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Selim KA, Haffner M, Mantovani O, Albrecht R, Zhu H, Hagemann M, Forchhammer K, Hartmann MD. Carbon signaling protein SbtB possesses atypical redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA. Proc Natl Acad Sci U S A 2023; 120:e2205882120. [PMID: 36800386 PMCID: PMC9974498 DOI: 10.1073/pnas.2205882120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 12/15/2022] [Indexed: 02/18/2023] Open
Abstract
The PII superfamily consists of widespread signal transduction proteins found in all domains of life. In addition to canonical PII proteins involved in C/N sensing, structurally similar PII-like proteins evolved to fulfill diverse, yet poorly understood cellular functions. In cyanobacteria, the bicarbonate transporter SbtA is co-transcribed with the conserved PII-like protein, SbtB, to augment intracellular inorganic carbon levels for efficient CO2 fixation. We identified SbtB as a sensor of various adenine nucleotides including the second messenger nucleotides cyclic AMP (cAMP) and c-di-AMP. Moreover, many SbtB proteins possess a C-terminal extension with a disulfide bridge of potential redox-regulatory function, which we call R-loop. Here, we reveal an unusual ATP/ADP apyrase (diphosphohydrolase) activity of SbtB that is controlled by the R-loop. We followed the sequence of hydrolysis reactions from ATP over ADP to AMP in crystallographic snapshots and unravel the structural mechanism by which changes of the R-loop redox state modulate apyrase activity. We further gathered evidence that this redox state is controlled by thioredoxin, suggesting that it is generally linked to cellular metabolism, which is supported by physiological alterations in site-specific mutants of the SbtB protein. Finally, we present a refined model of how SbtB regulates SbtA activity, in which both the apyrase activity and its redox regulation play a central role. This highlights SbtB as a central switch point in cyanobacterial cell physiology, integrating not only signals from the energy state (adenyl-nucleotide binding) and the carbon supply via cAMP binding but also from the day/night status reported by the C-terminal redox switch.
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Affiliation(s)
- Khaled A. Selim
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, 72076Tübingen, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
| | - Michael Haffner
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, 72076Tübingen, Germany
| | - Oliver Mantovani
- Plant Physiology Department, Institute of Biological Sciences, Rostock University, 18059Rostock, Germany
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
| | - Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, Rostock University, 18059Rostock, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, 72076Tübingen, Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, 72076Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076Tübingen, Germany
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Wen S, Yin F, Liu C, Dang Y, Sun D, Li P. Integrated analysis of transcriptomic and protein-protein interaction data reveals cadmium stress response in Geobacter sulfurreducens. ENVIRONMENTAL RESEARCH 2023; 218:115063. [PMID: 36528045 DOI: 10.1016/j.envres.2022.115063] [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: 10/15/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Bacteria have evolved several mechanisms to resist Cd toxicity, which are crucial for Cd detoxication and have the potential to be used for bioremediation of Cd. Geobacter species are widely found in anaerobic environments and play important roles in natural biogeochemical cycles. However, the transcriptomic response of Geobacter sulfurreducens under Cd stress have not been fully elucidated. Through integrated analysis of transcriptomic and protein-protein interaction (PPI) data, we uncovered a global view of mRNA changes in Cd-induced cellular processes in this study. We identified 182 differentially expressed genes (|log2(fold change)| > 1, adjusted P < 0.05) in G. sulfurreducens exposed to 0.1 mM CdCl2 using RNA sequencing (RNA-seq). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that CdCl2 significantly affected sulfur compound metabolic processes. In addition, through PPI network analysis, hub genes related to molecular chaperones were identified to play important role in Cd stress response. We also identified a Cd-responsive transcriptional regulator ArsR2 (coded by GSU2149) and verified the function of ArsR2-ParsR2 regulatory circuit in Escherichia coli. This study provides new insight into Cd stress response in G. sulfurreducens, and identified a potential sensor element for Cd detection.
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Affiliation(s)
- Su Wen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Fei Yin
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Chunmao Liu
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yan Dang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Dezhi Sun
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Pengsong Li
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
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Li X, Ke X, Qiao L, Sui Y, Chu J. Comparative genomic and transcriptomic analysis guides to further enhance the biosynthesis of erythromycin by an overproducer. Biotechnol Bioeng 2022; 119:1624-1640. [PMID: 35150130 DOI: 10.1002/bit.28059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 11/12/2022]
Abstract
Omics approaches have been applied to understand the boosted productivity of natural products by industrial high-producing microorganisms. Here, with the updated genome sequence and transcriptomic profiles derived from high-throughput sequencing, we exploited comparative omics analysis to further enhance the biosynthesis of erythromycin in an industrial overproducer, Saccharopolyspora erythraea HL3168 E3. By comparing the genome of E3 with the wild type NRRL23338, we identified fragment deletions inside 56 coding sequences and 255 single nucleotide polymorphisms over the genome of E3. A substantial number of genomic variations were observed in genes responsible for pathways which were interconnected to the biosynthesis of erythromycin by supplying precursors/cofactors or by signal transduction. Furthermore, the transcriptomic data suggested that genes involved in the biosynthesis of erythromycin were significantly up-regulated constantly, whereas some genes in biosynthesis clusters of other secondary metabolites contained nonsense mutations and were expressed at extremely low levels. Through comparative transcriptomic analysis, L-glutamine/L-glutamate and 2-oxoglutarate were identified as reporter metabolites. Around the node of 2-oxoglutarate, genomic mutations were also observed. Based on the omics association analysis, readily available strategies were proposed to engineer E3 by simultaneously overexpressing sucB (coding for 2-oxoglutarate dehydrogenase E2 component) and sucA (coding for 2-oxoglutarate dehydrogenase E1 component), which increased the erythromycin titer by 71% compared to E3 in batch culture. This work provides more promising molecular targets to engineer for enhanced production of erythromycin by the overproducer. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xiaobo Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Lijia Qiao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Yufei Sui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China
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4
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New views on PII signaling: from nitrogen sensing to global metabolic control. Trends Microbiol 2022; 30:722-735. [DOI: 10.1016/j.tim.2021.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/20/2022]
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5
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Wang P, Wang X, Yin Y, He M, Tan W, Gao W, Wen J. Increasing the Ascomycin Yield by Relieving the Inhibition of Acetyl/Propionyl-CoA Carboxylase by the Signal Transduction Protein GlnB. Front Microbiol 2021; 12:684193. [PMID: 34122395 PMCID: PMC8187598 DOI: 10.3389/fmicb.2021.684193] [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] [Received: 03/22/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Ascomycin (FK520) is a multifunctional antibiotic produced by Streptomyces hygroscopicus var. ascomyceticus. In this study, we demonstrated that the inactivation of GlnB, a signal transduction protein belonging to the PII family, can increase the production of ascomycin by strengthening the supply of the precursors malonyl-CoA and methylmalonyl-CoA, which are produced by acetyl-CoA carboxylase and propionyl-CoA carboxylase, respectively. Bioinformatics analysis showed that Streptomyces hygroscopicus var. ascomyceticus contains two PII family signal transduction proteins, GlnB and GlnK. Protein co-precipitation experiments demonstrated that GlnB protein could bind to the α subunit of acetyl-CoA carboxylase, and this binding could be disassociated by a sufficient concentration of 2-oxoglutarate. Coupled enzyme activity assays further revealed that the interaction between GlnB protein and the α subunit inhibited both the activity of acetyl-CoA carboxylase and propionyl-CoA carboxylase, and this inhibition could be relieved by 2-oxoglutarate in a concentration-dependent manner. Because GlnK protein can act redundantly to maintain metabolic homeostasis under the control of the global nitrogen regulator GlnR, the deletion of GlnB protein enhanced the supply of malonyl-CoA and methylmalonyl-CoA by restoring the activity of acetyl-CoA carboxylase and propionyl-CoA carboxylase, thereby improving the production of ascomycin to 390 ± 10 mg/L. On this basis, the co-overexpression of the β and ε subunits of propionyl-CoA carboxylase further increased the ascomycin yield to 550 ± 20 mg/L, which was 1.9-fold higher than that of the parent strain FS35 (287 ± 9 mg/L). Taken together, this study provides a novel strategy to increase the production of ascomycin, providing a reference for improving the yield of other antibiotics.
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Affiliation(s)
- Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Xin Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Mingliang He
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Wei Tan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Wenting Gao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
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Global control of bacterial nitrogen and carbon metabolism by a PTS Ntr-regulated switch. Proc Natl Acad Sci U S A 2020; 117:10234-10245. [PMID: 32341157 DOI: 10.1073/pnas.1917471117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The nitrogen-related phosphotransferase system (PTSNtr) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells "blind" to the cellular nitrogen status. PTSNtr constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTSNtr is widely conserved in proteobacteria, highlighting its global importance.
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7
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PII Signal Transduction Protein GlnK Alleviates Feedback Inhibition of N-Acetyl-l-Glutamate Kinase by l-Arginine in Corynebacterium glutamicum. Appl Environ Microbiol 2020; 86:AEM.00039-20. [PMID: 32060028 DOI: 10.1128/aem.00039-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
PII signal transduction proteins are ubiquitous and highly conserved in bacteria, archaea, and plants and play key roles in controlling nitrogen metabolism. However, research on biological functions and regulatory targets of PII proteins remains limited. Here, we illustrated experimentally that the PII protein Corynebacterium glutamicum GlnK (CgGlnK) increased l-arginine yield when glnK was overexpressed in Corynebacterium glutamicum Data showed that CgGlnK regulated l-arginine biosynthesis by upregulating the expression of genes of the l-arginine metabolic pathway and interacting with N-acetyl-l-glutamate kinase (CgNAGK), the rate-limiting enzyme in l-arginine biosynthesis. Further assays indicated that CgGlnK contributed to alleviation of the feedback inhibition of CgNAGK caused by l-arginine. In silico analysis of the binding interface of CgGlnK-CgNAGK suggested that the B and T loops of CgGlnK mainly interacted with C and N domains of CgNAGK. Moreover, F11, R47, and K85 of CgGlnK were identified as crucial binding sites that interact with CgNAGK via hydrophobic interaction and H bonds, and these interactions probably had a positive effect on maintaining the stability of the complex. Collectively, this study reveals PII-NAGK interaction in nonphotosynthetic microorganisms and further provides insights into the regulatory mechanism of PII on amino acid biosynthesis in corynebacteria.IMPORTANCE Corynebacteria are safe industrial producers of diverse amino acids, including l-glutamic acid and l-arginine. In this study, we showed that PII protein GlnK played an important role in l-glutamic acid and l-arginine biosynthesis in C. glutamicum Through clarifying the molecular mechanism of CgGlnK in l-arginine biosynthesis, the novel interaction between CgGlnK and CgNAGK was revealed. The alleviation of l-arginine inhibition of CgNAGK reached approximately 48.21% by CgGlnK addition, and the semi-inhibition constant of CgNAGK increased 1.4-fold. Furthermore, overexpression of glnK in a high-yield l-arginine-producing strain and fermentation of the recombinant strain in a 5-liter bioreactor led to a remarkably increased production of l-arginine, 49.978 g/liter, which was about 22.61% higher than that of the initial strain. In conclusion, this study provides a new strategy for modifying amino acid biosynthesis in C. glutamicum.
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Li X, Chen J, Andersen JM, Chu J, Jensen PR. Cofactor Engineering Redirects Secondary Metabolism and Enhances Erythromycin Production in Saccharopolyspora erythraea. ACS Synth Biol 2020; 9:655-670. [PMID: 32078772 DOI: 10.1021/acssynbio.9b00528] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Saccharopolyspora erythraea is used for industrial erythromycin production. To explore the physiological role of intracellular energy state in metabolic regulation by S. erythraea, we initially overexpressed the F1 part of the endogenous F1F0-ATPase in the high yielding erythromycin producing strain E3. The F1-ATPase expression resulted in lower [ATP]/[ADP] ratios, which was accompanied by a strong increase in the production of a reddish pigment and a decreased erythromycin production. Subsequent transcriptional analysis revealed that the lower intracellular [ATP]/[ADP] ratios exerted a pleotropic regulation on the metabolism of S. erythraea. The lower [ATP]/[ADP] ratios induced physiological changes to restore the energy balance, mainly via pathways that tend to produce ATP or regenerate NADH. The F1-ATPase overexpression strain exhibited a state of redox stress, which was correlated to an alteration of electron transport at the branch of the terminal oxidases, and S. erythraea channeled the enhanced glycolytic flux toward a reddish pigment in order to reduce NADH formation. The production of erythromycin was decreased, which is in accordance with the net ATP requirement and the excess NADH formed through this pathway. Partial growth inhibition by apramycin increased the intracellular [ATP]/[ADP] ratios and demonstrated a positive correlation between [ATP]/[ADP] ratios and erythromycin synthesis. Finally, overexpression of the entire F1F0-ATPase complex resulted in 28% enhanced erythromycin production and markedly reduced pigment synthesis in E3. The work illustrates a feasible strategy to optimize the distribution of fluxes in secondary metabolism.
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Affiliation(s)
- Xiaobo Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Jun Chen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Joakim M. Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Peter R. Jensen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
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A novel approach for production of an active N-terminally truncated Ulp1 (SUMO protease 1) catalytic domain from Escherichia coli inclusion bodies. Protein Expr Purif 2020; 166:105507. [DOI: 10.1016/j.pep.2019.105507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/23/2019] [Accepted: 10/02/2019] [Indexed: 01/21/2023]
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10
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Kaczmarski JA, Hong NS, Mukherjee B, Wey LT, Rourke L, Förster B, Peat TS, Price GD, Jackson CJ. Structural Basis for the Allosteric Regulation of the SbtA Bicarbonate Transporter by the P II-like Protein, SbtB, from Cyanobium sp. PCC7001. Biochemistry 2019; 58:5030-5039. [PMID: 31746199 DOI: 10.1021/acs.biochem.9b00880] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyanobacteria have evolved a suite of enzymes and inorganic carbon (Ci) transporters that improve photosynthetic performance by increasing the localized concentration of CO2 around the primary CO2-fixating enzyme, Rubisco. This CO2-concentrating mechanism (CCM) is highly regulated, responds to illumination/darkness cycles, and allows cyanobacteria to thrive under limiting Ci conditions. While the transcriptional control of CCM activity is well understood, less is known about how regulatory proteins might allosterically regulate Ci transporters in response to changing conditions. Cyanobacterial sodium-dependent bicarbonate transporters (SbtAs) are inhibited by PII-like regulatory proteins (SbtBs), with the inhibitory effect being modulated by adenylnucleotides. Here, we used isothermal titration calorimetry to show that SbtB from Cyanobium sp. PCC7001 (SbtB7001) binds AMP, ADP, cAMP, and ATP with micromolar-range affinities. X-ray crystal structures of apo and nucleotide-bound SbtB7001 revealed that while AMP, ADP, and cAMP have little effect on the SbtB7001 structure, binding of ATP stabilizes the otherwise flexible T-loop, and that the flexible C-terminal C-loop adopts several distinct conformations. We also show that ATP binding affinity is increased 10-fold in the presence of Ca2+, and we present an X-ray crystal structure of Ca2+ATP:SbtB7001 that shows how this metal ion facilitates additional stabilizing interactions with the apex of the T-loop. We propose that the Ca2+ATP-induced conformational change observed in SbtB7001 is important for allosteric regulation of SbtA activity by SbtB and is consistent with changing adenylnucleotide levels in illumination/darkness cycles.
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Affiliation(s)
- Joe A Kaczmarski
- Research School of Chemistry , The Australian National University , 137 Sullivans Creek Road , Canberra , ACT 0200 , Australia
| | - Nan-Sook Hong
- Research School of Chemistry , The Australian National University , 137 Sullivans Creek Road , Canberra , ACT 0200 , Australia
| | - Bratati Mukherjee
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Laura T Wey
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Loraine Rourke
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Britta Förster
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Thomas S Peat
- CSIRO Biomedical Program , 343 Royal Parade , Parkville , VIC 3052 , Australia
| | - G Dean Price
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology , The Australian National University , 134 Linnaeus Way , Canberra , ACT 0200 , Australia
| | - Colin J Jackson
- Research School of Chemistry , The Australian National University , 137 Sullivans Creek Road , Canberra , ACT 0200 , Australia
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Xu Z, You D, Tang LY, Zhou Y, Ye BC. Metabolic Engineering Strategies Based on Secondary Messengers (p)ppGpp and C-di-GMP To Increase Erythromycin Yield in Saccharopolyspora erythraea. ACS Synth Biol 2019; 8:332-345. [PMID: 30632732 DOI: 10.1021/acssynbio.8b00372] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Secondary messengers (such as (p)ppGpp and c-di-GMP) were proved to play important roles in antibiotic biosynthesis in actinobacteria. In this study, we found that transcription levels of erythromycin-biosynthetic ( ery) genes were upregulated in nutrient limitation, which depended on (p)ppGpp in Saccharopolyspora erythraea. Further study demonstrated that the expression of ery genes and intracellular concentrations of (p)ppGpp showed synchronization during culture process. The erythromycin yield was significantly improved (about 200%) by increasing intracellular concentration of (p)ppGpp through introduction of C-terminally truncated (p)ppGpp synthetase RelA (1.43 kb of the N-terminal segment) from Streptomyces coelicolor into S. erythraea strain NRRL2338 (named as WT/pIB-P BAD- relA1-489). As the intracellular concentration of (p)ppGpp in an industrial erythromycin-high-producing strain E3 was greatly higher (about 10- to 100-fold) than WT strain, the applications of the above-described strategy did not work in E3 strain. Further research revealed that low concentration of 2-oxoglutarate in E3 strain exerted a "nitrogen-rich" pseudosignal, leading to the downregulation of nitrogen metabolism genes, which limited the use of nitrogen sources and thus the high intracellular (p)ppGpp concentration. Furthermore, the secondary messenger, c-di-GMP, was proved to be able to activate ery genes transcription by enhancing binding of BldD to promoters of ery genes. Overexpressing the diguanylate cyclase CdgB from S. coelicolor in S. erythraea increased the intracellular c-di-GMP concentration, and improved erythromycin production. These findings demonstrated that increasing the concentration of intracellular secondary messengers can activate ery genes transcription, and provided new strategies for designing metabolic engineering based on secondary messengers to improve antibiotics yield in actinobacteria.
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Affiliation(s)
- Zhen Xu
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Di You
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Li-Ya Tang
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ying Zhou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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Forcada-Nadal A, Llácer JL, Contreras A, Marco-Marín C, Rubio V. The P II-NAGK-PipX-NtcA Regulatory Axis of Cyanobacteria: A Tale of Changing Partners, Allosteric Effectors and Non-covalent Interactions. Front Mol Biosci 2018; 5:91. [PMID: 30483512 PMCID: PMC6243067 DOI: 10.3389/fmolb.2018.00091] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 10/18/2018] [Indexed: 11/13/2022] Open
Abstract
PII, a homotrimeric very ancient and highly widespread (bacteria, archaea, plants) key sensor-transducer protein, conveys signals of abundance or poorness of carbon, energy and usable nitrogen, converting these signals into changes in the activities of channels, enzymes, or of gene expression. PII sensing is mediated by the PII allosteric effectors ATP, ADP (and, in some organisms, AMP), 2-oxoglutarate (2OG; it reflects carbon abundance and nitrogen scarcity) and, in many plants, L-glutamine. Cyanobacteria have been crucial for clarification of the structural bases of PII function and regulation. They are the subject of this review because the information gathered on them provides an overall structure-based view of a PII regulatory network. Studies on these organisms yielded a first structure of a PII complex with an enzyme, (N-acetyl-Lglutamate kinase, NAGK), deciphering how PII can cause enzyme activation, and how it promotes nitrogen stockpiling as arginine in cyanobacteria and plants. They have also revealed the first clear-cut mechanism by which PII can control gene expression. A small adaptor protein, PipX, is sequestered by PII when nitrogen is abundant and is released when is scarce, swapping partner by binding to the 2OG-activated transcriptional regulator NtcA, co-activating it. The structures of PII-NAGK, PII-PipX, PipX alone, of NtcA in inactive and 2OG-activated forms and as NtcA-2OG-PipX complex, explain structurally PII regulatory functions and reveal the changing shapes and interactions of the T-loops of PII depending on the partner and on the allosteric effectors bound to PII. Cyanobacterial studies have also revealed that in the PII-PipX complex PipX binds an additional transcriptional factor, PlmA, thus possibly expanding PipX roles beyond NtcA-dependency. Further exploration of these roles has revealed a functional interaction of PipX with PipY, a pyridoxal-phosphate (PLP) protein involved in PLP homeostasis whose mutations in the human ortholog cause epilepsy. Knowledge of cellular levels of the different components of this PII-PipX regulatory network and of KD values for some of the complexes provides the basic background for gross modeling of the system at high and low nitrogen abundance. The cyanobacterial network can guide searches for analogous components in other organisms, particularly of PipX functional analogs.
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Affiliation(s)
- Alicia Forcada-Nadal
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - José Luis Llácer
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras - Instituto de Salud Carlos III, Valencia, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Clara Marco-Marín
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras - Instituto de Salud Carlos III, Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras - Instituto de Salud Carlos III, Valencia, Spain
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13
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P II-like signaling protein SbtB links cAMP sensing with cyanobacterial inorganic carbon response. Proc Natl Acad Sci U S A 2018; 115:E4861-E4869. [PMID: 29735650 DOI: 10.1073/pnas.1803790115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria are phototrophic prokaryotes that evolved oxygenic photosynthesis ∼2.7 billion y ago and are presently responsible for ∼10% of total global photosynthetic production. To cope with the evolutionary pressure of dropping ambient CO2 concentrations, they evolved a CO2-concentrating mechanism (CCM) to augment intracellular inorganic carbon (Ci) levels for efficient CO2 fixation. However, how cyanobacteria sense the fluctuation in Ci is poorly understood. Here we present biochemical, structural, and physiological insights into SbtB, a unique PII-like signaling protein, which provides new insights into Ci sensing. SbtB is highly conserved in cyanobacteria and is coexpressed with CCM genes. The SbtB protein from the cyanobacterium Synechocystis sp. PCC 6803 bound a variety of adenosine nucleotides, including the second messenger cAMP. Cocrystal structures unraveled the individual binding modes of trimeric SbtB with AMP and cAMP. The nucleotide-binding pocket is located between the subunit clefts of SbtB, perfectly matching the structure of canonical PII proteins. This clearly indicates that proteins of the PII superfamily arose from a common ancestor, whose structurally conserved nucleotide-binding pocket has evolved to sense different adenyl nucleotides for various signaling functions. Moreover, we provide physiological and biochemical evidence for the involvement of SbtB in Ci acclimation. Collectively, our results suggest that SbtB acts as a Ci sensor protein via cAMP binding, highlighting an evolutionarily conserved role for cAMP in signaling the cellular carbon status.
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14
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Li Y, Liu W, Sun LP, Zhou ZG. Evidence for PII with NAGK interaction that regulates Arg synthesis in the microalga Myrmecia incisa in response to nitrogen starvation. Sci Rep 2017; 7:16291. [PMID: 29176648 PMCID: PMC5701185 DOI: 10.1038/s41598-017-16644-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 11/12/2022] Open
Abstract
To understand why most eukaryotic microalgae accumulate lipids during nitrogen starvation stress, a gene, MiglnB, encoding PII, a signal transduction protein, was cloned from the arachidonic acid-rich microalga Myrmecia incisa Reisigl. Similarly to its homologues, MiPII contains three conserved T-, B-, and C-loops. In the presence of abundant Mg2+, ATP, and Gln, MiPII upregulates Arg biosynthesis by interacting with the rate-limiting enzyme, MiNAGK, as evidenced by yeast two-hybrid, co-immunoprecipitation assays, and kinetics analysis of enzyme-catalyzed reactions. However, this interaction of MiPII with MiNAGK is reversed by addition of 2-oxoglutarate (2-OG). Moreover, this interaction is present in the chloroplasts of M. incisa, as illustrated cytologically by both immunoelectron microscopy and agroinfiltration of Nicotiana benthamiana leaves to determine the subcellular localization of MiPII with MiNAGK. During the process of nitrogen starvation, soluble Arg levels in M. incisa are modulated by a change in MiNAGK enzymatic activity, both of which are significantly correlated (r = 0.854). A model for the manipulation of Arg biosynthesis via MiPII in M. incisa chloroplasts in response to nitrogen starvation is proposed. The ATP and 2-OG saved from Arg biosynthesis is thus suggested to facilitate the accumulation of fatty acids and triacylglycerol in M. incisa during exposure to nitrogen starvation.
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Affiliation(s)
- Yan Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Li-Ping Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhi-Gang Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China. .,National Demonstration Center for the Experimental Teaching of Fisheries Science, Shanghai Ocean University, Shanghai, 201306, China. .,International Research Center for Marine Biosciences Conferred by Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
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15
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Parlati A, Valkov VT, D'Apuzzo E, Alves LM, Petrozza A, Summerer S, Costa A, Cellini F, Vavasseur A, Chiurazzi M. Ectopic Expression of PII Induces Stomatal Closure in Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2017; 8:1299. [PMID: 28791036 PMCID: PMC5524832 DOI: 10.3389/fpls.2017.01299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/10/2017] [Indexed: 05/20/2023]
Abstract
The PII protein in plants has been associated to many different tissue specialized roles concerning the Nitrogen assimilation pathways. We report here the further characterization of L. japonicus transgenic lines overexpressing the PII protein encoded by the LjGLB1 gene that is strongly expressed in the guard cells of Lotus plants. Consistently with a putative role played by PII in that specific cellular context we have observed an alteration of the patterns of stomatal movement in the overexpressing plants. An increased stomatal closure is measured in epidermal peels from detached leaves of normally watered overexpressing plants when compared to wild type plants and this effect was by-passed by Abscisic Acid application. The biochemical characterization of the transgenic lines indicates an increased rate of the Nitric Oxide biosynthetic route, associated to an induced Nitrate Reductase activity. The phenotypic characterization is completed by measures of the photosynthetic potential in plants grown under greenhouse conditions, which reveal a higher stress index of the PII overexpressing plants.
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Affiliation(s)
- Aurora Parlati
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Consiglio Nazionale delle RicercheNapoli, Italy
| | - Vladimir T. Valkov
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Consiglio Nazionale delle RicercheNapoli, Italy
| | - Enrica D'Apuzzo
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Consiglio Nazionale delle RicercheNapoli, Italy
| | - Ludovico M. Alves
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Consiglio Nazionale delle RicercheNapoli, Italy
| | | | | | - Alex Costa
- Department of Bioscience, University of MilanMilan, Italy
- Department of Physics, Institute of Biophysics, Consiglio Nazionale delle RicercheMilan, Italy
| | | | - Alain Vavasseur
- Unitè Mixte de Reserche 6191 Centre National de la Reserche Scientifique, Institute de Biologie Environnementales – Commissariat à l'Energie Atomique-Universitè Aix-Marseille IISt. Paul Lez Durance, France
| | - Maurizio Chiurazzi
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Consiglio Nazionale delle RicercheNapoli, Italy
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Abstract
The pancreatic β-cell secretes insulin in response to elevated plasma glucose. This review applies an external bioenergetic critique to the central processes of glucose-stimulated insulin secretion, including glycolytic and mitochondrial metabolism, the cytosolic adenine nucleotide pool, and its interaction with plasma membrane ion channels. The control mechanisms responsible for the unique responsiveness of the cell to glucose availability are discussed from bioenergetic and metabolic control standpoints. The concept of coupling factor facilitation of secretion is critiqued, and an attempt is made to unravel the bioenergetic basis of the oscillatory mechanisms controlling secretion. The need to consider the physiological constraints operating in the intact cell is emphasized throughout. The aim is to provide a coherent pathway through an extensive, complex, and sometimes bewildering literature, particularly for those unfamiliar with the field.
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Affiliation(s)
- David G Nicholls
- Buck Institute for Research on Aging, Novato, California; and Department of Clinical Sciences, Unit of Molecular Metabolism, Lund University Diabetes Centre, Malmo, Sweden
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17
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Boeckstaens M. [From the discovery of microbial Mep-Amt ammonium transporters to human Rhesus factors]. Med Sci (Paris) 2016; 32:394-400. [PMID: 27137697 DOI: 10.1051/medsci/20163204018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Ammonium, ubiquitous on Earth, plays major and distinct roles in most organisms. While it can be a nitrogen source for many microorganisms and plants, it is a cytotoxic metabolic product actively detoxified by the liver in animals. Furthermore, in the latter, ammonium synthesis in the kidney is involved in acid/base homeostasis. Ammonium transport is ensured by a family of proteins, called Mep-Amt-Rh. This family is conserved in all domains of life and comprises the human Rh factors, notably known in transfusional medicine. While the study of bacterial, fungal and vegetal Mep-Amt transporters reveals a fine-tuned and rapid regulation of these proteins in function of environmental changes, the regulation of animal Rh proteins has been poorly addressed. This review notably highlights the importance of the yeast model in the study of the regulation of these proteins as well as in the functional characterization of Mep-Amt-Rh members of diverse origins.
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Affiliation(s)
- Mélanie Boeckstaens
- Laboratoire de biologie du transport membranaire, IBMM, université Libre de Bruxelles, 12, rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgique
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18
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Abstract
The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.
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19
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Forchhammer K, Lüddecke J. Sensory properties of the PII signalling protein family. FEBS J 2015; 283:425-37. [PMID: 26527104 DOI: 10.1111/febs.13584] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/06/2015] [Accepted: 10/28/2015] [Indexed: 11/30/2022]
Abstract
PII signalling proteins constitute one of the largest families of signalling proteins in nature. An even larger superfamily of trimeric sensory proteins with the same architectural principle as PII proteins appears in protein structure databases. Large surface-exposed flexible loops protrude from the intersubunit faces, where effector molecules are bound that tune the conformation of the loops. Via this mechanism, PII proteins control target proteins in response to cellular ATP/ADP levels and the 2-oxoglutarate status, thereby coordinating the cellular carbon/nitrogen balance. The antagonistic (ATP versus ADP) and synergistic (2-oxoglutarate and ATP) mode of effector molecule binding is further affected by PII -receptor interaction, leading to a highly sophisticated signalling network organized by PII . Altogether, it appears that PII is a multitasking information processor that, depending on its interaction environment, differentially transmits information on the energy status and the cellular 2-oxoglutarate level. In addition to the basic mode of PII function, several bacterial PII proteins may transmit a signal of the cellular glutamine status via covalent modification. Remarkably, during the evolution of plant chloroplasts, glutamine signalling by PII proteins was re-established by acquisition of a short sequence extension at the C-terminus. This plant-specific C-terminus makes the interaction of plant PII proteins with one of its targets, the arginine biosynthetic enzyme N-acetyl-glutamate kinase, glutamine-dependent.
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Affiliation(s)
- Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen, Germany
| | - Jan Lüddecke
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard-Karls-Universität Tübingen, Germany
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20
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Kan CC, Chung TY, Juo YA, Hsieh MH. Glutamine rapidly induces the expression of key transcription factor genes involved in nitrogen and stress responses in rice roots. BMC Genomics 2015; 16:731. [PMID: 26407850 PMCID: PMC4582844 DOI: 10.1186/s12864-015-1892-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/01/2015] [Indexed: 12/02/2022] Open
Abstract
Background Glutamine is a major amino donor for the synthesis of amino acids, nucleotides, and other nitrogen-containing compounds in all organisms. In addition to its role in nutrition and metabolism, glutamine can also function as a signaling molecule in bacteria, yeast, and humans. By contrast, the functions of glutamine in nutrition and as a signaling molecule remain unclear in plants. Results We demonstrated that glutamine could effectively support the growth of rice seedlings. In glutamine-treated rice roots, the glutamine contents increased dramatically, whereas levels of glutamate remained relatively constant. Transcriptome analysis of rice roots revealed that glutamine induced the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses within 30 min. Interestingly, 10 of the 35 early glutamine responsive genes encode putative transcription factors, including two LBD37-like genes that are involved in the regulation of nitrogen metabolism. Glutamine also rapidly induced the expression of the DREB1A, IRO2, and NAC5 transcription factor genes, which are involved in the regulation of stress responses. Conclusions In addition to its role as a metabolic fuel, glutamine may also function as a signaling molecule to regulate gene expression in plants. The rapid induction of transcription factor genes suggests that glutamine may efficiently amplify its signal and interact with the other signal transduction pathways to regulate plant growth and stress responses. Thus, glutamine is a functional amino acid that plays important roles in plant nutrition and signal transduction. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1892-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chia-Cheng Kan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Tsui-Yun Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Yan-An Juo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
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Lüddecke J, Forchhammer K. Energy Sensing versus 2-Oxoglutarate Dependent ATPase Switch in the Control of Synechococcus PII Interaction with Its Targets NAGK and PipX. PLoS One 2015; 10:e0137114. [PMID: 26317540 PMCID: PMC4552645 DOI: 10.1371/journal.pone.0137114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/07/2015] [Indexed: 12/20/2022] Open
Abstract
PII proteins constitute a superfamily of highly conserved signaling devices, common in all domains of life. Through binding of the metabolites ATP, ADP and 2-oxoglutarate (2-OG), they undergo conformational changes which allow them to regulate a variety of target proteins including enzymes, transport proteins and transcription factors. But, in reverse, these target proteins also modulate the metabolite sensing properties of PII, as has been recently shown. We used this effect to refine our PII based Förster resonance energy transfer (FRET) sensor and amplify its sensitivity towards ADP. With this enhanced sensor setup we addressed the question whether the PII protein from the model organism Synechococcus elongatus autonomously switches into the ADP conformation through ATPase activity as proposed in a recently published model. The present study disproves ATPase activity as a relevant mechanism for the transition of PII into the ADP state. In the absence of 2-OG, only the ATP/ADP ratio and concentration of ADP directs the competitive interaction of PII with two targets, one of which preferentially binds PII in the ATP-state, the other in the ADP-state.
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Affiliation(s)
- Jan Lüddecke
- Interfaculty Institute for Microbiology and Infection Medicine, Division Organismic Interactions, University of Tübingen, Auf der Morgenstelle 28, D-72076, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Division Organismic Interactions, University of Tübingen, Auf der Morgenstelle 28, D-72076, Tübingen, Germany
- * E-mail:
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22
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Boeckstaens M, Merhi A, Llinares E, Van Vooren P, Springael JY, Wintjens R, Marini AM. Identification of a Novel Regulatory Mechanism of Nutrient Transport Controlled by TORC1-Npr1-Amu1/Par32. PLoS Genet 2015; 11:e1005382. [PMID: 26172854 PMCID: PMC4501750 DOI: 10.1371/journal.pgen.1005382] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 06/22/2015] [Indexed: 01/12/2023] Open
Abstract
Fine-tuning the plasma-membrane permeability to essential nutrients is fundamental to cell growth optimization. Nutritional signals including nitrogen availability are integrated by the TORC1 complex which notably regulates arrestin-mediated endocytosis of amino-acid transporters. Ammonium is a ubiquitous compound playing key physiological roles in many, if not all, organisms. In yeast, it is a preferred nitrogen source transported by three Mep proteins which are orthologues of the mammalian Rhesus factors. By combining genetic, kinetic, biochemical and cell microscopy analyses, the current study reveals a novel mechanism enabling TORC1 to regulate the inherent activity of ammonium transport proteins, independently of arrestin-mediated endocytosis, identifying the still functional orphan Amu1/Par32 as a selective regulator intermediate. We show that, under poor nitrogen supply, the TORC1 effector kinase' Npr1' promotes phosphorylation of Amu1/Par32 which appears mainly cytosolic while ammonium transport proteins are active. Upon preferred nitrogen supplementation, like glutamine or ammonium addition, TORC1 upregulation enables Npr1 inhibition and Amu1/Par32 dephosphorylation. In these conditions, as in Npr1-lacking cells, hypophosphorylated Amu1/Par32 accumulates at the cell surface and mediates the inhibition of specific ammonium transport proteins. We show that the integrity of a conserved repeated motif of Amu1/Par32 is required for the interaction with these transport proteins. This study underscores the diversity of strategies enabling TORC1-Npr1 to selectively monitor cell permeability to nutrients by discriminating between transporters to be degraded or transiently inactivated and kept stable at the plasma membrane. This study further identifies the function of Amu1/Par32 in acute control of ammonium transport in response to variations in nitrogen availability. Cells have evolved a variety of mechanisms to control the permeability of the plasma membrane to face environmental perturbations. Transcriptional regulation, endocytosis, gating and activity control of channels and transporters enable global or specific responses to stressful conditions and focused variations in nutrient availability. Emerging data from the yeast model reveal that the conserved TORC1 pathway regulates arrestin-mediated endocytosis of amino-acid transporters. We provide genetic and biochemical evidence for a novel mechanism enabling TORC1 to regulate the inherent activity of transport proteins via the Amu1/Par32 regulator intermediate. This low complexity protein mediates inhibition of specific proteins dedicated to the transport of ammonium, a favored nitrogen source, underscoring that TORC1 selects transporters to be degraded or transiently inactivated and preserved at the cell surface according to the environmental situation. The here-revealed mechanism of transport inhibition by Amu/Par32 is reminiscent to the inhibition of prokaryotic ammonium transport proteins mediated by PII-type proteins, key nitrogen signal transducers widespread in bacteria and Archaea.
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Affiliation(s)
- Mélanie Boeckstaens
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | - Ahmad Merhi
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | - Elisa Llinares
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | - Pascale Van Vooren
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
| | | | - René Wintjens
- Laboratoire des Biopolymères et des nanomatériaux supramoléculaires, Université Libre de Bruxelles, Brussels, Belgium
| | - Anna Maria Marini
- Biology of Membrane Transport, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
- * E-mail:
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23
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Chantranupong L, Wolfson RL, Sabatini DM. Nutrient-sensing mechanisms across evolution. Cell 2015; 161:67-83. [PMID: 25815986 DOI: 10.1016/j.cell.2015.02.041] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 12/11/2022]
Abstract
For organisms to coordinate their growth and development with nutrient availability, they must be able to sense nutrient levels in their environment. Here, we review select nutrient-sensing mechanisms in a few diverse organisms. We discuss how these mechanisms reflect the nutrient requirements of specific species and how they have adapted to the emergence of multicellularity in eukaryotes.
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Affiliation(s)
- Lynne Chantranupong
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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24
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D'Apuzzo E, Valkov VT, Parlati A, Omrane S, Barbulova A, Sainz MM, Lentini M, Esposito S, Rogato A, Chiurazzi M. PII Overexpression in Lotus japonicus Affects Nodule Activity in Permissive Low-Nitrogen Conditions and Increases Nodule Numbers in High Nitrogen Treated Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:432-42. [PMID: 25390190 DOI: 10.1094/mpmi-09-14-0285-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We report here the first characterization of a GLNB1 gene coding for the PII protein in leguminous plants. The main purpose of this work was the investigation of the possible roles played by this multifunctional protein in nodulation pathways. The Lotus japonicus LjGLB1 gene shows a significant transcriptional regulation during the light-dark cycle and different nitrogen availability, conditions that strongly affect nodule formation, development, and functioning. We also report analysis of the spatial profile of expression of LjGLB1 in root and nodule tissues and of the protein's subcellular localization. Transgenic L. japonicus lines overexpressing the PII protein were obtained and tested for the analysis of the symbiotic responses in different conditions. The uncoupling of PII from its native regulation affects nitrogenase activity and nodule polyamine content. Furthermore, our results suggest the involvement of PII in the signaling of the nitrogen nutritional status affecting the legumes' predisposition for nodule formation.
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Affiliation(s)
- Enrica D'Apuzzo
- 1 Institute of Biosciences and Bioresources, CNR, Via P. Castellino 111, Napoli, Italy
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25
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Chellamuthu VR, Ermilova E, Lapina T, Lüddecke J, Minaeva E, Herrmann C, Hartmann MD, Forchhammer K. A widespread glutamine-sensing mechanism in the plant kingdom. Cell 2015; 159:1188-1199. [PMID: 25416954 DOI: 10.1016/j.cell.2014.10.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/13/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022]
Abstract
Glutamine is the primary metabolite of nitrogen assimilation from inorganic nitrogen sources in microorganisms and plants. The ability to monitor cellular nitrogen status is pivotal for maintaining metabolic homeostasis and sustaining growth. The present study identifies a glutamine-sensing mechanism common in the entire plant kingdom except Brassicaceae. The plastid-localized PII signaling protein controls, in a glutamine-dependent manner, the key enzyme of the ornithine synthesis pathway, N-acetyl-l-glutamate kinase (NAGK), that leads to arginine and polyamine formation. Crystal structures reveal that the plant-specific C-terminal extension of PII, which we term the Q loop, forms a low-affinity glutamine-binding site. Glutamine binding alters PII conformation, promoting interaction and activation of NAGK. The binding motif is highly conserved in plants except Brassicaceae. A functional Q loop restores glutamine sensing in a recombinant Arabidopsis thaliana PII protein, demonstrating the modular concept of the glutamine-sensing mechanism adopted by PII proteins during the evolution of plant chloroplasts.
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Affiliation(s)
- Vasuki-Ranjani Chellamuthu
- Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Elena Ermilova
- Lab Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia
| | - Tatjana Lapina
- Lab Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia
| | - Jan Lüddecke
- Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ekaterina Minaeva
- Lab Adaptation in Microorganisms, Biological Faculty, Saint-Petersburg State University, Universitetskaya em. 7/9, 199034 Saint-Petersburg, Russia
| | - Christina Herrmann
- Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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26
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Merrick M. Post-translational modification of P II signal transduction proteins. Front Microbiol 2015; 5:763. [PMID: 25610437 PMCID: PMC4285133 DOI: 10.3389/fmicb.2014.00763] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/15/2014] [Indexed: 11/13/2022] Open
Abstract
The PII proteins constitute one of the most widely distributed families of signal transduction proteins in nature. They are pivotal players in the control of nitrogen metabolism in bacteria and archaea, and are also found in the plastids of plants. Quite remarkably PII proteins control the activities of a diverse range of enzymes, transcription factors and membrane transport proteins, and in all known cases they achieve their regulatory effect by direct interaction with their target. PII proteins in the Proteobacteria and the Actinobacteria are subject to post-translational modification by uridylylation or adenylylation respectively, whilst in some Cyanobacteria they can be modified by phosphorylation. In all these cases the protein's modification state is influenced by the cellular nitrogen status and is thought to regulate its activity. However, in many organisms there is no evidence for modification of PII proteins and indeed the ability of these proteins to respond to the cellular nitrogen status is fundamentally independent of post-translational modification. In this review we explore the role of post-translational modification in PII proteins in the light of recent studies.
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Affiliation(s)
- Mike Merrick
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
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27
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Radchenko MV, Thornton J, Merrick M. Association and dissociation of the GlnK-AmtB complex in response to cellular nitrogen status can occur in the absence of GlnK post-translational modification. Front Microbiol 2014; 5:731. [PMID: 25566239 PMCID: PMC4274968 DOI: 10.3389/fmicb.2014.00731] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/04/2014] [Indexed: 11/20/2022] Open
Abstract
PII proteins are pivotal players in the control of nitrogen metabolism in bacteria and archaea, and are also found in the plastids of plants. PII proteins control the activities of a diverse range of enzymes, transcription factors and membrane transport proteins, and their regulatory effect is achieved by direct interaction with their target. Many, but by no means all, PII proteins are subject to post-translational modification of a residue within the T-loop of the protein. The protein’s modification state is influenced by the cellular nitrogen status and in the past this has been considered to regulate PII activity by controlling interaction with target proteins. However, the fundamental ability of PII proteins to respond to the cellular nitrogen status has been shown to be dependent on binding of key effector molecules, ATP, ADP, and 2-oxoglutarate which brings into question the precise role of post-translational modification. In this study we have used the Escherichia coli PII protein GlnK to examine the influence of post-translational modification (uridylylation) on the interaction between GlnK and its cognate target the ammonia channel protein AmtB. We have compared the interaction with AmtB of wild-type GlnK and a variant protein, GlnKTyr51Ala, that cannot be uridylylated. This analysis was carried out both in vivo and in vitro and showed that association and dissociation of the GlnK–AmtB complex is not dependent on the uridylylation state of GlnK. However, our in vivo studies show that post-translational modification of GlnK does influence the dynamics of its interaction with AmtB.
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Affiliation(s)
| | - Jeremy Thornton
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Mike Merrick
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
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Palanca C, Pedro-Roig L, Llácer JL, Camacho M, Bonete MJ, Rubio V. The structure of a PII signaling protein from a halophilic archaeon reveals novel traits and high-salt adaptations. FEBS J 2014; 281:3299-314. [PMID: 24946894 DOI: 10.1111/febs.12881] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/06/2014] [Accepted: 06/17/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED To obtain insights into archaeal nitrogen signaling and haloadaptation of the nitrogen/carbon/energy-signaling protein PII, we determined crystal structures of recombinantly produced GlnK2 from the extreme halophilic archaeon Haloferax mediterranei, complexed with AMP or with the PII effectors ADP or ATP, at respective resolutions of 1.49 Å, 1.45 Å, and 2.60 Å. A unique trait of these structures was a three-tongued crown protruding from the trimer body convex side, formed by an 11-residue, N-terminal, highly acidic extension that is absent from structurally studied PII proteins. This extension substantially contributed to the very low pI value, which is a haloadaptive trait of H. mediterranei GlnK2, and participated in hexamer-forming contacts in one crystal. Similar acidic N-extensions are shown here to be common among PII proteins from halophilic organisms. Additional haloadaptive traits prominently represented in H. mediterranei GlnK2 are a very high ratio of small residues to large hydrophobic aliphatic residues, and the highest ratio of polar to nonpolar exposed surface for any structurally characterized PII protein. The presence of a dense hydration layer in the region between the three T-loops might also be a haloadaptation. Other unique findings revealed by the GlnK2 structure that might have functional relevance are: the adoption by its T-loop of a three-turn α-helical conformation, perhaps related to the ability of GlnK2 to directly interact with glutamine synthetase; and the firm binding of AMP, confirmed by biochemical binding studies with ATP, ADP, and AMP, raising the possibility that AMP could be an important PII effector, at least in archaea. DATABASE The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession numbers 4OZL (hmGlnK2-AMP), 4OZJ (hmGlnK2-ADP), and 4OZN (hmGlnK2-ATP). STRUCTURED DIGITAL ABSTRACT hmGlnK2 and hmGlnK2 bind by x-ray crystallography (View interaction).
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Affiliation(s)
- Carles Palanca
- Instituto de Biomedicina de Valencia of the CSIC (IBV-CSIC), Spain
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29
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Truan D, Bjelić S, Li XD, Winkler FK. Structure and thermodynamics of effector molecule binding to the nitrogen signal transduction PII protein GlnZ from Azospirillum brasilense. J Mol Biol 2014; 426:2783-99. [PMID: 24846646 DOI: 10.1016/j.jmb.2014.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/23/2014] [Accepted: 05/08/2014] [Indexed: 10/25/2022]
Abstract
The trimeric PII signal transduction proteins regulate the function of a variety of target proteins predominantly involved in nitrogen metabolism. ATP, ADP and 2-oxoglutarate (2-OG) are key effector molecules influencing PII binding to targets. Studies of PII proteins have established that the 20-residue T-loop plays a central role in effector sensing and target binding. However, the specific effects of effector binding on T-loop conformation have remained poorly documented. We present eight crystal structures of the Azospirillum brasilense PII protein GlnZ, six of which are cocrystallized and liganded with ADP or ATP. We find that interaction with the diphosphate moiety of bound ADP constrains the N-terminal part of the T-loop in a characteristic way that is maintained in ADP-promoted complexes with target proteins. In contrast, the interactions with the triphosphate moiety in ATP complexes are much more variable and no single predominant interaction mode is apparent except for the ternary MgATP/2-OG complex. These conclusions can be extended to most investigated PII proteins of the GlnB/GlnK subfamily. Unlike reported for other PII proteins, microcalorimetry reveals no cooperativity between the three binding sites of GlnZ trimers for any of the three effectors under carefully controlled experimental conditions.
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Affiliation(s)
- Daphné Truan
- Macromolecular Crystallography, Swiss Light Source, CH-5232 Villigen PSI, Switzerland
| | - Saša Bjelić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Xiao-Dan Li
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Fritz K Winkler
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.
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Abstract
Beyond fuelling cellular activities with building blocks and energy, metabolism also integrates environmental conditions into intracellular signals. The underlying regulatory network is complex and multifaceted: it ranges from slow interactions, such as changing gene expression, to rapid ones, such as the modulation of protein activity via post-translational modification or the allosteric binding of small molecules. In this Review, we outline the coordination of common metabolic tasks, including nutrient uptake, central metabolism, the generation of energy, the supply of amino acids and protein synthesis. Increasingly, a set of key metabolites is recognized to control individual regulatory circuits, which carry out specific functions of information input and regulatory output. Such a modular view of microbial metabolism facilitates an intuitive understanding of the molecular mechanisms that underlie cellular decision making.
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31
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Zeth K, Fokina O, Forchhammer K. Structural basis and target-specific modulation of ADP sensing by the Synechococcus elongatus PII signaling protein. J Biol Chem 2014; 289:8960-72. [PMID: 24519945 DOI: 10.1074/jbc.m113.536557] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PII signaling proteins comprise one of the most versatile signaling devices in nature and have a highly conserved structure. In cyanobacteria, PipX and N-acetyl-L-glutamate kinase are receptors of PII signaling, and these interactions are modulated by ADP, ATP, and 2-oxoglutarate. These effector molecules bind interdependently to three anti-cooperative binding sites on the trimeric PII protein and thereby affect its structure. Here we used the PII protein from Synechococcus elongatus PCC 7942 to reveal the structural basis of anti-cooperative ADP binding. Furthermore, we clarified the mutual influence of PII-receptor interaction and sensing of the ATP/ADP ratio. The crystal structures of two forms of trimeric PII, one with one ADP bound and the other with all three ADP-binding sites occupied, revealed significant differences in the ADP binding mode: at one site (S1) ADP is tightly bound through side-chain and main-chain interactions, whereas at the other two sites (S2 and S3) the ADP molecules are only bound by main-chain interactions. In the presence of the PII-receptor PipX, the affinity of ADP to the first binding site S1 strongly increases, whereas the affinity for ATP decreases due to PipX favoring the S1 conformation of PII-ADP. In consequence, the PII-PipX interaction is highly sensitive to subtle fluctuations in the ATP/ADP ratio. By contrast, the PII-N-acetyl-L-glutamate kinase interaction, which is negatively affected by ADP, is insensitive to these fluctuations. Modulation of the metabolite-sensing properties of PII by its receptors allows PII to differentially perceive signals in a target-specific manner and to perform multitasking signal transduction.
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Affiliation(s)
- Kornelius Zeth
- From the Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, 72076 Tübingen, Germany and
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32
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Chen HL, Bernard CS, Hubert P, My L, Zhang CC. Fluorescence resonance energy transfer based on interaction of PII and PipX proteins provides a robust and specific biosensor for 2-oxoglutarate, a central metabolite and a signalling molecule. FEBS J 2014; 281:1241-55. [DOI: 10.1111/febs.12702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/22/2013] [Accepted: 12/17/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Hai-Lin Chen
- Laboratoire de Chimie Bactérienne; UMR 7283; Aix-Marseille Université and CNRS; France
| | - Christophe S. Bernard
- Laboratoire de Chimie Bactérienne; UMR 7283; Aix-Marseille Université and CNRS; France
| | - Pierre Hubert
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires; UMR 7255; Aix-Marseille Université and CNRS; France
| | - Laetitia My
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires; UMR 7255; Aix-Marseille Université and CNRS; France
| | - Cheng-Cai Zhang
- Laboratoire de Chimie Bactérienne; UMR 7283; Aix-Marseille Université and CNRS; France
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33
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Rodrigues TE, Gerhardt ECM, Oliveira MA, Chubatsu LS, Pedrosa FO, Souza EM, Souza GA, Müller-Santos M, Huergo LF. Search for novel targets of the PII signal transduction protein in Bacteria identifies the BCCP component of acetyl-CoA carboxylase as a PII binding partner. Mol Microbiol 2014; 91:751-61. [PMID: 24329683 DOI: 10.1111/mmi.12493] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2013] [Indexed: 11/29/2022]
Abstract
The PII family comprises a group of widely distributed signal transduction proteins. The archetypal function of PII is to regulate nitrogen metabolism in bacteria. As PII can sense a range of metabolic signals, it has been suggested that the number of metabolic pathways regulated by PII may be much greater than described in the literature. In order to provide experimental evidence for this hypothesis a PII protein affinity column was used to identify PII targets in Azospirillum brasilense. One of the PII partners identified was the biotin carboxyl carrier protein (BCCP), a component of the acetyl-CoA carboxylase which catalyses the committed step in fatty acid biosynthesis. As BCCP had been previously identified as a PII target in Arabidopsis thaliana we hypothesized that the PII -BCCP interaction would be conserved throughout Bacteria. In vitro experiments using purified proteins confirmed that the PII -BCCP interaction is conserved in Escherichia coli. The BCCP-PII interaction required MgATP and was dissociated by increasing 2-oxoglutarate. The interaction was modestly affected by the post-translational uridylylation status of PII ; however, it was completely dependent on the post-translational biotinylation of BCCP.
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Affiliation(s)
- Thiago E Rodrigues
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
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Jain S, Mandal RS, Anand S, Maiti S, Ramachandran S. Probing the amino acids critical for protein oligomerisation and protein-nucleotide interaction in Mycobacterium tuberculosis PII protein through integration of computational and experimental approaches. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2736-49. [PMID: 24129075 DOI: 10.1016/j.bbapap.2013.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 10/05/2013] [Accepted: 10/07/2013] [Indexed: 11/26/2022]
Abstract
We investigated the interacting amino acids critical for the stability and ATP binding of Mycobacterium tuberculosis PII protein through a series of site specific mutagenesis experiments. We assessed the effect of mutants using glutaraldehyde crosslinking and size exclusion chromatography and isothermal titration calorimetry. Mutations in the amino acid pair R60-E62 affecting central electrostatic interaction resulted in insoluble proteins. Multiple sequence alignment of PII orthologs displayed a conserved pattern of charged residues at these positions. Mutation of amino acid D97 to a neutral residue was tolerated whereas positive charge was not acceptable. Mutation of R107 alone had no effect on trimer formation. However, the combination of neutral residues both at positions 97 and 107 was not acceptable even with the pair at 60-62 intact. Reversal of charge polarity could partially restore the interaction. The residues including K90, R101 and R103 with potential to form H-bonds to ATP are conserved throughout across numerous orthologs of PII but when mutated to Alanine, they did not show significant differences in the total free energy change of the interaction as examined through isothermal titration calorimetry. The ATP binding pattern showed anti-cooperativity using three-site binding model. We observed compensatory effect in enthalpy and entropy changes and these may represent structural adjustments to accommodate ATP in the cavity even in absence of some interactions to perform the requisite function. In this respect these small differences between the PII orthologs may have evolved to suite species specific physiological niches.
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Affiliation(s)
- Sriyans Jain
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, New Delhi 110 007, India
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