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Spampinato A, Leone DL, Pohl R, Tarábek J, Šoltysová M, Polák M, Kádek A, Sýkorová V, Řezáčová P, Hocek M. ABNOH-Linked Nucleotides and DNA for Bioconjugation and Cross-linking with Tryptophan-Containing Peptides and Proteins. Chemistry 2024; 30:e202402151. [PMID: 38924659 DOI: 10.1002/chem.202402151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024]
Abstract
Reactive N-hydroxy-9-azabicyclo[3.3.1]nonane (ABNOH) linked 2'-deoxyuridine 5'-O-mono- and triphosphates were synthesized through a CuAAC reaction of ABNOH-PEG4-N3 with 5-ethynyl-dUMP or -dUTP. The modified triphosphate was used as substrate for enzymatic synthesis of modified DNA probes with KOD XL DNA polymerase. The keto-ABNO radical reacted with tryptophan (Trp) and Trp-containing peptides to form a stable tricyclic fused hexahydropyrrolo-indole conjugates. Similarly modified ABNOH-linked nucleotides reacted with Trp-containing peptides to form a stable conjugate in the presence but surprisingly even in the absence of NaNO2 (presumably through activation by O2). The reactive ABNOH-modified DNA probe was used for bioconjugations and crosslinking with Trp-containing peptides or proteins.
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Affiliation(s)
- Ambra Spampinato
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| | - Denise-Liu' Leone
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Ján Tarábek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Markéta Šoltysová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Marek Polák
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Alan Kádek
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
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Arya G, Pal M, Sharma M, Singh B, Singh S, Agrawal V, Chaba R. Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli. Mol Microbiol 2020; 115:591-609. [PMID: 33068046 DOI: 10.1111/mmi.14625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023]
Abstract
Several GntR/FadR transcriptional regulators govern sugar acid metabolism in bacteria. Although effectors have been identified for a few sugar acid regulators, the mode of effector binding is unknown. Even in the overall FadR subfamily, there are limited details on effector-regulator interactions. Here, we identified the effector-binding cavity in Escherichia coli DgoR, a FadR subfamily transcriptional repressor of D-galactonate metabolism that employs D-galactonate as its effector. Using a genetic screen, we isolated several dgoR superrepressor alleles. Blind docking suggested eight amino acids corresponding to these alleles to form a part of the effector-binding cavity. In vivo and in vitro assays showed that these mutations compromise the inducibility of DgoR without affecting its oligomeric status or affinity for target DNA. Taking Bacillus subtilis GntR as a representative, we demonstrated that the effector-binding cavity is similar among FadR subfamily sugar acid regulators. Finally, a comparison of sugar acid regulators with other FadR members suggested conserved features of effector-regulator recognition within the FadR subfamily. Sugar acid metabolism is widely implicated in bacterial colonization and virulence. The present study sets the basis to investigate the influence of natural genetic variations in FadR subfamily regulators on their sensitivity to sugar acids and ultimately on host-bacterial interactions.
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Affiliation(s)
- Garima Arya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Mohinder Pal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Vishal Agrawal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
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Molecular and Functional Insights into the Regulation of d-Galactonate Metabolism by the Transcriptional Regulator DgoR in Escherichia coli. J Bacteriol 2019; 201:JB.00281-18. [PMID: 30455279 DOI: 10.1128/jb.00281-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022] Open
Abstract
d-Galactonate, an aldonic sugar acid, is used as a carbon source by Escherichia coli, and the structural dgo genes involved in its metabolism have previously been investigated. Here, using genetic, biochemical and bioinformatics approaches, we present the first detailed molecular and functional insights into the regulation of d-galactonate metabolism in E. coli K-12 by the transcriptional regulator DgoR. We found that dgoR deletion accelerates the growth of E. coli in d-galactonate concomitant with the strong constitutive expression of dgo genes. In the dgo locus, sequence upstream of dgoR alone harbors the d-galactonate-inducible promoter that likely drives the expression of all dgo genes. DgoR exerts repression on the dgo operon by binding two inverted repeats overlapping the dgo promoter. Binding of d-galactonate induces a conformational change in DgoR to derepress the dgo operon. The findings from our work firmly place DgoR in the GntR family of transcriptional regulators: DgoR binds an operator sequence [5'-TTGTA(G/C)TACA(A/T)-3'] matching the signature of GntR family members that recognize inverted repeats [5'-(N) y GT(N) x AC(N) y -3', where x and y indicate the number of nucleotides, which varies], and it shares critical protein-DNA contacts. We also identified features in DgoR that are otherwise less conserved in the GntR family. Recently, missense mutations in dgoR were recovered in a natural E. coli isolate adapted to the mammalian gut. Our results show these mutants to be DNA binding defective, emphasizing that mutations in the dgo-regulatory elements are selected in the host to allow simultaneous induction of dgo genes. The present study sets the basis to explore the regulation of dgo genes in additional enterobacterial strains where they have been implicated in host-bacterium interactions.IMPORTANCE d-Galactonate is a widely prevalent aldonic sugar acid. Despite the proposed significance of the d-galactonate metabolic pathway in the interaction of enteric bacteria with their hosts, there are no details on its regulation even in Escherichia coli, which has been known to utilize d-galactonate since the 1970s. Here, using multiple methodologies, we identified the promoter, operator, and effector of DgoR, the transcriptional repressor of d-galactonate metabolism in E. coli We establish DgoR as a GntR family transcriptional regulator. Recently, a human urinary tract isolate of E. coli introduced in the mouse gut was found to accumulate missense mutations in dgoR Our results show these mutants to be DNA binding defective, hence emphasizing the role of the d-galactonate metabolic pathway in bacterial colonization of the mammalian gut.
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Daddaoua A, Corral-Lugo A, Ramos JL, Krell T. Identification of GntR as regulator of the glucose metabolism in Pseudomonas aeruginosa. Environ Microbiol 2017; 19:3721-3733. [PMID: 28752954 DOI: 10.1111/1462-2920.13871] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/26/2017] [Accepted: 07/24/2017] [Indexed: 11/29/2022]
Abstract
In contrast to Escherichia coli, glucose metabolism in pseudomonads occurs exclusively through the Entner-Doudoroff (ED) pathway. This pathway, as well as the three routes to generate the initial ED pathway substrate, 6-phosphogluconate, is regulated by the PtxS, HexR and GtrS/GltR systems. With GntR (PA2320) we report here the identification of an additional regulator in Pseudomonas aeruginosa PAO1. GntR repressed its own expression as well as that of the GntP gluconate permease. In contrast to PtxS and GtrS/GltR, GntR did not modulate expression of the toxA gene encoding the exotoxin A virulence factor. GntR was found to bind to promoters PgntR and PgntP and the consensus sequence of its operator was defined as 5'-AC-N-AAG-N-TAGCGCT-3'. Both operator sites overlapped with the RNA polymerase binding site and we show that GntR employs an effector mediated de-repression mechanism. The release of promoter bound GntR is induced by gluconate and 6-phosphogluconate that bind with similar apparent affinities to the GntR/DNA complex. GntR and PtxS are paralogous and may have evolved from a common ancestor. The concerted action of four regulatory systems in the regulation of glucose metabolism in Pseudomonas can be considered as a model to understand complex regulatory circuits in bacteria.
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Affiliation(s)
- A Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - A Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - J-L Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Toyoda K, Inui M. Regulons of global transcription factors in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2015; 100:45-60. [DOI: 10.1007/s00253-015-7074-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/03/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
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6
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Bardot C, Besse-Hoggan P, Carles L, Le Gall M, Clary G, Chafey P, Federici C, Broussard C, Batisson I. How the edaphic Bacillus megaterium strain Mes11 adapts its metabolism to the herbicide mesotrione pressure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 199:198-208. [PMID: 25679981 DOI: 10.1016/j.envpol.2015.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/23/2014] [Accepted: 01/24/2015] [Indexed: 05/26/2023]
Abstract
Toxicity of pesticides towards microorganisms can have a major impact on ecosystem function. Nevertheless, some microorganisms are able to respond quickly to this stress by degrading these molecules. The edaphic Bacillus megaterium strain Mes11 can degrade the herbicide mesotrione. In order to gain insight into the cellular response involved, the intracellular proteome of Mes11 exposed to mesotrione was analyzed using the two-dimensional differential in-gel electrophoresis (2D-DIGE) approach coupled with mass spectrometry. The results showed an average of 1820 protein spots being detected. The gel profile analyses revealed 32 protein spots whose abundance is modified after treatment with mesotrione. Twenty spots could be identified, leading to 17 non redundant proteins, mainly involved in stress, metabolic and storage mechanisms. These findings clarify the pathways used by B. megaterium strain Mes11 to resist and adapt to the presence of mesotrione.
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Affiliation(s)
- Corinne Bardot
- Clermont Université, Université Blaise Pascal, LMGE, F-63000 Clermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, F-63177 Aubière, France
| | - Pascale Besse-Hoggan
- Clermont Université, Université Blaise Pascal, ICCF, F-63000 Clermont Ferrand, France; CNRS, UMR 6296, Institut de Chimie de Clermont-Ferrand, BP 80026, F-63171 Aubière Cedex, France
| | - Louis Carles
- Clermont Université, Université Blaise Pascal, LMGE, F-63000 Clermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, F-63177 Aubière, France
| | - Morgane Le Gall
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, France; Plate-forme Protéomique 3P5, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Guilhem Clary
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, France; Plate-forme Protéomique 3P5, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Philippe Chafey
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, France; Plate-forme Protéomique 3P5, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Christian Federici
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, France; Plate-forme Protéomique 3P5, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Cédric Broussard
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes, Paris, France; Plate-forme Protéomique 3P5, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Batisson
- Clermont Université, Université Blaise Pascal, LMGE, F-63000 Clermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et Environnement, F-63177 Aubière, France.
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CcpA-mediated catabolite activation of the Bacillus subtilis ilv-leu operon and its negation by either CodY- or TnrA-mediated negative regulation. J Bacteriol 2014; 196:3793-806. [PMID: 25157083 DOI: 10.1128/jb.02055-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis ilv-leu operon functions in the biosynthesis of branched-chain amino acids. It undergoes catabolite activation involving a promoter-proximal cre which is mediated by the complex of CcpA and P-Ser-HPr. This activation of ilv-leu expression is negatively regulated through CodY binding to a high-affinity site in the promoter region under amino acid-rich growth conditions, and it is negatively regulated through TnrA binding to the TnrA box under nitrogen-limited growth conditions. The CcpA-mediated catabolite activation of ilv-leu required a helix face-dependent interaction of the complex of CcpA and P-Ser-HPr with RNA polymerase and needed a 19-nucleotide region upstream of cre for full activation. DNase I footprinting indicated that CodY binding to the high-affinity site competitively prevented the binding of the complex of CcpA and P-Ser-HPr to cre. This CodY binding not only negated catabolite activation but also likely inhibited transcription initiation from the ilv-leu promoter. The footprinting also indicated that TnrA and the complex of CcpA and P-Ser-HPr simultaneously bound to the TnrA box and the cre site, respectively, which are 112 nucleotides apart; TnrA binding to its box was likely to induce DNA bending. This implied that interaction of TnrA bound to its box with the complex of CcpA and P-Ser-HPr bound to cre might negate catabolite activation, but TnrA bound to its box did not inhibit transcription initiation from the ilv-leu promoter. Moreover, this negation of catabolite activation by TnrA required a 26-nucleotide region downstream of the TnrA box.
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Crystal structure of PhnF, a GntR-family transcriptional regulator of phosphate transport in Mycobacterium smegmatis. J Bacteriol 2014; 196:3472-81. [PMID: 25049090 DOI: 10.1128/jb.01965-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Bacterial uptake of phosphate is usually accomplished via high-affinity transporters that are commonly regulated by two-component systems, which are activated when the concentration of phosphate is low. Mycobacterium smegmatis possesses two such transporters, the widely distributed PstSCAB system and PhnDCE, a transporter that in other bacteria mediates the uptake of alternative phosphorus sources. We previously reported that the transcriptional regulator PhnF controls the production of the Phn system, acting as a repressor under high-phosphate conditions. Here we show that the phnDCE genes are common among environmental mycobacteria, where they are often associated with phnF-like genes. In contrast, pathogenic mycobacteria were not found to encode Phn-like systems but instead were found to possess multiple copies of the pst genes. A detailed biochemical analysis of PhnF binding to its identified binding sites in the phnD-phnF intergenic region of M. smegmatis has allowed us to propose a quantitative model for repressor binding, which shows that a PhnF dimer binds independently to each site. We present the crystal structure of M. smegmatis PhnF at 1.8-Å resolution, showing a homodimer with a helix-turn-helix N-terminal domain and a C-terminal domain with a UbiC transcription regulator-associated fold. The C-terminal domain crystallized with a bound sulfate ion instead of the so far unidentified physiological ligand, allowing the identification of residues involved in effector binding. Comparison of the positioning of the DNA binding domains in PhnF with that in homologous proteins suggests that its DNA binding activity is regulated via a conformational change in the linker region, triggering a movement of the N-terminal domains.
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Mycobacterium smegmatis RoxY is a repressor of oxyS and contributes to resistance to oxidative stress and bactericidal ubiquitin-derived peptides. J Bacteriol 2011; 193:6824-33. [PMID: 21984791 DOI: 10.1128/jb.05492-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mycobactericidal properties of macrophages include the generation of reactive oxygen intermediates and the delivery of bacteria to a hydrolytic lysosome enriched in bactericidal ubiquitin-derived peptides (Ub-peptides). To better understand the interactions of ubiquitin-derived peptides with mycobacteria and identify putative mycobacterial intrinsic resistance mechanisms, we screened for transposon mutants with increased susceptibility to the bactericidal Ub-peptide Ub2. We isolated 27 Mycobacterium smegmatis mutants that were hypersusceptible to Ub2. Two mutants were isolated that possessed mutations in the msmeg_0166 gene, which encodes a transcriptional regulator. The msmeg_0166 mutants were also hypersusceptible to other host antimicrobial peptides and oxidative stress. In characterizing msmeg_0166, we found that it encodes a repressor of oxyS, and therefore we have renamed the gene roxY. We demonstrate that RoxY and OxyS contribute to M. smegmatis resistance to oxidative stress. An ahpD transposon mutant was also isolated in our screen for Ub-peptide hypersusceptibility. Overexpression of oxyS in M. smegmatis reduced transcription of the ahpCD genes, which encode a peroxide detoxification system. Our data indicate that RoxY, OxyS, and AhpD play a role in the mycobacterial oxidative stress response and are important for resistance to host antimicrobial peptides.
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Genetic analysis around aminoalcohol dehydrogenase gene of Rhodococcus erythropolis MAK154: a putative GntR transcription factor in transcriptional regulation. Appl Microbiol Biotechnol 2010; 89:739-46. [DOI: 10.1007/s00253-010-2924-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 09/27/2010] [Accepted: 09/29/2010] [Indexed: 02/05/2023]
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Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli. J Bacteriol 2008; 190:2997-3005. [PMID: 18263722 DOI: 10.1128/jb.02013-07] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lldPRD operon of Escherichia coli, involved in L-lactate metabolism, is induced by growth in this compound. We experimentally identified that this system is transcribed from a single promoter with an initiation site located 110 nucleotides upstream of the ATG start codon. On the basis of computational data, it had been proposed that LldR and its homologue PdhR act as regulators of the lldPRD operon. Nevertheless, no experimental data on the function of these regulators have been reported so far. Here we show that induction of an lldP-lacZ fusion by L-lactate is lost in an Delta lldR mutant, indicating the role of LldR in this induction. Expression analysis of this construct in a pdhR mutant ruled out the participation of PdhR in the control of lldPRD. Gel shift experiments showed that LldR binds to two operator sites, O1 (positions -105 to -89) and O2 (positions +22 to +38), with O1 being filled at a lower concentration of LldR. L-Lactate induced a conformational change in LldR that did not modify its DNA binding activity. Mutations in O1 and O2 enhanced the basal transcriptional level. However, only mutations in O1 abolished induction by L-lactate. Mutants with a change in helical phasing between O1 and O2 behaved like O2 mutants. These results were consistent with the hypothesis that LldR has a dual role, acting as a repressor or an activator of lldPRD. We propose that in the absence of L-lactate, LldR binds to both O1 and O2, probably leading to DNA looping and the repression of transcription. Binding of L-lactate to LldR promotes a conformational change that may disrupt the DNA loop, allowing the formation of the transcription open complex.
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Frunzke J, Engels V, Hasenbein S, Gätgens C, Bott M. Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2. Mol Microbiol 2008; 67:305-22. [PMID: 18047570 PMCID: PMC2230225 DOI: 10.1111/j.1365-2958.2007.06020.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2007] [Indexed: 11/28/2022]
Abstract
Corynebacterium glutamicum is a Gram-positive soil bacterium that prefers the simultaneous catabolism of different carbon sources rather than their sequential utilization. This type of metabolism requires an adaptation of the utilization rates to the overall metabolic capacity. Here we show how two functionally redundant GntR-type transcriptional regulators, designated GntR1 and GntR2, co-ordinately regulate gluconate catabolism and glucose uptake. GntR1 and GntR2 strongly repress the genes encoding gluconate permease (gntP), gluconate kinase (gntK), and 6-phosphogluconate dehydrogenase (gnd) and weakly the pentose phosphate pathway genes organized in the tkt-tal-zwf-opcA-devB cluster. In contrast, ptsG encoding the EII(Glc) permease of the glucose phosphotransferase system (PTS) is activated by GntR1 and GntR2. Gluconate and glucono-delta-lactone interfere with binding of GntR1 and GntR2 to their target promoters, leading to a derepression of the genes involved in gluconate catabolism and reduced ptsG expression. To our knowledge, this is the first example for gluconate-dependent transcriptional control of PTS genes. A mutant lacking both gntR1 and gntR2 shows a 60% lower glucose uptake rate and growth rate than the wild type when cultivated on glucose as sole carbon source. This growth defect can be complemented by plasmid-encoded GntR1 or GntR2.
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Affiliation(s)
- Julia Frunzke
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany.
| | - Verena Engels
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany.
| | | | - Cornelia Gätgens
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany.
| | - Michael Bott
- Institut für Biotechnologie 1, Forschungszentrum JülichD-52425 Jülich, Germany.
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Gorelik M, Lunin VV, Skarina T, Savchenko A. Structural characterization of GntR/HutC family signaling domain. Protein Sci 2006; 15:1506-11. [PMID: 16672238 PMCID: PMC2242532 DOI: 10.1110/ps.062146906] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The crystal structure of Escherichia coli PhnF C-terminal domain (C-PhnF) was solved at 1.7 A resolution by the single wavelength anomalous dispersion (SAD) method. The PhnF protein belongs to the HutC subfamily of the large GntR transcriptional regulator family. Members of this family share similar N-terminal DNA-binding domains, but are divided into four subfamilies according to their heterogenic C-terminal domains, which are involved in effector binding and oligomerization. The C-PhnF structure provides for the first time the scaffold of this domain for the HutC subfamily, which covers about 31% of GntR-like regulators. The structure represents a mixture of alpha-helices and beta-strands, with a six-stranded antiparallel beta-sheet at the core. C-PhnF monomers form a dimer by establishing interdomain eight-strand beta-sheets that include core antiparallel and N-terminal two-strand parallel beta-sheets from each monomer. C-PhnF shares strong structural similarity with the chorismate lyase fold, which features a buried active site locked behind two helix-turn-helix loops. The structural comparison of the C-PhnF and UbiC proteins allows us to propose that a similar site in the PhnF structure is adapted for effector binding.
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Affiliation(s)
- Marina Gorelik
- Ontario Center for Structural Proteomics, University Health Network, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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Abstract
In the murine model of infection, a Mycobacterium tuberculosis mce1 operon mutant elicits an aberrant granulomatous response, resulting in uncontrolled replication and failure to enter a persistent state. In this study, we demonstrate that the mce1 genes can be transcribed as a 13-gene polycistronic message encompassing Rv0166 to Rv0178. Quantitative reverse transcriptase PCR and immunoblot analyses revealed that the mce1 genes and proteins are expressed during in vitro growth but are significantly down-regulated in intracellular bacilli isolated from murine macrophages. A homologue of the FadR subfamily of GntR transcriptional regulators, Rv0165c (designated Mce1R), lies upstream and is divergently transcribed from the operon. To investigate whether this gene plays a role in regulation of mce1 expression, we created an M. tuberculosis mce1R deletion mutant. There was no difference in expression of mce1 operon genes in Deltamce1R compared to expression in the wild type during logarithmic growth in vitro. However, in bacilli isolated from murine macrophages, expression of mce1 genes was significantly higher in Deltamce1R. In addition, overexpression of mce1R resulted in repression of the mce1 genes. These data demonstrate that Mce1R is a negative regulator that acts intracellularly to repress expression of the mce1 operon. We propose that Mce1R facilitates balanced temporal expression of the mce1 products required for organized granuloma formation, which is both protective to the host and necessary for the persistence of M. tuberculosis.
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Affiliation(s)
- Nicola Casali
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, 140 Warren Hall, Berkeley, CA 94720, USA
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Tsunedomi R, Izu H, Kawai T, Matsushita K, Ferenci T, Yamada M. The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli. J Bacteriol 2003; 185:1783-95. [PMID: 12618441 PMCID: PMC150117 DOI: 10.1128/jb.185.6.1783-1795.2003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gluconate is one of the preferred carbon sources of Escherichia coli, and two sets of gnt genes (encoding the GntI and GntII systems) are involved in its transport and metabolism. GntR represses the GntI genes gntKU and gntT, whereas GntH was previously suggested to be an activator for the GntII genes gntV and idnDO-gntWH. The helix-turn-helix residues of the two regulators GntR and GntH exhibit extensive homologies. The similarity between the two regulators prompted analysis of the cross-regulation of the GntI genes by GntH. Repression of gntKU and gntT by GntH, as well as GntR, was indeed observed using transcriptional fusions and RNA analysis. High GntH expression, from cloned gntH or induced through 5-ketogluconate, was required to observe repression of GntI genes. Two GntR-binding elements were identified in the promoter-operator region of gntKU and were also shown to be the target sites of GntH by mutational analysis. However, the GntI genes were not induced by gluconate in the presence of enhanced amounts of GntH, whereas repression by GntR was relieved by gluconate. The repression of GntI genes by GntH is thus unusual in that it is not relieved by the availability of substrate. These results led us to propose that GntH activates GntII and represses the GntI genes in the presence of metabolites derived from gluconate, allowing the organism to switch from the GntI to the GntII system. This cross-regulation may explain the progressive changes in gnt gene expression along with phases of cell growth in the presence of gluconate.
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Affiliation(s)
- Ryouichi Tsunedomi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan
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16
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Chhabra SR, Shockley KR, Conners SB, Scott KL, Wolfinger RD, Kelly RM. Carbohydrate-induced differential gene expression patterns in the hyperthermophilic bacterium Thermotoga maritima. J Biol Chem 2003; 278:7540-52. [PMID: 12475972 DOI: 10.1074/jbc.m211748200] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic bacterium Thermotoga maritima MSB8 was grown on a variety of carbohydrates to determine the influence of carbon and energy source on differential gene expression. Despite the fact that T. maritima has been phylogenetically characterized as a primitive microorganism from an evolutionary perspective, results here suggest that it has versatile and discriminating mechanisms for regulating and effecting complex carbohydrate utilization. Growth of T. maritima on monosaccharides was found to be slower than growth on polysaccharides, although growth to cell densities of 10(8) to 10(9) cells/ml was observed on all carbohydrates tested. Differential expression of genes encoding carbohydrate-active proteins encoded in the T. maritima genome was followed using a targeted cDNA microarray in conjunction with mixed model statistical analysis. Coordinated regulation of genes responding to specific carbohydrates was noted. Although glucose generally repressed expression of all glycoside hydrolase genes, other sugars induced or repressed these genes to varying extents. Expression profiles of most endo-acting glycoside hydrolase genes correlated well with their reported biochemical properties, although exo-acting glycoside hydrolase genes displayed less specific expression patterns. Genes encoding selected putative ABC sugar transporters were found to respond to specific carbohydrates, and in some cases putative oligopeptide transporter genes were also found to respond to specific sugar substrates. Several genes encoding putative transcriptional regulators were expressed during growth on specific sugars, thus suggesting functional assignments. The transcriptional response of T. maritima to specific carbohydrate growth substrates indicated that sugar backbone- and linkage-specific regulatory networks are operational in this organism during the uptake and utilization of carbohydrate substrates. Furthermore, the wide ranging collection of such networks in T. maritima suggests that this organism is capable of adapting to a variety of growth environments containing carbohydrate growth substrates.
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Affiliation(s)
- Swapnil R Chhabra
- Department of Chemical Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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17
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Teramoto M, Harayama S, Watanabe K. PhcS represses gratuitous expression of phenol-metabolizing enzymes in Comamonas testosteroni R5. J Bacteriol 2001; 183:4227-34. [PMID: 11418563 PMCID: PMC95312 DOI: 10.1128/jb.183.14.4227-4234.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified an open reading frame, designated phcS, downstream of the transcriptional activator gene (phcR) for the expression of multicomponent phenol hydroxylase (mPH) in Comamonas testosteroni R5. The deduced product of phcS was homologous to AphS of C. testosteroni TA441, which belongs to the GntR family of transcriptional regulators. The transformation of Pseudomonas aeruginosa PAO1c (phenol negative, catechol positive) with pROR502 containing phcR and the mPH genes conferred the ability to grow on phenol, while transformation with pROR504 containing phcS, phcR, and mPH genes did not confer this ability. The disruption of phcS in strain R5 had no effect on its phenol-oxygenating activity in a chemostat culture with phenol. The phenol-oxygenating activity was not expressed in strain R5 grown in a chemostat with acetate. In contrast, the phenol-oxygenating activity in the strain with a knockout phcS gene when grown in a chemostat with acetate as the limiting growth factor was 66% of that obtained in phenol-grown cells of the strain with a knockout in the phcS gene. The disruption of phcS and/or phcR and the complementation in trans of these defects confirm that PhcS is a trans-acting repressor and that the unfavorable expression of mPH in the phcS knockout cells grown on acetate requires PhcR. These results show that the PhcS protein repressed the gratuitous expression of phenol-metabolizing enzymes in the absence of the genuine substrate and that strain R5 acted by an unknown mechanism in which the PhcS-mediated repression was overcome in the presence of the pathway substrate.
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Affiliation(s)
- M Teramoto
- Marine Biotechnology Institute, Kamaishi Laboratories, Kamaishi City, Iwate 026-0001, Japan
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18
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van Aalten DM, DiRusso CC, Knudsen J, Wierenga RK. Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold. EMBO J 2000; 19:5167-77. [PMID: 11013219 PMCID: PMC302096 DOI: 10.1093/emboj/19.19.5167] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
FadR is a dimeric acyl coenzyme A (acyl CoA)-binding protein and transcription factor that regulates the expression of genes encoding fatty acid biosynthetic and degrading enzymes in Escherichia coli. Here, the 2.0 A crystal structure of full-length FadR is described, determined using multi-wavelength anomalous dispersion. The structure reveals a dimer and a two-domain fold, with DNA-binding and acyl-CoA-binding sites located in an N-terminal and C-terminal domain, respectively. The N-terminal domain contains a winged helix-turn-helix prokaryotic DNA-binding fold. Comparison with known structures and analysis of mutagenesis data delineated the site of interaction with DNA. The C-terminal domain has a novel fold, consisting of a seven-helical bundle with a crossover topology. Careful analysis of the structure, together with mutational and biophysical data, revealed a putative hydrophobic acyl-CoA-binding site, buried in the core of the seven-helical bundle. This structure aids in understanding FadR function at a molecular level, provides the first structural scaffold for the large GntR family of transcription factors, which are keys in the control of metabolism in bacterial pathogens, and could thus be a possible target for novel chemotherapeutic agents.
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Affiliation(s)
- D M van Aalten
- Wellcome Trust Biocentre, Department of Biochemistry, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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19
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Yoshida KI, Fujita Y, Ehrlich SD. An operon for a putative ATP-binding cassette transport system involved in acetoin utilization of Bacillus subtilis. J Bacteriol 2000; 182:5454-61. [PMID: 10986249 PMCID: PMC110989 DOI: 10.1128/jb.182.19.5454-5461.2000] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ytrABCDEF operon of Bacillus subtilis was deduced to encode a putative ATP-binding cassette (ABC) transport system. YtrB and YtrE could be the ABC subunits, and YtrC and YtrD are highly hydrophobic and could form a channel through the cell membrane, while YtrF could be a periplasmic lipoprotein for substrate binding. Expression of the operon was examined in cells grown in a minimal medium. The results indicate that the expression was induced only early in the stationary phase. The six ytr genes form a single operon, transcribed from a putative sigma(A)-dependent promoter present upstream of ytrA. YtrA, which possesses a helix-turn-helix motif of the GntR family, acts probably as a repressor and regulates its own transcription. Inactivation of the operon led to a decrease in maximum cell yield and less-efficient sporulation, suggesting its involvement in the growth in stationary phase and sporulation. It is known that B. subtilis produces acetoin as an external carbon storage compound and then reuses it later during stationary phase and sporulation. When either the entire ytr operon or its last gene, ytrF, was inactivated, the production of acetoin was not affected, but the reuse of acetoin became less efficient. We suggest that the Ytr transport system plays a role in acetoin utilization during stationary phase and sporulation.
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Affiliation(s)
- K I Yoshida
- Department of Biotechnology, Fukuyama University, Fukuyama, Hiroshima 729-0292, Japan.
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20
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DiRusso CC, Black PN, Weimar JD. Molecular inroads into the regulation and metabolism of fatty acids, lessons from bacteria. Prog Lipid Res 1999; 38:129-97. [PMID: 10396600 DOI: 10.1016/s0163-7827(98)00022-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- C C DiRusso
- Department of Biochemistry and Molecular Biology, Albany Medical College, New York, USA.
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21
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Yoshida K, Miwa Y, Ohmori H, Fujita Y. Analysis of an insertional operator mutation (gntOi) that affects the expression level of the Bacillus subtilis gnt operon, and characterization of gntOi suppressor mutations. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:583-91. [PMID: 7476858 DOI: 10.1007/bf02423454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The Bacillus subtilis gnt operon is negatively regulated via interaction of the gnt repressor (GntR) with an operator upstream of gntR, which is antagonized by gluconate. An 8 bp insertional operator mutation (gntOi) of the gnt operon was constructed which affected the expression level of this operon. Two suppressors of this gntOi mutation, exhibiting normal expression, were also isolated; one involved a threonine substitution for the Ala-48 residue (gntR48T) within the helix-turn-helix DNA-binding motif of GntR, and the other an adenine substitution for the guanine at nucleotide -4 within the gntOi operator (gntOiM4A) (+ 1 is the transcription initiation site). The gntR48T mutation by itself rendered the gnt operon partially constitutive. When the gntR43L mutation, which renders the gnt operon fully constitutive, was introduced into the gntOi or gntOiM4A mutant, the operator mutations were found not to affect the promoter activity of the gnt operon. These in vivo results indicate that the gntOi mutation affects the operator interaction with GntR, causing a low expression level even in the presence of gluconate. In vitro gel retardation and DNase I footprint analyses demonstrated that even when gluconate was present, GntR still bound to the gntOi operator region.
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Affiliation(s)
- K Yoshida
- Department of Biotechnology, Faculty of Engineering, Fukuyama University, Hiroshima, Japan
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22
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Yoshida K, Ohmori H, Miwa Y, Fujita Y. Bacillus subtilis gnt repressor mutants that diminish gluconate-binding ability. J Bacteriol 1995; 177:4813-6. [PMID: 7642511 PMCID: PMC177250 DOI: 10.1128/jb.177.16.4813-4816.1995] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The Bacillus subtilis gnt operon is negatively regulated by GntR, which is antagonized by gluconate. Three GntR mutants with diminished gluconate-binding ability were obtained. Two were missense mutants (Met-209 to Ile and Ser-230 to Leu), whereas the third had a deletion of the C-terminal 23 amino acids. The mutant GntR proteins were unable to become properly detached from the gnt operator even in the presence of gluconate.
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Affiliation(s)
- K Yoshida
- Department of Biotechnology, Faculty of Engineering, Fukuyama University, Hiroshima, Japan
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23
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Yoshisue H, Ihara K, Nishimoto T, Sakai H, Komano T. Cloning and characterization of a Bacillus thuringiensis homolog of the spoIIID gene from Bacillus subtilis. Gene 1995; 154:23-9. [PMID: 7867944 DOI: 10.1016/0378-1119(94)00822-a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The SpoIIID protein of Bacillus subtilis (Bs) is a small DNA-binding protein that is essential for gene expression of the mother cell compartment during sporulation. We have cloned a DNA fragment from Bacillus thuringiensis (Bt) that showed a specific hybridization with the Bs spoIIID gene. Sequence analysis found an open reading frame encoding 90 amino acids (aa), which are 89% identical to the deduced aa sequence of Bs spoIIID. Upstream from the transcription start point (tsp), a nucleotide sequence highly homologous to the consensus sequence motif for the sigma 35-recognized promoters was found. Northern blot analysis has indicated that the expression of the gene is induced only at the midsporulation stage, and that the gene constitutes an operon with a downstream gene, mreB. The Bs strain carrying the spoIIID delta erm or spoIIID83 mutation completely restored sporulation ability upon introduction of the spoIIID homologous gene from Bt. These results strongly suggest that the gene we have cloned is a Bt homolog of spoIIID.
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Affiliation(s)
- H Yoshisue
- Department of Agricultural Chemistry, Faculty of Agriculture, Kyoto University, Japan
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24
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Quail MA, Guest JR. Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli. Mol Microbiol 1995; 15:519-29. [PMID: 7783622 DOI: 10.1111/j.1365-2958.1995.tb02265.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The repressor of the pdhR-aceEF-lpd operon of Escherichia coli, PdhR, was amplified to 23% of total cell protein and purified to homogeneity by heparin-agarose and cation-exchange chromatography. The purified protein is a monomer (M(r) 29,300) which binds specifically to DNA fragments containing the pdh promoter (Ppdh) in the absence of pyruvate. The pdh operator was identified by DNase I footprinting as a region of hyphenated dyad symmetry, +11AATTGGTaagACCAATT+27, situated just downstream of the transcript start site. In vitro transcription from Ppdh was repressed > 1000-fold by PdhR and this repression was antagonized in a concentration-dependent manner by its co-effector, pyruvate. Studies on RNA polymerase binding at Ppdh showed that RNA polymerase protects the -44 to +21 region in the absence of PdhR, but no RNA polymerase binding or protection upstream of +9 could be detected in the presence of PdhR. It is concluded that PdhR represses transcription by binding to an operator site centred at +19 such that effective binding of RNA polymerase is prevented.
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Affiliation(s)
- M A Quail
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
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25
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Quail MA, Haydon DJ, Guest JR. The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. Mol Microbiol 1994; 12:95-104. [PMID: 8057842 DOI: 10.1111/j.1365-2958.1994.tb00998.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transcript mapping and studies with lacZ translational fusions have shown that the pdhR gene (formerly genA) is the proximal gene of the pdhR-aceE-aceF-lpd operon encoding the pyruvate dehydrogenase (PDH) complex of Escherichia coli. A pdhR-lpd read-through transcript (7.4 kb) initiating at the pyruvate-inducible pdh promoter, and a smaller lpd transcript (1.7 kb) initiating at the independent lpd promoter, were identified. Evidence showing that the pdhR gene product negatively regulates the synthesis of the PdhR protein and the PDH complex via the pdh promoter was obtained, with pyruvate (or a derivative) serving as the putative inducing coeffector. The partially purified PdhR protein was also found to specifically retard and protect DNA fragments containing the pdh promoter region. The pdh promoter was not strongly controlled by ArcA, FNR or CRP.
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Affiliation(s)
- M A Quail
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
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26
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Abstract
The gluconate (gnt) operon of Bacillus subtilis includes the gntR, gntK, gntP, and gntZ genes, respectively encoding the transcriptional repressor of the operon, gluconate kinase, the gluconate permease, and an unidentified open reading frame (Fujita and Fujita, 1987). We have compared the proteins encoded by the gnt operon of B.subtilis with published sequences and showed that (i) the gluconate repressor is homologous to several putative regulatory proteins in Escherichia coli, (ii) the gluconate kinase of B. subtilis is homologous to xylulose kinase, glycerol kinase and fucose kinase in E. coli (20-26% identity; 12-59 S.D.), (iii) the gluconate permease exhibits a C-terminal domain which is homologous to a hydrophobic protein encoded by an unidentified open reading frame (dsdAp) which precedes the dsdA gene of E. coli (39% identity; 19 S.D.), and (iv) the gntZ gene product is homologous to 6-phosphogluconate dehydrogenases of other bacteria and of animals (48-56%; 82-178 S.D.), thereby suggesting that the B. subtilis gntZ encodes 6-phosphogluconate dehydrogenase. Several conserved regions of the sequenced 6-phosphogluconate dehydrogenases can serve as signature patterns of this protein. Computer analyses have indicated that the previously reported sequences of the porcine and ovine 6-phosphogluconate dehydrogenases, as well as the hypothetical DsdAp protein, are probably erroneous. The probable reasons for the errors are reported along with the proposed revised sequences.
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Affiliation(s)
- A Reizer
- Department of Biology, University of California, San Diego, La Jolla 92093-0116
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27
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Fujita Y, Fujita T, Miwa Y. Evidence for posttranscriptional regulation of synthesis of the Bacillus subtilis Gnt repressor. FEBS Lett 1990; 267:71-4. [PMID: 2163901 DOI: 10.1016/0014-5793(90)80290-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcription of the Bacillus subtilis gnt operon results in a polycistronic mRNA that encodes from the 5' end the Gnt repressor, gluconate kinase and permease. The RNA is drastically induced through inactivation of the Gnt repressor by gluconate. The results of deletion analysis of the gnt promoter region upstream of the repressor gene indicated that no other promoter except the gnt promoter was present for expression of the gluconate kinase gene. In contrast to the synthesis of gluconate kinase and permease, which was markedly induced by gluconate, the results of a radioimmunoassay for the Gnt repressor indicated that synthesis of the Gnt repressor from the induced mRNA was posttranscriptionally repressed.
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Affiliation(s)
- Y Fujita
- Department of Biotechnology, Faculty of Engineering, Fukuyama University, Japan
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28
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29
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Fujita Y, Fujita T. Effect of mutations causing gluconate kinase or gluconate permease deficiency on expression of the Bacillus subtilis gnt operon. J Bacteriol 1989; 171:1751-4. [PMID: 2537826 PMCID: PMC209811 DOI: 10.1128/jb.171.3.1751-1754.1989] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The gluconate (gnt) operon contains genes for a repressor of the operon, gluconate kinase, and gluconate permease. A nonleaky kinase mutation (gntK4) induced the gnt operon constitutively through interaction of the repressor with an inducer of gluconate which had been endogenously formed and accumulated in the cell owing to the complete deficiency of the kinase even in the absence of gluconate in the medium. In contrast, a nonleaky permease mutation (gntP9) never induced the operon by gluconate likely because it cannot give rise to its inducing concentration in the cell even in the presence of gluconate in the medium.
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Affiliation(s)
- Y Fujita
- Department of Biotechnology, Faculty of Engineering, Fukuyama University, Japan
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30
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Ebbole DJ, Zalkin H. Interaction of a Putative Repressor Protein with an Extended Control Region of the Bacillus subtilis pur Operon. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)94101-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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