1
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Travis BA, Peck JV, Salinas R, Dopkins B, Lent N, Nguyen VD, Borgnia MJ, Brennan RG, Schumacher MA. Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria. Nat Commun 2022; 13:3793. [PMID: 35778410 PMCID: PMC9249791 DOI: 10.1038/s41467-022-31573-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium into glutamine, and the GlnR repressor. GlnR detects nitrogen excess indirectly by binding glutamine-feedback-inhibited-GS (FBI-GS), which activates its transcription-repression function. The molecular mechanisms behind this regulatory circuitry, however, are unknown. Here we describe biochemical and structural analyses of GS and FBI-GS-GlnR complexes from pathogenic and non-pathogenic Gram-positive bacteria. The structures show FBI-GS binds the GlnR C-terminal domain within its active-site cavity, juxtaposing two GlnR monomers to form a DNA-binding-competent GlnR dimer. The FBI-GS-GlnR interaction stabilizes the inactive GS conformation. Strikingly, this interaction also favors a remarkable dodecamer to tetradecamer transition in some GS, breaking the paradigm that all bacterial GS are dodecamers. These data thus unveil unique structural mechanisms of transcription and enzymatic regulation.
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Affiliation(s)
- Brady A Travis
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jared V Peck
- Cryo-EM core, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Brandon Dopkins
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Nicholas Lent
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Viet D Nguyen
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Richard G Brennan
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA.
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2
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Chou KT, Lee DYD, Chiou JG, Galera-Laporta L, Ly S, Garcia-Ojalvo J, Süel GM. A segmentation clock patterns cellular differentiation in a bacterial biofilm. Cell 2022; 185:145-157.e13. [PMID: 34995513 PMCID: PMC8754390 DOI: 10.1016/j.cell.2021.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023]
Abstract
Contrary to multicellular organisms that display segmentation during development, communities of unicellular organisms are believed to be devoid of such sophisticated patterning. Unexpectedly, we find that the gene expression underlying the nitrogen stress response of a developing Bacillus subtilis biofilm becomes organized into a ring-like pattern. Mathematical modeling and genetic probing of the underlying circuit indicate that this patterning is generated by a clock and wavefront mechanism, similar to that driving vertebrate somitogenesis. We experimentally validated this hypothesis by showing that predicted nutrient conditions can even lead to multiple concentric rings, resembling segments. We additionally confirmed that this patterning mechanism is driven by cell-autonomous oscillations. Importantly, we show that the clock and wavefront process also spatially patterns sporulation within the biofilm. Together, these findings reveal a biofilm segmentation clock that organizes cellular differentiation in space and time, thereby challenging the paradigm that such patterning mechanisms are exclusive to plant and animal development.
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Affiliation(s)
- Kwang-Tao Chou
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Dong-Yeon D Lee
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jian-Geng Chiou
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - San Ly
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California San Diego, La Jolla, CA 92093-0380, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093-0380, USA.
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3
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Wang T, Zhao X, Shi H, Sun L, Li Y, Li Q, Zhang H, Chen S, Li J. Positive and negative regulation of transferred nif genes mediated by indigenous GlnR in Gram-positive Paenibacillus polymyxa. PLoS Genet 2018; 14:e1007629. [PMID: 30265664 PMCID: PMC6191146 DOI: 10.1371/journal.pgen.1007629] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 10/16/2018] [Accepted: 08/14/2018] [Indexed: 12/29/2022] Open
Abstract
Ammonia is a major signal that regulates nitrogen fixation in most diazotrophs. Regulation of nitrogen fixation by ammonia in the Gram-negative diazotrophs is well-characterized. In these bacteria, this regulation occurs mainly at the level of nif (nitrogen fixation) gene transcription, which requires a nif-specific activator, NifA. Although Gram-positive and diazotrophic Paenibacilli have been extensively used as a bacterial fertilizer in agriculture, how nitrogen fixation is regulated in response to nitrogen availability in these bacteria remains unclear. An indigenous GlnR and GlnR/TnrA-binding sites in the promoter region of the nif cluster are conserved in these strains, indicating the role of GlnR as a regulator of nitrogen fixation. In this study, we for the first time reveal that GlnR of Paenibacillus polymyxa WLY78 is essentially required for nif gene transcription under nitrogen limitation, whereas both GlnR and glutamine synthetase (GS) encoded by glnA within glnRA operon are required for repressing nif expression under excess nitrogen. Dimerization of GlnR is necessary for binding of GlnR to DNA. GlnR in P. polymyxa WLY78 exists in a mixture of dimers and monomers. The C-terminal region of GlnR monomer is an autoinhibitory domain that prevents GlnR from binding DNA. Two GlnR-biding sites flank the -35/-10 regions of the nif promoter of the nif operon (nifBHDKENXhesAnifV). The GlnR-binding site Ⅰ (located upstream of -35/-10 regions of the nif promoter) is specially required for activating nif transcription, while GlnR-binding siteⅡ (located downstream of -35/-10 regions of the nif promoter) is for repressing nif expression. Under nitrogen limitation, GlnR dimer binds to GlnR-binding siteⅠ in a weak and transient association way and then activates nif transcription. During excess nitrogen, glutamine binds to and feedback inhibits GS by forming the complex FBI-GS. The FBI-GS interacts with the C-terminal domain of GlnR and stabilizes the binding affinity of GlnR to GlnR-binding site Ⅱ and thus represses nif transcription. GlnR is a global transcription regulator of nitrogen metabolism in Bacillus and other Gram-positive bacteria. GlnR generally functions as repressor and inhibits gene transcription under excess nitrogen. Our study for the first time reveals that GlnR simultaneously acted as an activator and a repressor for nitrogen fixation of Paenibacillus by binding to different loci of the single nif promoter region according to nitrogen availability. In excess glutamine, the feedback inhibited form of glutamine synthetase (GS) encoded by glnA within glnRA operon directly interacts with the C-terminal domain of GlnR and then controls the GlnR activity. Also, overexpression of glnR or deletion of glnA or mutagenesis of GlnR-binding site Ⅱ led to constitutive nif expression in the absence or presence of high (100 mM) concentration of ammonia. This work represents the first instance of a dual positive and negative regulatory mechanism of nitrogen fixation.
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Affiliation(s)
- Tianshu Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
| | - Xiyun Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
| | - Haowen Shi
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
| | - Li Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
| | - Yongbin Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
| | - Qin Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
- * E-mail:
| | - Jilun Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, P. R. China
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Annapurna K, Govindasamy V, Sharma M, Ghosh A, Chikara SK. Whole genome shotgun sequence of Bacillus paralicheniformis strain KMS 80, a rhizobacterial endophyte isolated from rice ( Oryza sativa L.). 3 Biotech 2018; 8:223. [PMID: 29692960 DOI: 10.1007/s13205-018-1242-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 04/03/2018] [Indexed: 11/26/2022] Open
Abstract
Bacillus paralicheniformis strain KMS 80 (MTCC No. 12704) is an isolate from the root tissues of rice (Oryza sativa L.) that displays biological nitrogen fixation and plant growth promoting abilities. Here, we report the complete genome sequence of this strain, which contains 4,566,040 bp, 4424 protein-coding genes, 8692 promoter sequences, 67 tRNAs, 20 rRNA genes with six copies of 5S rRNAs along with a single copy of 16S-23S rRNA and genome average GC-content of 45.50%. Twenty one genes involved in nitrogen metabolism pathway and two main transcriptional factor genes, glnR and tnrA responsible for regulation of nitrogen fixation in Bacillus sp. were predicted from the whole genome of strain KMS 80. Analysis of the ~ 4.57 Mb genome sequence will give support to understand the genetic determinants of host range, endophytic colonization behaviour as well as to enhance endophytic nitrogen fixation and other plant beneficial role of B. paralicheniformis in rice.
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Affiliation(s)
- Kannepalli Annapurna
- 1Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Venkadasamy Govindasamy
- 1Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Meenakshi Sharma
- 1Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Arpita Ghosh
- Eurofins Genomics India Private Limited, Bangalore, 560048 Karnataka India
| | - Surendra K Chikara
- Eurofins Genomics India Private Limited, Bangalore, 560048 Karnataka India
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5
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Hauf K, Kayumov A, Gloge F, Forchhammer K. The Molecular Basis of TnrA Control by Glutamine Synthetase in Bacillus subtilis. J Biol Chem 2015; 291:3483-95. [PMID: 26635369 DOI: 10.1074/jbc.m115.680991] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 12/16/2022] Open
Abstract
TnrA is a master regulator of nitrogen assimilation in Bacillus subtilis. This study focuses on the mechanism of how glutamine synthetase (GS) inhibits TnrA function in response to key metabolites ATP, AMP, glutamine, and glutamate. We suggest a model of two mutually exclusive GS conformations governing the interaction with TnrA. In the ATP-bound state (A-state), GS is catalytically active but unable to interact with TnrA. This conformation was stabilized by phosphorylated L-methionine sulfoximine (MSX), fixing the enzyme in the transition state. When occupied by glutamine (or its analogue MSX), GS resides in a conformation that has high affinity for TnrA (Q-state). The A- and Q-state are mutually exclusive, and in agreement, ATP and glutamine bind to GS in a competitive manner. At elevated concentrations of glutamine, ATP is no longer able to bind GS and to bring it into the A-state. AMP efficiently competes with ATP and prevents formation of the A-state, thereby favoring GS-TnrA interaction. Surface plasmon resonance analysis shows that TnrA bound to a positively regulated promoter fragment binds GS in the Q-state, whereas it rapidly dissociates from a negatively regulated promoter fragment. These data imply that GS controls TnrA activity at positively controlled promoters by shielding the transcription factor in the DNA-bound state. According to size exclusion and multiangle light scattering analysis, the dodecameric GS can bind three TnrA dimers. The highly interdependent ligand binding properties of GS reveal this enzyme as a sophisticated sensor of the nitrogen and energy state of the cell to control the activity of DNA-bound TnrA.
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Affiliation(s)
- Ksenia Hauf
- From the Interfaculty Institute for Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
| | - Airat Kayumov
- the Department of Genetics, Kazan Federal University, Kremlevskaya 18, 420008, Kazan, Russia, and
| | - Felix Gloge
- Wyatt Technology Europe, Hochstrasse 12a, 56307 Dernbach, Germany
| | - Karl Forchhammer
- From the Interfaculty Institute for Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany,
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6
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Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK, Whitfill T. Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis. Genes Dev 2015; 29:451-64. [PMID: 25691471 PMCID: PMC4335299 DOI: 10.1101/gad.254714.114] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA and the repressor GlnR. Here, Schumacher et al. describe a comprehensive molecular dissection of this network that reveals novel mechanisms, including oligomeric transformations, by which their inducible signal transduction domains are employed to provide a readout of nitrogen levels. All cells must sense and adapt to changing nutrient availability. However, detailed molecular mechanisms coordinating such regulatory pathways remain poorly understood. In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA, which is deactivated by feedback-inhibited glutamine synthetase (GS) during nitrogen excess and stabilized by GlnK upon nitrogen depletion, and the repressor GlnR. Here we describe a complete molecular dissection of this network. TnrA and GlnR, the global nitrogen homeostatic transcription regulators, are revealed as founders of a new structural family of dimeric DNA-binding proteins with C-terminal, flexible, effector-binding sensors that modulate their dimerization. Remarkably, the TnrA sensor domains insert into GS intersubunit catalytic pores, destabilizing the TnrA dimer and causing an unprecedented GS dodecamer-to-tetradecamer conversion, which concomitantly deactivates GS. In contrast, each subunit of the GlnK trimer “templates” active TnrA dimers. Unlike TnrA, GlnR sensors mediate an autoinhibitory dimer-destabilizing interaction alleviated by GS, which acts as a GlnR chaperone. Thus, these studies unveil heretofore unseen mechanisms by which inducible sensor domains drive metabolic reprograming in the model Gram-positive bacterium B. subtilis.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Naga Babu Chinnam
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Bonnie Cuthbert
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Nam K Tonthat
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Travis Whitfill
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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7
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Fedorova K, Kayumov A, Woyda K, Ilinskaja O, Forchhammer K. Transcription factor TnrA inhibits the biosynthetic activity of glutamine synthetase in Bacillus subtilis. FEBS Lett 2013; 587:1293-8. [PMID: 23535029 DOI: 10.1016/j.febslet.2013.03.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 03/11/2013] [Accepted: 03/11/2013] [Indexed: 11/25/2022]
Abstract
The Bacillus subtilis glutamine synthetase (GS) plays a dual role in cell metabolism by functioning as catalyst and regulator. GS catalyses the ATP-dependent synthesis of glutamine from glutamate and ammonium. Under nitrogen-rich conditions, GS becomes feedback-inhibited by high intracellular glutamine levels and then binds transcription factors GlnR and TnrA, which control the genes of nitrogen assimilation. While GS-bound TnrA is no longer able to interact with DNA, GlnR-DNA binding is shown to be stimulated by GS complex formation. In this paper we show a new physiological feature of the interaction between glutamine synthetase and TnrA. The transcription factor TnrA inhibits the biosynthetic activity of glutamine synthetase in vivo and in vitro, while the GlnR protein does not affect the activity of the enzyme.
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Affiliation(s)
- Ksenia Fedorova
- Kazan (Volga region) Federal University, Department of Microbiology, Kremlevskaya 18, 420008 Kazan, Russia
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8
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Fedorova KP, Scharafutdinov IS, Turbina EY, Bogachev MI, Ilinskaja ON, Kayumov AR. C-terminus of transcription factor TnrA from Bacillus subtilis controls DNA-binding domain activity but is not required for dimerization. Mol Biol 2013. [DOI: 10.1134/s0026893313020052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Gunka K, Commichau FM. Control of glutamate homeostasis in Bacillus subtilis: a complex interplay between ammonium assimilation, glutamate biosynthesis and degradation. Mol Microbiol 2012; 85:213-24. [DOI: 10.1111/j.1365-2958.2012.08105.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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10
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Wei Y, Thompson J, Floudas CA. CONCORD: a consensus method for protein secondary structure prediction via mixed integer linear optimization. Proc Math Phys Eng Sci 2011. [DOI: 10.1098/rspa.2011.0514] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most of the protein structure prediction methods use a multi-step process, which often includes secondary structure prediction, contact prediction, fragment generation, clustering, etc. For many years, secondary structure prediction has been the workhorse for numerous methods aimed at predicting protein structure and function. This paper presents a new mixed integer linear optimization (MILP)-based consensus method: a Consensus scheme based On a mixed integer liNear optimization method for seCOndary stRucture preDiction (CONCORD). Based on seven secondary structure prediction methods, SSpro, DSC, PROF, PROFphd, PSIPRED, Predator and GorIV, the MILP-based consensus method combines the strengths of different methods, maximizes the number of correctly predicted amino acids and achieves a better prediction accuracy. The method is shown to perform well compared with the seven individual methods when tested on the PDBselect25 training protein set using sixfold cross validation. It also performs well compared with another set of 10 online secondary structure prediction servers (including several recent ones) when tested on the CASP9 targets (
http://predictioncenter.org/casp9/
). The average Q3 prediction accuracy is 83.04 per cent for the sixfold cross validation of the PDBselect25 set and 82.3 per cent for the CASP9 targets. We have developed a MILP-based consensus method for protein secondary structure prediction. A web server, CONCORD, is available to the scientific community at
http://helios.princeton.edu/CONCORD
.
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Affiliation(s)
- Y. Wei
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - J. Thompson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - C. A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
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11
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Kayumov A, Heinrich A, Fedorova K, Ilinskaya O, Forchhammer K. Interaction of the general transcription factor TnrA with the PII-like protein GlnK and glutamine synthetase in Bacillus subtilis. FEBS J 2011; 278:1779-89. [DOI: 10.1111/j.1742-4658.2011.08102.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Kayumov A, Heinrich A, Sharipova M, Iljinskaya O, Forchhammer K. Inactivation of the general transcription factor TnrA in Bacillus subtilis by proteolysis. MICROBIOLOGY-SGM 2008; 154:2348-2355. [PMID: 18667567 DOI: 10.1099/mic.0.2008/019802-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Under conditions of nitrogen limitation, the general transcription factor TnrA in Bacillus subtilis activates the expression of genes involved in assimilation of various nitrogen sources. Previously, TnrA activity has been shown to be controlled by protein-protein interaction with glutamine synthetase, the key enzyme of ammonia assimilation. Furthermore, depending on ATP and 2-oxoglutarate levels, TnrA can bind to the GlnK-AmtB complex. Here, we report that upon transfer of nitrate-grown cells to combined nitrogen-depleted medium, TnrA is rapidly eliminated from the cells by proteolysis. As long as TnrA is membrane-bound through GlnK-AmtB interaction it seems to be protected from degradation. Upon removal of nitrogen sources, the localization of TnrA becomes cytosolic and degradation occurs. The proteolytic activity against TnrA was detected in the cytosolic fraction but not in the membrane, and its presence does not depend on the nitrogen regime of cell growth. The proteolytic degradation of TnrA as a response to complete nitrogen starvation might represent a novel mechanism of TnrA control in B. subtilis.
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Affiliation(s)
- Airat Kayumov
- Department of Microbiology, Kazan State University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Annette Heinrich
- Institut für Mikrobiologie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Margarita Sharipova
- Department of Microbiology, Kazan State University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Olga Iljinskaya
- Department of Microbiology, Kazan State University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Karl Forchhammer
- Institut für Mikrobiologie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
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13
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Wray LV, Fisher SH. Bacillus subtilis GlnR contains an autoinhibitory C-terminal domain required for the interaction with glutamine synthetase. Mol Microbiol 2008; 68:277-85. [DOI: 10.1111/j.1365-2958.2008.06162.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Ter Beek A, Keijser BJF, Boorsma A, Zakrzewska A, Orij R, Smits GJ, Brul S. Transcriptome analysis of sorbic acid-stressed Bacillus subtilis reveals a nutrient limitation response and indicates plasma membrane remodeling. J Bacteriol 2008; 190:1751-61. [PMID: 18156260 PMCID: PMC2258692 DOI: 10.1128/jb.01516-07] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 12/13/2007] [Indexed: 11/20/2022] Open
Abstract
The weak organic acid sorbic acid is a commonly used food preservative, as it inhibits the growth of bacteria, yeasts, and molds. We have used genome-wide transcriptional profiling of Bacillus subtilis cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance mechanisms. Our analysis demonstrated that sorbic acid-stressed cells induce responses normally seen upon nutrient limitation. This is indicated by the strong derepression of the CcpA, CodY, and Fur regulon and the induction of tricarboxylic acid cycle genes, SigL- and SigH-mediated genes, and the stringent response. Intriguingly, these conditions did not lead to the activation of sporulation, competence, or the general stress response. The fatty acid biosynthesis (fab) genes and BkdR-regulated genes are upregulated, which may indicate plasma membrane remodeling. This was further supported by the reduced sensitivity toward the fab inhibitor cerulenin upon sorbic acid stress. We are the first to present a comprehensive analysis of the transcriptional response of B. subtilis to sorbic acid stress.
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Affiliation(s)
- Alex Ter Beek
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.
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15
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Cheng H, Sen TZ, Jernigan RL, Kloczkowski A. Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM). Bioinformatics 2007; 23:2628-30. [PMID: 17660202 PMCID: PMC2553684 DOI: 10.1093/bioinformatics/btm379] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we propose a novel approach to surpass this barrier. Instead of using a single algorithm that relies on a limited data set for training, we combine two complementary methods having different strengths: Fragment Database Mining (FDM) and GOR V. FDM harnesses the availability of the known protein structures in the Protein Data Bank and provides highly accurate secondary structure predictions when sequentially similar structural fragments are identified. In contrast, the GOR V algorithm is based on information theory, Bayesian statistics, and PSI-BLAST multiple sequence alignments to predict the secondary structure of residues inside a sliding window along a protein chain. A combination of these two different methods benefits from the large number of structures in the PDB and significantly improves the secondary structure prediction accuracy, resulting in Q3 ranging from 67.5 to 93.2%, depending on the availability of highly similar fragments in the Protein Data Bank.
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Affiliation(s)
- Haitao Cheng
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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