated interface with a particular biocatalyst (e.g., oxidoreductase), which remains an empirical but try-and-error process. Herein, we present the computer-aided exploration of interactions between a flavin-containing reductive synthase and structurally diverse π-extended (hetero)cyclic mediators to realize reversed bioelectrocatalytic oxidation at low overpotentials. Compared to ring-fused systems with unbroken molecular planarity, heteroatom-bridged cyclic, and rotatable conjugated structures (e.g., indophenols) can experience unusually large dynamic torsion under biased forces of hydrogen bonding with enzyme residues. This behavior led to fast intraprotein reorientation (<50 ps) that shortened the electron-tunneling distance from 12 to 9 Å. Meanwhile, the lowest unoccupied molecular orbital level upon molecular torsion was decreased by 0.5 eV to further promote electron abstraction from the reduced flavin cofactor. An efficient distant electron tunneling also obviated mediator transport through the substrate channel, thus avoiding competitive inhibition on enzyme kinetics to broaden the operating concentration range. The resulting bioelectrocatalytic interface enables low-potential biosensing of glutamate with improved selectivity. Our finding provides new structural insights into constructing efficient long-range heterogeneous charge transport with biomacromolecular catalysts.
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Affiliation(s)
- Zhongjie Han
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,College of Chemistry, Beijing Normal University, Beijing 100875, China
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13
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Nguyen S, Jovcevski B, Pukala TL, Bruning JB. Structural insights into the antifungal drug target guanosine monophosphate synthase from Aspergillus fumigatus. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:248-259. [DOI: 10.1107/s2059798321012031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/11/2021] [Indexed: 11/10/2022]
Abstract
Purine biosynthesis is a fundamental cellular process that sustains life by maintaining the intracellular pool of purines for DNA/RNA synthesis and signal transduction. As an integral determinant of fungal survival and virulence, the enzymes in this metabolic pathway have been pursued as potential antifungal targets. Guanosine monophosphate (GMP) synthase has been identified as an attractive target as it is essential for virulence in the clinically prominent fungal pathogens Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans. However, a lack of structural information on GMP synthase has hindered drug-design efforts. Here, the first structure of a GMP synthase of fungal origin, that from A. fumigatus (at 2.3 Å resolution), is presented. Structural analysis of GMP synthase shows a distinct absence of the D1 dimerization domain that is present in the human homologue. Interestingly, A. fumigatus GMP synthase adopts a dimeric state, as determined by native mass spectrometry and gel-filtration chromatography, in contrast to the monomeric human homologue. Analysis of the substrate-binding pockets of A. fumigatus GMP synthase reveals key differences in the ATP- and XMP-binding sites that can be exploited for species-specific inhibitor drug design. Furthermore, the inhibitory activities of the glutamine analogues acivicin (IC50 = 16.6 ± 2.4 µM) and 6-diazo-5-oxo-L-norleucine (IC50 = 29.6 ± 5.6 µM) against A. fumigatus GMP synthase are demonstrated. Together, these data provide crucial structural information required for specifically targeting A. fumigatus GMP synthase for future antifungal drug-discovery endeavours.
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Vanoni MA. Iron-sulfur flavoenzymes: the added value of making the most ancient redox cofactors and the versatile flavins work together. Open Biol 2021; 11:210010. [PMID: 33947244 PMCID: PMC8097209 DOI: 10.1098/rsob.210010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) flavoproteins form a broad and growing class of complex, multi-domain and often multi-subunit proteins coupling the most ancient cofactors (the Fe-S clusters) and the most versatile coenzymes (the flavin coenzymes, FMN and FAD). These enzymes catalyse oxidoreduction reactions usually acting as switches between donors of electron pairs and acceptors of single electrons, and vice versa. Through selected examples, the enzymes' structure−function relationships with respect to rate and directionality of the electron transfer steps, the role of the apoprotein and its dynamics in modulating the electron transfer process will be discussed.
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Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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15
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Daval S, Gazengel K, Belcour A, Linglin J, Guillerm‐Erckelboudt A, Sarniguet A, Manzanares‐Dauleux MJ, Lebreton L, Mougel C. Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes. Microb Biotechnol 2020; 13:1648-1672. [PMID: 32686326 PMCID: PMC7415369 DOI: 10.1111/1751-7915.13634] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
The contribution of surrounding plant microbiota to disease development has led to the 'pathobiome' concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time-course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defence-related genes (glucosinolate metabolism) in B. napus.
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Affiliation(s)
- Stéphanie Daval
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
| | - Kévin Gazengel
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
| | | | - Juliette Linglin
- INRAEAgrocampus OuestUniversité de RennesIGEPPPloudanielF‐29260France
| | | | - Alain Sarniguet
- INRAEAgrocampus OuestUniversité d'AngersIRHSBeaucouzéF‐49071France
| | | | - Lionel Lebreton
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
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16
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Li P, Li K, Li X, Zhao F, Wang R, Wang J. Improving enzyme activity of glucosamine-6-phosphate synthase by semi-rational design strategy and computer analysis. Biotechnol Lett 2020; 42:2319-2332. [PMID: 32601959 DOI: 10.1007/s10529-020-02949-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 06/24/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To improve enzyme activity of Glucosamine-6-phosphate synthase (Glms) of Bacillus subtilis by site saturation mutagenesis at Leu593, Ala594, Lys595, Ser596 and Val597 based on computer-aided semi-rational design. RESULTS The results indicated that L593S had the greatest effect on the activity of BsGlms and the enzyme activity increased from 5 to 48 U/mL. The mutation of L593S increased the yield of glucosamine by 1.6 times that of the original strain. The binding energy of the mutant with substrate was reduced from - 743.864 to - 768.246 kcal/mol. Molecular dynamics simulation results showed that Ser593 enhanced the flexibility of the protein, which ultimately led to increased enzyme activity. CONCLUSION We successfully improved BsGlms activity through computer simulation and site saturation mutagenesis. This combination of methodologies may fit into an efficient workflow for improving Glms and other proteins activity.
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Affiliation(s)
- Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan, 250353, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Kang Li
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Xu Li
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Fei Zhao
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan, 250353, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan, 250353, Shandong, People's Republic of China. .,Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
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17
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Li W, Ni J, Cai S, Liu Y, Shen C, Yang H, Chen Y, Tao J, Yu Y, Liu Q. Variations in microbial community structure and functional gene expression in bio-treatment processes with odorous pollutants. Sci Rep 2019; 9:17870. [PMID: 31780738 PMCID: PMC6883040 DOI: 10.1038/s41598-019-54281-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
Engineered microbial ecosystems in biofilters have been widely applied to treat odorous gases from industrial emissions. Variations in microbial community structure and function associated with the removal of odorous gases by biofilters are largely unknown. This study performed a metagenomic analysis to discover shifts in microbial community structures in a commercial scale biofilter after treating odorous gas. Our study identified 175,675 functional genes assigned into 43 functional KEGG pathways. Based on the unigene sequences, there were significant changes in microbial community structures in the biofilter after treating odorous gas. The dominant genera were Thiobacillus and Oceanicaulis before the treatment, and were Acidithiobacillus and Ferroplasma after the treatment. A clustering analysis showed that the number of down-regulated microbes exceeded the number of up-regulated microbes, suggesting that odorous gas treatment reduced in microbial community structures. A differential expression analysis identified 29,975 up- and 452,599 down-regulated genes. An enrichment analysis showed 17 classic types of xenobiotic biodegradation pathways. The results identified 16 and 15 genes involved in ammonia and sulfite metabolism, respectively; an analysis of their relative abundance identified several up-regulated genes, which may be efficient genes involved in removing odorous gases. The data provided in this study demonstrate the changes in microbial communities and help identify the dominant microflora and genes that play key roles in treating odorous gases.
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Affiliation(s)
- Weidong Li
- College of Qianjiang, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
| | - Jianguo Ni
- Hangzhou Ecological Environment Bureau of Xiaoshan Branch, Hangzhou, 311201, Zhejiang, People's Republic of China
| | - Shaoqin Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China.,College of Environment, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Ying Liu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
| | - Chenjia Shen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
| | - Huayun Yang
- College of Qianjiang, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
| | - Yuquan Chen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
| | - Jia Tao
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
| | - Yunfeng Yu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
| | - Qi Liu
- College of Qianjiang, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China. .,College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China.
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18
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Wu F, Yu P, Yang X, Han Z, Wang M, Mao L. Exploring Ferredoxin-Dependent Glutamate Synthase as an Enzymatic Bioelectrocatalyst. J Am Chem Soc 2018; 140:12700-12704. [DOI: 10.1021/jacs.8b08020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Xiaoti Yang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Zhongjie Han
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Ming Wang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
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19
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part II. [4Fe-4S] and [3Fe-4S] iron-sulfur proteins. J Struct Biol 2018; 202:250-263. [DOI: 10.1016/j.jsb.2018.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/11/2018] [Accepted: 01/29/2018] [Indexed: 01/27/2023]
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20
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Fam RR, Hiong KC, Choo CY, Wong WP, Chew SF, Ip YK. Molecular characterization of a novel algal glutamine synthetase (GS) and an algal glutamate synthase (GOGAT) from the colorful outer mantle of the giant clam, Tridacna squamosa , and the putative GS-GOGAT cycle in its symbiotic zooxanthellae. Gene 2018; 656:40-52. [DOI: 10.1016/j.gene.2018.02.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/09/2018] [Accepted: 02/23/2018] [Indexed: 12/25/2022]
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21
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Chan CYL, Hiong KC, Boo MV, Choo CYL, Wong WP, Chew SF, Ip YK. Light exposure enhances urea absorption in the fluted giant clam, Tridacna squamosa, and up-regulates the protein abundance of a light-dependent urea active transporter, DUR3-like, in its ctenidium. J Exp Biol 2018; 221:jeb176313. [PMID: 29540461 DOI: 10.1242/jeb.176313] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/12/2018] [Indexed: 12/26/2022]
Abstract
Giant clams live in nutrient-poor reef waters of the Indo-Pacific and rely on symbiotic dinoflagellates (Symbiodinium spp., also known as zooxanthellae) for nutrients. As the symbionts are nitrogen deficient, the host clam has to absorb exogenous nitrogen and supply it to them. This study aimed to demonstrate light-enhanced urea absorption in the fluted giant clam, Tridacna squamosa, and to clone and characterize the urea active transporter DUR3-like from its ctenidium (gill). The results indicate that T. squamosa absorbs exogenous urea, and the rate of urea uptake in the light was significantly higher than that in darkness. The DUR3-like coding sequence obtained from its ctenidium comprised 2346 bp, encoding a protein of 782 amino acids and 87.0 kDa. DUR3-like was expressed strongly in the ctenidium, outer mantle and kidney. Twelve hours of exposure to light had no significant effect on the transcript level of ctenidial DUR3-like However, between 3 and 12 h of light exposure, DUR3-like protein abundance increased progressively in the ctenidium, and became significantly greater than that in the control at 12 h. DUR3-like had an apical localization in the epithelia of the ctenidial filaments and tertiary water channels. Taken together, these results indicate that DUR3-like might participate in light-enhanced urea absorption in the ctenidium of T. squamosa When made available to the symbiotic zooxanthellae that are known to possess urease, the absorbed urea can be metabolized to NH3 and CO2 to support amino acid synthesis and photosynthesis, respectively, during insolation.
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Affiliation(s)
- Christabel Y L Chan
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Kum C Hiong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Mel V Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Celine Y L Choo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Wai P Wong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
- The Tropical Marine Science Institute, National University of Singapore, Kent Ridge, Singapore 119227, Republic of Singapore
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22
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García-Gutiérrez Á, Cánovas FM, Ávila C. Glutamate synthases from conifers: gene structure and phylogenetic studies. BMC Genomics 2018; 19:65. [PMID: 29351733 PMCID: PMC5775586 DOI: 10.1186/s12864-018-4454-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/15/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC 1.4.1.14) and Fd-GOGAT (EC 1.4.7.1), which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants. In conifers, partial cDNA sequences for GOGATs have been isolated and used for gene expression studies. However, knowledge of the gene structure and of phylogenetic relationships with other plant enzymes is quite scant. RESULTS Technological advances in conifer megagenomes sequencing have made it possible to obtain full-length cDNA sequences encoding Fd- and NADH-GOGAT from maritime pine, as well as BAC clones containing sequences for NADH-GOGAT and Fd-GOGAT genes. In the current study, we studied the genomic organization of pine GOGAT genes, the size of their exons/introns, copy numbers in the pine genome and relationships with other plant genes. Phylogenetic analysis was performed, and the degree of preservation and dissimilarity of key domains for the catalytic activities of these enzymes in different taxa were determined. CONCLUSIONS Fd- and NADH-GOGAT are encoded by single-copy genes in the maritime pine genome. The Fd-GOGAT gene is extremely large spanning more than 330 kb and the presence of very long introns highlights the important contribution of LTR retrotransposons to the gene size in conifers. In contrast, the structure of the NADH-GOGAT gene is similar to the orthologous genes in angiosperms. Our phylogenetic analysis indicates that these two genes had different origins during plant evolution. The results provide new insights into the structure and molecular evolution of these essential genes.
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Affiliation(s)
- Ángel García-Gutiérrez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
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23
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Hirasawa M, Solis J, Vaidyanathan N, Srivastava AP, Wynn RM, Sutton RB, Knaff DB. Identification of the ferredoxin interaction sites on ferredoxin-dependent glutamate synthase from Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2017; 134:317-328. [PMID: 28975508 DOI: 10.1007/s11120-017-0446-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Based on in silico docking methods, five amino acids in glutamate synthase (Gln-467, His-1144, Asn-1147, Arg-1162, and Trp-676) likely constitute key binding residues in the interface of a glutamate synthase:ferredoxin complex. Although all interfacial mutants studied showed the ability to form a complex under low ionic strength, these docking mutations showed significantly less ferredoxin-dependent activities, while still retaining enzymatic activity. Furthermore, isothermal titration calorimetry showed a possible 1:2 molar ratio between the wild-type glutamate synthase and ferredoxin. However, each of our interfacial mutants showed only a 1:1 complex with ferredoxin, suggesting that the mutations directly affect the glutamate synthase:ferredoxin heterodimer interface.
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Affiliation(s)
- Masakazu Hirasawa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Jacaranda Solis
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Science Center, Lubbock, TX, 79430-6591, USA
| | - Nanditha Vaidyanathan
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
- Depuy Synthes Companies, 1302 Wrights Lane East, West Chester, PA, 19380, USA
| | - Anurag P Srivastava
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinoi, 60064, USA
| | - R Max Wynn
- Departments of Internal Medicine and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9038, USA.
| | - Roger B Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech Health Science Center, Lubbock, TX, 79430-6551, USA
| | - David B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
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Muñoz-Nortes T, Pérez-Pérez JM, Sarmiento-Mañús R, Candela H, Micol JL. Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis. Sci Rep 2017; 7:6164. [PMID: 28733652 PMCID: PMC5522406 DOI: 10.1038/s41598-017-06335-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/29/2017] [Indexed: 11/29/2022] Open
Abstract
Biomass production requires the coordination between growth and metabolism. In a large-scale screen for mutants affected in leaf morphology, we isolated the orbiculata1 (orb1) mutants, which exhibit a pale green phenotype and reduced growth. The combination of map-based cloning and next-generation sequencing allowed us to establish that ORB1 encodes the GLUTAMATE SYNTHASE 1 (GLU1) enzyme, also known as FERREDOXIN-DEPENDENT GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1 (Fd-GOGAT1). We performed an RNA-seq analysis to identify global gene expression changes in the orb1–3 mutant. We found altered expression levels of genes encoding enzymes involved in nitrogen assimilation and amino acid biosynthesis, such as glutamine synthetases, asparagine synthetases and glutamate dehydrogenases, showing that the expression of these genes depends on the levels of glutamine and/or glutamate. In addition, we observed a concerted upregulation of genes encoding subunits of the cytosolic ribosome. A gene ontology (GO) analysis of the differentially expressed genes between Ler and orb1–3 showed that the most enriched GO terms were ‘translation’, ‘cytosolic ribosome’ and ‘structural constituent of ribosome’. The upregulation of ribosome-related functions might reflect an attempt to keep protein synthesis at optimal levels even when the pool of glutamate is reduced.
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Affiliation(s)
- Tamara Muñoz-Nortes
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - José Manuel Pérez-Pérez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Raquel Sarmiento-Mañús
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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Sun Y, De Vos P, Willems A. Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581 T. Antonie van Leeuwenhoek 2017; 110:1613-1626. [PMID: 28726125 DOI: 10.1007/s10482-017-0911-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/12/2017] [Indexed: 11/27/2022]
Abstract
Until recently, it has not been generally known that some bacteria can contain the gene inventory for both denitrification and dissimilatory nitrate (NO3-)/nitrite (NO2-) reduction to ammonium (NH4+) (DNRA). Detailed studies of these microorganisms could shed light on the differentiating environmental drivers of both processes without interference of organism-specific variation. Genome analysis of Bacillus azotoformans LMG 9581T shows a remarkable redundancy of dissimilatory nitrogen reduction, with multiple copies of each denitrification gene as well as DNRA genes nrfAH, but a reduced capacity for nitrogen assimilation, with no nas operon nor amtB gene. Here, we explored nitrogen assimilation in detail using growth experiments in media with different organic and inorganic nitrogen sources at different concentrations. Monitoring of growth, NO3- NO2-, NH4+ concentration and N2O production revealed that B. azotoformans LMG 9581T could not grow with NH4+ as sole nitrogen source and confirmed the hypothesis of reduced nitrogen assimilation pathways. However, NH4+ could be assimilated and contributed up to 50% of biomass if yeast extract was also provided. NH4+ also had a significant but concentration-dependent influence on growth rate. The mechanisms behind these observations remain to be resolved but hypotheses for this deficiency in nitrogen assimilation are discussed. In addition, in all growth conditions tested a denitrification phenotype was observed, with all supplied NO3- converted to nitrous oxide (N2O).
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Affiliation(s)
- Yihua Sun
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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Liu LK, Becker DF, Tanner JJ. Structure, function, and mechanism of proline utilization A (PutA). Arch Biochem Biophys 2017; 632:142-157. [PMID: 28712849 DOI: 10.1016/j.abb.2017.07.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/13/2023]
Abstract
Proline has important roles in multiple biological processes such as cellular bioenergetics, cell growth, oxidative and osmotic stress response, protein folding and stability, and redox signaling. The proline catabolic pathway, which forms glutamate, enables organisms to utilize proline as a carbon, nitrogen, and energy source. FAD-dependent proline dehydrogenase (PRODH) and NAD+-dependent glutamate semialdehyde dehydrogenase (GSALDH) convert proline to glutamate in two sequential oxidative steps. Depletion of PRODH and GSALDH in humans leads to hyperprolinemia, which is associated with mental disorders such as schizophrenia. Also, some pathogens require proline catabolism for virulence. A unique aspect of proline catabolism is the multifunctional proline utilization A (PutA) enzyme found in Gram-negative bacteria. PutA is a large (>1000 residues) bifunctional enzyme that combines PRODH and GSALDH activities into one polypeptide chain. In addition, some PutAs function as a DNA-binding transcriptional repressor of proline utilization genes. This review describes several attributes of PutA that make it a remarkable flavoenzyme: (1) diversity of oligomeric state and quaternary structure; (2) substrate channeling and enzyme hysteresis; (3) DNA-binding activity and transcriptional repressor function; and (4) flavin redox dependent changes in subcellular location and function in response to proline (functional switching).
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Affiliation(s)
- Li-Kai Liu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Donald F Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, United States.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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The competition between chemistry and biology in assembling iron-sulfur derivatives. Molecular structures and electrochemistry. Part IV. {[Fe3S4](SγCys)3} proteins. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Zeng DD, Qin R, Li M, Alamin M, Jin XL, Liu Y, Shi CH. The ferredoxin-dependent glutamate synthase (OsFd-GOGAT) participates in leaf senescence and the nitrogen remobilization in rice. Mol Genet Genomics 2016; 292:385-395. [DOI: 10.1007/s00438-016-1275-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 11/21/2016] [Indexed: 10/20/2022]
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Meng L, Li W, Zhang S, Wu C, Wang K. Effects of sucrose amendment on ammonia assimilation during sewage sludge composting. BIORESOURCE TECHNOLOGY 2016; 210:160-166. [PMID: 26852272 DOI: 10.1016/j.biortech.2016.01.094] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 06/05/2023]
Abstract
The aim of this study was to evaluate the laboratory-scale composting of sewage sludge and pumice mixtures that were amended with sucrose. The variation in temperature, pH, NH4(+)-N, ammonia emission, bacterial community, ammonia assimilating bacteria (AAB) populations and enzymatic activity related to ammonia assimilation were detected. The addition of sucrose increased the AAB population by 2.5-3.5 times, reduced ammonia emission by 24.7-31.1% compared with the control treatment, and promoted the growth of Bacillus and Wautersiella. The activities of glutamate dehydrogenase (GDH), glutamate synthase (GS) and glutamine synthetase (GOGAT), were enhanced by the addition of sucrose. GDH made a substantial contribution to ammonia assimilation when the ammonia concentration was high (⩾1.5g/kg) in the thermophilic phase. The GS/GOGAT cycle played an important role at low ammonia concentrations (⩽1.1g/kg) in the cooling phase. These results suggested that adding sucrose to sludge compost could promote ammonia assimilation and reduce ammonia emission.
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Affiliation(s)
- Liqiang Meng
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, 150090 Harbin, China; Institute of Microbiology, Heilongjiang Academy of Sciences, 150010 Harbin, China; Institute of Advanced Technology, Heilongjiang Academy of Sciences, 150020 Harbin, China
| | - Weiguang Li
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, 150090 Harbin, China.
| | - Shumei Zhang
- Institute of Microbiology, Heilongjiang Academy of Sciences, 150010 Harbin, China; Institute of Advanced Technology, Heilongjiang Academy of Sciences, 150020 Harbin, China
| | - Chuandong Wu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, 150090 Harbin, China
| | - Ke Wang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, 150090 Harbin, China
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Salminen A, Jouhten P, Sarajärvi T, Haapasalo A, Hiltunen M. Hypoxia and GABA shunt activation in the pathogenesis of Alzheimer's disease. Neurochem Int 2015; 92:13-24. [PMID: 26617286 DOI: 10.1016/j.neuint.2015.11.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022]
Abstract
We have previously observed that the conversion of mild cognitive impairment to definitive Alzheimer's disease (AD) is associated with a significant increase in the serum level of 2,4-dihydroxybutyrate (2,4-DHBA). The metabolic generation of 2,4-DHBA is linked to the activation of the γ-aminobutyric acid (GABA) shunt, an alternative energy production pathway activated during cellular stress, when the function of Krebs cycle is compromised. The GABA shunt can be triggered by local hypoperfusion and subsequent hypoxia in AD brains caused by cerebral amyloid angiopathy. Succinic semialdehyde dehydrogenase (SSADH) is a key enzyme in the GABA shunt, converting succinic semialdehyde (SSA) into succinate, a Krebs cycle intermediate. A deficiency of SSADH activity stimulates the conversion of SSA into γ-hydroxybutyrate (GHB), an alternative route from the GABA shunt. GHB can exert not only acute neuroprotective activities but unfortunately also chronic detrimental effects which may lead to cognitive impairment. Subsequently, GHB can be metabolized to 2,4-DHBA and secreted from the brain. Thus, the activation of the GABA shunt and the generation of GHB and 2,4-DHBA can have an important role in the early phase of AD pathogenesis.
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Affiliation(s)
- Antero Salminen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland.
| | - Paula Jouhten
- VTT Technical Research Centre of Finland, FIN-00014 Helsinki, Finland; EMBL European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Timo Sarajärvi
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Annakaisa Haapasalo
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 100, FI-70029 KYS, Finland
| | - Mikko Hiltunen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 100, FI-70029 KYS, Finland; Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
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31
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Wang P, Tan Z, Guan L, Tang S, Zhou C, Han X, Kang J, He Z. Ammonia and amino acids modulates enzymes associated with ammonia assimilation pathway by ruminal microbiota in vitro. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.05.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Deschoenmaeker F, Facchini R, Leroy B, Badri H, Zhang CC, Wattiez R. Proteomic and cellular views of Arthrospira sp. PCC 8005 adaptation to nitrogen depletion. MICROBIOLOGY-SGM 2014; 160:1224-1236. [PMID: 24648480 DOI: 10.1099/mic.0.074641-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes that play a crucial role in the Earth's nitrogen and carbon cycles. Nitrogen availability is one of the most important factors in cyanobacterial growth. Interestingly, filamentous non-diazotrophic cyanobacteria, such as Arthrospira sp. PCC 8005, have developed survival strategies that enable them to adapt to nitrogen deprivation. Metabolic studies recently demonstrated a substantial synthesis and accumulation of glycogen derived from amino acids during nitrogen starvation. Nevertheless, the regulatory mechanism of this adaptation is poorly understood. To the best of our knowledge, this study is the first proteomic and cellular analysis of Arthrospira sp. PCC 8005 under nitrogen depletion. Label-free differential proteomic analysis indicated the global carbon and nitrogen reprogramming of the cells during nitrogen depletion as characterized by an upregulation of glycogen synthesis and the use of endogenous nitrogen sources. The degradation of proteins and cyanophycin provided endogenous nitrogen when exogenous nitrogen was limited. Moreover, formamides, cyanates and urea were also potential endogenous nitrogen sources. The transporters of some amino acids and alternative nitrogen sources such as ammonium permease 1 were induced under nitrogen depletion. Intriguingly, although Arthrospira is a non-diazotrophic cyanobacterium, we observed the upregulation of HetR and HglK proteins, which are involved in heterocyst differentiation. Moreover, after a long period without nitrate, only a few highly fluorescent cells in each trichome were observed, and they might be involved in the long-term survival mechanism of this non-diazotrophic cyanobacterium under nitrogen deprivation.
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Affiliation(s)
- Frédéric Deschoenmaeker
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - Raphaël Facchini
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - Hanène Badri
- Expert Group for Molecular and Cellular Biology MCB, Belgian Nuclear Research Center SCK.CEN, B-2400 Mol, Belgium.,Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - C-C Zhang
- Laboratoire de Chimie Bactérienne, CNRS-UMR 7283, Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, B-7000 Mons, Belgium
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Dance I. A molecular pathway for the egress of ammonia produced by nitrogenase. Sci Rep 2013; 3:3237. [PMID: 24241241 PMCID: PMC3831235 DOI: 10.1038/srep03237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/01/2013] [Indexed: 01/19/2023] Open
Abstract
Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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34
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35
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Susanti D, Mukhopadhyay B. An intertwined evolutionary history of methanogenic archaea and sulfate reduction. PLoS One 2012; 7:e45313. [PMID: 23028926 PMCID: PMC3448663 DOI: 10.1371/journal.pone.0045313] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 08/20/2012] [Indexed: 12/29/2022] Open
Abstract
Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420))-dependent sulfite reductase (Fsr) where N- and C-terminal halves (Fsr-N and Fsr-C) are homologs of F(420)H(2) dehydrogenase and dissimilatory sulfite reductase (Dsr), respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP), both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest), carrying a coupled siroheme-[Fe(4)-S(4)] cluster and sulfite-binding Arg/Lys residues; Group III (most complex), with group I features, a Dsr-type peripheral [Fe(4)-S(4)] cluster and an additional [Fe(4)-S(4)] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe(4)-S(4)] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F(420)H(2) dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago) biologically produced sulfide deposit.
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Affiliation(s)
- Dwi Susanti
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
- Genetics, Bioinformatics and Computational Biology Ph.D Program, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Biswarup Mukhopadhyay
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
- Departments of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
- Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail:
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Kaur H, Ganguli D, Bachhawat AK. Glutathione degradation by the alternative pathway (DUG pathway) in Saccharomyces cerevisiae is initiated by (Dug2p-Dug3p)2 complex, a novel glutamine amidotransferase (GATase) enzyme acting on glutathione. J Biol Chem 2012; 287:8920-31. [PMID: 22277648 DOI: 10.1074/jbc.m111.327411] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The recently identified, fungi-specific alternative pathway of glutathione degradation requires the participation of three genes, DUG1, DUG2, and DUG3. Dug1p has earlier been shown to function as a Cys-Gly-specific dipeptidase. In the present study, we describe the characterization of Dug2p and Dug3p. Dug3p has a functional glutamine amidotransferase (GATase) II domain that is catalytically important for glutathione degradation as demonstrated through mutational analysis. Dug2p, which has an N-terminal WD40 and a C-terminal M20A peptidase domain, has no peptidase activity. The previously demonstrated Dug2p-Dug3p interaction was found to be mediated through the WD40 domain of Dug2p. Dug2p was also shown to be able to homodimerize, and this was mediated by its M20A peptidase domain. In vitro reconstitution assays revealed that Dug2p and Dug3p were required together for the cleavage of glutathione into glutamate and Cys-Gly. Purification through gel filtration chromatography confirmed the formation of a Dug2p-Dug3p complex. The functional complex had a molecular weight that corresponded to (Dug2p-Dug3p)(2) in addition to higher molecular weight oligomers and displayed Michaelis-Menten kinetics. (Dug2p-Dug3p)(2) had a K(m) for glutathione of 1.2 mm, suggesting a novel GATase enzyme that acted on glutathione. Dug1p activity in glutathione degradation was found to be restricted to its Cys-Gly peptidase activity, which functioned downstream of the (Dug2p-Dug3p)(2) GATase. The DUG2 and DUG3 genes, but not DUG1, were derepressed by sulfur limitation. Based on these studies and the functioning of GATases, a mechanism is proposed for the functioning of the Dug proteins in the degradation of glutathione.
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Affiliation(s)
- Hardeep Kaur
- Institute of Microbial Technology, Chandigarh, India
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Bhat JY, Venkatachala R, Balaram H. Substrate-induced conformational changes in Plasmodium falciparum guanosine monophosphate synthetase. FEBS J 2011; 278:3756-68. [PMID: 21827625 DOI: 10.1111/j.1742-4658.2011.08296.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GMP synthetase is a glutamine amidotransferase that incorporates ammonia derived from glutamine into the nucleotide xanthosine 5'-monophosphate (XMP) to form guanosine 5'-monophosphate (GMP). Functional coordination of domains in glutamine amidotransferases leads to upregulation of glutamine hydrolysis in the presence of acceptor substrates and is a common feature in this class of enzymes. We have shown earlier that binding of substrates to the acceptor domain of Plasmodium falciparum GMP synthetase (PfGMPS) leads to enhancement in both glutaminase activity and rate of glutaminase inactivation, by the irreversible inhibitors acivicin and diazo-oxonorleucine [Bhat JY et al. (2008) Biochem J409, 263-273], a process that must be driven by conformational alterations. In this paper, through the combined use of biochemical assays, optical spectroscopy and mass spectrometry, we demonstrate that PfGMPS undergoes conformational transitions upon binding of substrates to the acceptor domain. Limited proteolysis and hydrogen-deuterium exchange in conjunction with mass spectrometry unveil region-specific conformational changes in the ATP + XMP bound state of PfGMPS. Decreased accessibility of R294 and K428 residues to trypsin in the ATP pyrophosphatase domain and reduced deuterium incorporation in the 143-155 region, pertaining to the glutaminase domain, suggest that in PfGMPS ligand-induced conformational changes are not only local but also transmitted over a long range across the domains. Overall, these results provide a detailed understanding of the substrate-induced changes in PfGMPS that could be essential for the overall catalytic process.
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Affiliation(s)
- Javaid Y Bhat
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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Scaraffia PY, Zhang Q, Thorson K, Wysocki VH, Miesfeld RL. Differential ammonia metabolism in Aedes aegypti fat body and midgut tissues. JOURNAL OF INSECT PHYSIOLOGY 2010; 56:1040-9. [PMID: 20206632 PMCID: PMC2910787 DOI: 10.1016/j.jinsphys.2010.02.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 02/25/2010] [Accepted: 02/25/2010] [Indexed: 05/04/2023]
Abstract
In order to understand at the tissue level how Aedes aegypti copes with toxic ammonia concentrations that result from the rapid metabolism of blood meal proteins, we investigated the incorporation of (15)N from (15)NH(4)Cl into amino acids using an in vitro tissue culture system. Fat body or midgut tissues from female mosquitoes were incubated in an Aedes saline solution supplemented with glucose and (15)NH(4)Cl for 10-40min. The media were then mixed with deuterium-labeled amino acids, dried and derivatized. The (15)N-labeled and unlabeled amino acids in each sample were quantified by mass spectrometry techniques. The results demonstrate that both tissues efficiently incorporate ammonia into amino acids, however, the specific metabolic pathways are distinct. In the fat body, the (15)N from (15)NH(4)Cl is first incorporated into the amide side chain of Gln and then into the amino group of Gln, Glu, Ala and Pro. This process mainly occurs via the glutamine synthetase (GS) and glutamate synthase (GltS) pathway. In contrast, (15)N in midgut is first incorporated into the amino group of Glu and Ala, and then into the amide side chain of Gln. Interestingly, our data show that the GS/GltS pathway is not functional in the midgut. Instead, midgut cells detoxify ammonia by glutamate dehydrogenase, alanine aminotransferase and GS. These data provide new insights into ammonia metabolism in A. aegypti mosquitoes.
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Affiliation(s)
- Patricia Y Scaraffia
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721-0088, USA.
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Tcherkez G. Natural 15N/ 14N isotope composition in C 3 leaves: are enzymatic isotope effects informative for predicting the 15N-abundance in key metabolites? FUNCTIONAL PLANT BIOLOGY : FPB 2010; 38:1-12. [PMID: 32480857 DOI: 10.1071/fp10091] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 10/24/2010] [Indexed: 06/11/2023]
Abstract
Although nitrogen isotopes are viewed as important tools for understanding plant N acquisition and allocation, the current interpretation of natural 15N-abundances (δ15N values) is often impaired by substantial variability among individuals or between species. Such variability is likely to stem from the fact that 15N-abundance of assimilated N is not preserved during N metabolism and redistribution within the plant; that is, 14N/15N isotope effects associated with N metabolic reactions are certainly responsible for isotopic shifts between organic-N (amino acids) and absorbed inorganic N (nitrate). Therefore, to gain insights into the metabolic origin of 15N-abundance in plants, the present paper reviews enzymatic isotope effects and integrates them into a metabolic model at the leaf level. Using simple steady-state equations which satisfactorily predict the δ15N value of amino acids, it is shown that the sensitivity of δ15N values to both photorespiratory and N-input (reduction by nitrate reductase) rates is quite high. In other words, the variability in δ15N values observed in nature might originate from subtle changes in metabolic fluxes or environment-driven effects, such as stomatal closure that in turn changes v0, the Rubisco-catalysed oxygenation rate.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay Cedex, France. Email
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40
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Vanoni MA, Curti B. Structure-function studies of glutamate synthases: a class of self-regulated iron-sulfur flavoenzymes essential for nitrogen assimilation. IUBMB Life 2008; 60:287-300. [PMID: 18421771 DOI: 10.1002/iub.52] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Glutamate synthases play with glutamine synthetase an essential role in nitrogen assimilation processes in microorganisms, plants, and lower animals by catalyzing the net synthesis of one molecule of L-glutamate from L-glutamine and 2-oxoglutarate. They exhibit a modular architecture with a common subunit or region, which is responsible for the L-glutamine-dependent glutamate synthesis from 2-oxoglutarate. Here, a PurF- (Type II- or Ntn-) type amidotransferase domain is coupled to the synthase domain, a (beta/alpha)8 barrel containing FMN and one [3Fe-4S]0,+1 cluster, through a approximately 30 angstroms-long intramolecular tunnel for the transfer of ammonia between the sites. In bacterial and eukaryotic GltS, reducing equivalents are provided by reduced pyridine nucleotides thanks to the stable association with a second subunit or region, which acts as a FAD-dependent NAD(P)H oxidoreductase and is responsible for the formation of the two low potential [4Fe-4S]+1,+2 clusters of the enzyme. In photosynthetic cells, reduced ferredoxin is the physiological reductant. This review focus on the mechanism of cross-activation of the synthase and glutaminase reactions in response to the bound substrates and the redox state of the enzyme cofactors, as well as on recent information on the structure of the alphabeta protomer of the NADPH-dependent enzyme, which sheds light on the intramolecular electron transfer pathway between the flavin cofactors.
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Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, Milano, Italy.
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41
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Durand P, Golinelli-Pimpaneau B, Mouilleron S, Badet B, Badet-Denisot MA. Highlights of glucosamine-6P synthase catalysis. Arch Biochem Biophys 2008; 474:302-17. [PMID: 18279655 DOI: 10.1016/j.abb.2008.01.026] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 01/30/2008] [Accepted: 01/31/2008] [Indexed: 10/22/2022]
Abstract
L-Glutamine:d-fructose-6-phosphate amidotransferase, also known as glucosamine-6-phosphate synthase (GlcN6P synthase), which catalyzes the first step in a pathway leading to the formation of uridine 5'-diphospho-N-acetyl-d-glucosamine (UDP-GlcNAc), is a key point in the metabolic control of the biosynthesis of amino sugar-containing macromolecules. The molecular mechanism of the reaction catalyzed by GlcN6P synthase is complex and involves amide bond cleavage followed by ammonia channeling and sugar isomerization. This article provides a comprehensive overview of the present knowledge on this multi-faceted enzyme emphasizing the progress made during the last five years.
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Affiliation(s)
- Philippe Durand
- Institut de Chimie des Substances Naturelles-CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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42
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Cottevieille M, Larquet E, Jonic S, Petoukhov MV, Caprini G, Paravisi S, Svergun DI, Vanoni MA, Boisset N. The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications. J Biol Chem 2008; 283:8237-49. [PMID: 18199747 DOI: 10.1074/jbc.m708529200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional structure of the hexameric (alphabeta)(6) 1.2-MDa complex formed by glutamate synthase has been determined at subnanometric resolution by combining cryoelectron microscopy, small angle x-ray scattering, and molecular modeling, providing for the first time a molecular model of this complex iron-sulfur flavoprotein. In the hexameric species, interprotomeric alpha-alpha and alpha-beta contacts are mediated by the C-terminal domain of the alpha subunit, which is based on a beta helical fold so far unique to glutamate synthases. The alphabeta protomer extracted from the hexameric model is fully consistent with it being the minimal catalytically active form of the enzyme. The structure clarifies the electron transfer pathway from the FAD cofactor on the beta subunit, to the FMN on the alpha subunit, through the low potential [4Fe-4S](1+/2+) centers on the beta subunit and the [3Fe-4S](0/1+) cluster on the alpha subunit. The (alphabeta)(6) hexamer exhibits a concentration-dependent equilibrium with alphabeta monomers and (alphabeta)(2) dimers, in solution, the hexamer being destabilized by high ionic strength and, to a lower extent, by the reaction product NADP(+). Hexamerization seems to decrease the catalytic efficiency of the alphabeta protomer only 3-fold by increasing the K(m) values measured for l-Gln and 2-OG. However, it cannot be ruled out that the (alphabeta)(6) hexamer acts as a scaffold for the assembly of multienzymatic complexes of nitrogen metabolism or that it provides a means to regulate the activity of the enzyme through an as yet unknown ligand.
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Affiliation(s)
- Magali Cottevieille
- Département de Biologie Structurale, IMPMC-UMR 7590, CNRS, Universités Paris 6 et Paris 7, IPGP, Paris, France
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Mouilleron S, Golinelli-Pimpaneau B. Conformational changes in ammonia-channeling glutamine amidotransferases. Curr Opin Struct Biol 2007; 17:653-64. [PMID: 17951049 DOI: 10.1016/j.sbi.2007.09.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 09/04/2007] [Accepted: 09/06/2007] [Indexed: 11/28/2022]
Abstract
Glutamine amidotransferases (GATs), which catalyze the synthesis of different aminated products, channel ammonia over 10-40 A from a glutamine substrate at the glutaminase site to an acceptor substrate at the synthase site. Ammonia production usually uses a cysteine-histidine-glutamate triad or a N-terminal cysteine residue. Crystal structures of several amidotransferase ligand complexes, mimicking intermediates along the catalytic cycle, have now been determined. In most cases, acceptor binding triggers glutaminase activation through domain-hinged movements and other conformational changes. Structural information shows how flexible loops of the synthase and glutaminase domains move to shield the two catalytic sites and anchor the substrates, and how the ammonia channel forms and opens or closes.
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Affiliation(s)
- Stéphane Mouilleron
- Laboratoire d'Enzymologie et Biochimie structurales, CNRS Bâtiment 34, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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Choudhury R, Noor S, Varadarajalu LP, Punekar NS. Delineation of an in vivo inhibitor for Aspergillus glutamate dehydrogenase. Enzyme Microb Technol 2007; 42:151-9. [PMID: 22578865 DOI: 10.1016/j.enzmictec.2007.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 08/29/2007] [Accepted: 08/30/2007] [Indexed: 11/18/2022]
Abstract
NADP-glutamate dehydrogenase (NADP-GDH) along with glutamine synthetase plays a pivotal role in ammonium assimilation. Specific inhibitors were valuable in defining the importance of glutamine synthetase in nitrogen metabolism. Selective in vivo inhibition of NADP-GDH has so far been an elusive desideratum. Isophthalate, a potent in vitro inhibitor of Aspergillus niger NADP-GDH [Noor S, Punekar NS. Allosteric NADP-glutamate dehydrogenase from aspergilli: purification, characterization and implications for metabolic regulation at the carbon-nitrogen interface. Microbiology 2005;151:1409-19], was evaluated for its efficacy in vivo. Dimethyl ester of isophthalate (DMIP), but not isophthalate, inhibited A. niger growth on agar as well as in liquid culture. This was ascribed to the inability of isophthalate to enter fungal mycelia. Subsequent to DMIP addition however, intracellular isophthalate could be demonstrated. Apart from NAD-GDH, no other enzyme including NAD-glutamate synthase was inhibited by isophthalate. A cross-over at NADP-GDH step of metabolism was observed as a direct consequence of isophthalate (formed in vivo from DMIP) inhibiting this enzyme. Addition of ammonium to DMIP-treated A. niger mycelia resulted in intensive vacuolation, retraction of cytoplasm and autolysis. Taken together, these results implicate glutamate dehydrogenase and NADP-GDH in particular, as a key target of in vivo isophthalate inhibition during ammonium assimilation.
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Affiliation(s)
- Rajarshi Choudhury
- Biotechnology Group, School of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
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Hu P, Brodie EL, Suzuki Y, McAdams HH, Andersen GL. Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J Bacteriol 2006; 187:8437-49. [PMID: 16321948 PMCID: PMC1317002 DOI: 10.1128/jb.187.24.8437-8449.2005] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterium Caulobacter crescentus and related stalk bacterial species are known for their distinctive ability to live in low-nutrient environments, a characteristic of most heavy metal-contaminated sites. Caulobacter crescentus is a model organism for studying cell cycle regulation with well-developed genetics. We have identified the pathways responding to heavy-metal toxicity in C. crescentus to provide insights for the possible application of Caulobacter to environmental restoration. We exposed C. crescentus cells to four heavy metals (chromium, cadmium, selenium, and uranium) and analyzed genome-wide transcriptional activities postexposure using an Affymetrix GeneChip microarray. C. crescentus showed surprisingly high tolerance to uranium, a possible mechanism for which may be the formation of extracellular calcium-uranium-phosphate precipitates. The principal response to these metals was protection against oxidative stress (up-regulation of manganese-dependent superoxide dismutase sodA). Glutathione S-transferase, thioredoxin, glutaredoxins, and DNA repair enzymes responded most strongly to cadmium and chromate. The cadmium and chromium stress response also focused on reducing the intracellular metal concentration, with multiple efflux pumps employed to remove cadmium, while a sulfate transporter was down-regulated to reduce nonspecific uptake of chromium. Membrane proteins were also up-regulated in response to most of the metals tested. A two-component signal transduction system involved in the uranium response was identified. Several differentially regulated transcripts from regions previously not known to encode proteins were identified, demonstrating the advantage of evaluating the transcriptome by using whole-genome microarrays.
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Affiliation(s)
- Ping Hu
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A3317, Berkeley, CA 94720, USA
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van Breukelen B, Barendregt A, Heck AJR, van den Heuvel RHH. Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:2490-6. [PMID: 16862623 DOI: 10.1002/rcm.2620] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A complicating factor in analyzing electrospray ionization mass spectra of intact macromolecular heterogeneous protein complexes is the potential overlap of ions from different species present in solution. Therefore, it is often not possible to assign all ion signals. With the aim of allowing the more efficient and comprehensive analysis of very complex mass spectra of intact heterogeneous protein complexes we developed a software program: SOMMS. The program uses simple user input parameters together with Gaussian curve fitting to simulate putative mass spectra of protein (sub)complexes within a specified charge state window. In addition, the program can simulate spectra for heterogeneous protein complexes using bi- and multinomial distributions and it can calculate zero-charge spectra and relatively quantify the abundance of each component in a mixture. As a proof of concept we analyzed the complex mass spectra of alpha-glutamate synthase and alphabeta-glutamate synthase from Azosprillum brasilense. Using our program we could determine that alpha-glutamate synthase is in equilibrium between its dimeric, tetrameric, hexameric and dodecameric conformation, whereas alphabeta-glutamate synthase forms up to 15 different heterooligomeric assemblies composed of alpha- and beta-subunits. Thus, SOMMS allows resolving stoichiometries and oligomeric states of protein complexes even from very complicated mass spectra. These complexes could not be assigned by using maximum entropy calculations. We compared our mass spectrometry data on glutamate synthases with available X-ray, small-angle X-ray scattering and size-exclusion chromatography data.
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Affiliation(s)
- Bas van Breukelen
- Utrecht University, Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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Abstract
Modern clinical treatments of childhood acute lymphoblastic leukemia (ALL) employ enzyme-based methods for depletion of blood asparagine in combination with standard chemotherapeutic agents. Significant side effects can arise in these protocols and, in many cases, patients develop drug-resistant forms of the disease that may be correlated with up-regulation of the enzyme glutamine-dependent asparagine synthetase (ASNS). Though the precise molecular mechanisms that result in the appearance of drug resistance are the subject of active study, potent ASNS inhibitors may have clinical utility in treating asparaginase-resistant forms of childhood ALL. This review provides an overview of recent developments in our understanding of (a) the structure and catalytic mechanism of ASNS, and (b) the role that ASNS may play in the onset of drug-resistant childhood ALL. In addition, the first successful, mechanism-based efforts to prepare and characterize nanomolar ASNS inhibitors are discussed, together with the implications of these studies for future efforts to develop useful drugs.
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Affiliation(s)
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32611;
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Mouilleron S, Badet-Denisot MA, Golinelli-Pimpaneau B. Glutamine binding opens the ammonia channel and activates glucosamine-6P synthase. J Biol Chem 2005; 281:4404-12. [PMID: 16339762 DOI: 10.1074/jbc.m511689200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glucosamine-6P synthase catalyzes the synthesis of glucosamine-6P from fructose-6P and glutamine and uses a channel to transfer ammonia from its glutaminase to its synthase active site. X-ray structures of glucosamine-6P synthase have been determined at 2.05 Angstroms resolution in the presence of fructose-6P and at 2.35 Angstroms resolution in the presence of fructose-6P and 6-diazo-5-oxo-L-norleucine, a glutamine affinity analog that covalently modifies the N-terminal catalytic cysteine, therefore mimicking the gamma-glutamyl-thioester intermediate formed during hydrolysis of glutamine. The fixation of the glutamine analog activates the enzyme through several major structural changes: 1) the closure of a loop to shield the glutaminase site accompanied by significant domain hinging, 2) the activation of catalytic residues involved in glutamine hydrolysis, i.e. the alpha-amino group of Cys-1 and Asn-98 that is positioned to form the oxyanion hole, and 3) a 75 degrees rotation of the Trp-74 indole group that opens the ammonia channel.
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Affiliation(s)
- Stéphane Mouilleron
- Laboratoire d'Enzymologie et de Biochimie Structurales, Unite Propre de Recherche 9063, France
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Agnelli P, Dossena L, Colombi P, Mulazzi S, Morandi P, Tedeschi G, Negri A, Curti B, Vanoni MA. The unexpected structural role of glutamate synthase [4Fe-4S](+1,+2) clusters as demonstrated by site-directed mutagenesis of conserved C residues at the N-terminus of the enzyme beta subunit. Arch Biochem Biophys 2005; 436:355-66. [PMID: 15797248 DOI: 10.1016/j.abb.2005.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2005] [Revised: 02/02/2005] [Indexed: 12/19/2022]
Abstract
Azospirillum brasilense glutamate synthase (GltS) is a complex iron-sulfur flavoprotein whose catalytically active alphabeta protomer (alpha subunit, 162kDa; beta subunit, 52.3 kDa) contains one FAD, one FMN, one [3Fe-4S](0,+1), and two [4Fe-4S](+1,+2) clusters. The structure of the alpha subunit has been determined providing information on the mechanism of ammonia transfer from L-glutamine to 2-oxoglutarate through a 30 A-long intramolecular tunnel. On the contrary, details of the electron transfer pathway from NADPH to the postulated 2-iminoglutarate intermediate through the enzyme flavin co-factors and [Fe-S] clusters are largely indirect. To identify the location and role of each one of the GltS [4Fe-4S] clusters, we individually substituted the four cysteinyl residues forming the first of two conserved C-rich regions at the N-terminus of GltS beta subunit with alanyl residues. The engineered genes encoding the beta subunit variants (and derivatives carrying C-terminal His6-tags) were co-expressed with the wild-type alpha subunit gene. In all cases the C/A substitutions prevented alpha and beta subunits association to yield the GltS alphabeta protomer. This result is consistent with the fact that these residues are responsible for the formation of glutamate synthase [4Fe-4S](+1,+2) clusters within the N-terminal region of the beta subunit, and that these clusters are implicated not only in electron transfer between the GltS flavins, but also in alphabeta heterodimer formation by structuring an N-terminal [Fe-S] beta subunit interface subdomain, as suggested by the three-dimensional structure of dihydropyrimidine dehydrogenase, an enzyme containing an N-terminal beta subunit-like domain.
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Affiliation(s)
- Paola Agnelli
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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Scaraffia PY, Isoe J, Murillo A, Wells MA. Ammonia metabolism in Aedes aegypti. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2005; 35:491-503. [PMID: 15804581 DOI: 10.1016/j.ibmb.2005.01.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 12/13/2004] [Accepted: 01/26/2005] [Indexed: 05/24/2023]
Abstract
We investigated the mechanisms by which Aedes aegypti mosquitoes are able to metabolize ammonia. When females were given access to solutions containing NH(4)Cl or to a blood meal, hemolymph glutamine and proline concentrations increased markedly, indicating that ammonium/ammonia can be removed from the body through the synthesis of these two amino acids. The importance of glutamine synthetase was shown when an inhibitor of the enzyme was added to the meal causing the glutamine concentration in hemolymph to decrease significantly, while the proline concentration increased dramatically. Unexpectedly, we found an important role for glutamate synthase. When mosquitoes were fed azaserine, an inhibitor of glutamate synthase, the glutamine concentration increased and the proline concentration decreased significantly. This confirms the presence of glutamate synthase in mosquitoes and suggests that this enzyme contributes to the production of glutamate for proline synthesis. Several key enzymes related to ammonium/ammonia metabolism showed activity in homogenates of mosquito fat body and midgut. The mosquito genes encoding glutamate dehydrogenase, glutamine synthetase, glutamate synthase, pyrroline-5-carboxylate synthase were cloned and sequenced. The mRNA expression patterns of these genes were examined by a real-time RT-PCR in fat body and midgut. The results show that female mosquitoes have evolved efficient mechanisms to detoxify large loads of ammonium/ammonia.
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Affiliation(s)
- Patricia Y Scaraffia
- Department of Biochemistry and Molecular Biophysics, The University of Arizona, Tucson, AZ 85721-0088, USA
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