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Metabolomic and transcriptional profiling of oleuropein bioconversion into hydroxytyrosol during table olive fermentation by Lactiplantibacillus plantarum. Appl Environ Microbiol 2022; 88:e0201921. [PMID: 35170988 PMCID: PMC8939334 DOI: 10.1128/aem.02019-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
This study aims to elucidate the mechanisms responsible for the bioconversion of oleuropein into low-molecular-weight phenolic compounds in two selected Lactiplantibacillus plantarum strains, namely, C11C8 and F3.5, under stress brine conditions and at two different temperatures (16°C and 30°C). For this purpose, we adopted an experimental strategy that combined high-resolution mass spectrometry, in silico functional analysis of glycoside hydrolase family 1 (GH1)-encoding candidate genes, and gene expression studies. The oleuropein hydrolysis products and the underlying enzymatic steps were identified, and a novel putative bgl gene was detected, using seven strains belonging to the same species as controls. According to metabolomic analysis, a new intermediate compound (decarboxymethyl dialdehydic form of oleuropein aglycone) was revealed. In addition, strain C11C8 showed a decrease in the oleuropein content greater than that of the F3.5 strain (30% versus 15%) at a temperature of 16°C. The highest increase in hydroxytyrosol was depicted by strain C11C8 at a temperature of 30°C. PCR assays and sequencing analyses revealed that both strains possess bglH1, bglH2, and bglH3 genes. Furthermore, a reverse transcription-PCR (RT-PCR) assay showed that bglH3 is the only gene transcribed under all tested conditions, while bglH2 is switched off in strain C11C8 grown at cold temperatures, and no transcription was detected for the bglH1 gene. The bglH3 gene encodes a 6-phospho-β-glucosidase, suggesting how phospho-β-glucosidase activity could belong to the overall metabolic strategy undertaken by L. plantarum to survive in an environment poor in free sugars, like table olives. IMPORTANCE In the present study, a new candidate gene, bglH3, responsible for the β-glucosidase-positive phenotype in L. plantarum was detected, providing the basis for the future marker-assisted selection of L. plantarum starter strains with a β-glucosidase-positive phenotype. Furthermore, the ability of selected strains to hydrolyze oleuropein at low temperatures is important for application as starter cultures on an industrial scale.
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Zhang Z, Zhou K, Tran D, Saier M. Insertion Sequence (IS) Element-Mediated Activating Mutations of the Cryptic Aromatic β-Glucoside Utilization ( BglGFB) Operon Are Promoted by the Anti-Terminator Protein (BglG) in Escherichia coli. Int J Mol Sci 2022; 23:ijms23031505. [PMID: 35163427 PMCID: PMC8836124 DOI: 10.3390/ijms23031505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 01/24/2023] Open
Abstract
The cryptic β-glucoside GFB (bglGFB) operon in Escherichia coli (E. coli) can be activated by mutations arising under starvation conditions in the presence of an aromatic β-glucoside. This may involve the insertion of an insertion sequence (IS) element into a "stress-induced DNA duplex destabilization" (SIDD) region upstream of the operon promoter, although other types of mutations can also activate the bgl operon. Here, we show that increased expression of the bglG gene, encoding a well-characterized transcriptional antiterminator, dramatically increases the frequency of both IS-mediated and IS-independent Bgl+ mutations occurring on salicin- and arbutin-containing agar plates. Both mutation rates increased with increasing levels of bglG expression but IS-mediated mutations were more prevalent at lower BglG levels. Mutations depended on the presence of both BglG and an aromatic β-glucoside, and bglG expression did not influence IS insertion in other IS-activated operons tested. The N-terminal mRNA-binding domain of BglG was essential for mutational activation, and alteration of BglG's binding site in the mRNA nearly abolished Bgl+ mutant appearances. Increased bglG expression promoted residual bgl operon expression in parallel with the increases in mutation rates. Possible mechanisms are proposed explaining how BglG enhances the frequencies of bgl operon activating mutations.
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Amster-Choder O. The bgl sensory system: a transmembrane signaling pathway controlling transcriptional antitermination. Curr Opin Microbiol 2005; 8:127-34. [PMID: 15802242 DOI: 10.1016/j.mib.2005.02.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bgl system represents a family of sensory systems composed of membrane-bound sugar-sensors and transcriptional antiterminators, which regulate expression of genes involved in sugar utilization in response to the presence of the corresponding sugar in the growth medium. The BglF sensor catalyzes different activities depending on its stimulation state: in its non-stimulated state, it phosphorylates the BglG transcriptional regulator, thus inactivating it; in the presence of the stimulating sugar, it transports the sugar and phosphorylates it and also activates BglG by dephosphorylation, leading to bgl operon expression. The sugar stimulates BglF by inducing a change in its membrane topology. BglG exists in several conformations: a dimer, which is active, and compact and non-compact monomers, which are inactive. BglF modulates the transition of BglG from one conformation to another, depending on sugar availability. The two Bgl proteins form a pre-complex at the membrane that dissociates upon stimulation, enabling BglG to exert its effect on transcription.
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Affiliation(s)
- Orna Amster-Choder
- Department of Molecular Biology, The Hebrew University, Hadassah Medical School, P.O.Box 12272, Jerusalem 91120, Israel.
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Ben-Zeev E, Fux L, Amster-Choder O, Eisenstein M. Experimental and Computational Characterization of the Dimerization of the PTS-regulation Domains of BglG from Escherichia coli. J Mol Biol 2005; 347:693-706. [PMID: 15769463 DOI: 10.1016/j.jmb.2005.01.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Revised: 01/24/2005] [Accepted: 01/27/2005] [Indexed: 11/18/2022]
Abstract
BglG and LicT are transcriptional antiterminators from Escherichia coli and Bacillus subtilis, respectively, that control the expression of genes and operons involved in transport and catabolism of carbohydrates. Both proteins contain a duplicate conserved domain, the PTS-regulation domain (PRD), and they are regulated by phosphorylation on specific, highly conserved histidine residues located in the PRDs. However, despite their similar function and the high sequence identity, experimental evidence implies different modes of regulation. Thus, BglG must be de-phosphorylated on PRD2 in order to form active dimers, whereas activation of LicT requires de-phosphorylation on PRD1 and phosphorylation on PRD2. Here we address two goals. First, we test in vivo and in silico the effect of point mutations in the PRDs of BglG on the PRD-PRD dimerization. Second, we explore computationally the effect of histidine phosphorylation on PRD dimerization in BglG and LicT. We find excellent correspondence between the experimental and computational measures of the influence of mutations on PRD dimerization in BglG. This establishes that the geometric-electrostatic complementarity scores computed with the program MolFit provide a good measure of the effects of mutations in this system. In addition, it indicates that the dimerization mode of the separately expressed PRDs of BglG is similar to the dimers formed by activated LicT. The computations also show that phosphorylation of the histidine residues in PRD1 of either BglG or LicT leads to a strong electrostatic repulsion. Conversely, the phosphorylation of one histidine residue in PRD2 of LicT leads to improved electrostatic complementarity at the PRD2-PRD2 interface, whereas the corresponding phosphorylation in BglG has negligible contribution. This different conduct may be attributed to a single replacement in the sequence of PRD2 in BglG compared to LicT, Ala262 versus Asp261, respectively.
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Affiliation(s)
- Efrat Ben-Zeev
- Department of Chemical Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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5
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Fux L, Nussbaum-Shochat A, Lopian L, Amster-Choder O. Modulation of monomer conformation of the BglG transcriptional antiterminator from Escherichia coli. J Bacteriol 2004; 186:6775-81. [PMID: 15466029 PMCID: PMC522206 DOI: 10.1128/jb.186.20.6775-6781.2004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2004] [Accepted: 07/17/2004] [Indexed: 11/20/2022] Open
Abstract
The BglG protein positively regulates expression of the bgl operon in Escherichia coli by binding as a dimer to the bgl transcript and preventing premature termination of transcription in the presence of beta-glucosides. BglG activity is negatively controlled by BglF, the beta-glucoside phosphotransferase, which reversibly phosphorylates BglG according to beta-glucoside availability, thus modulating its dimeric state. BglG consists of an RNA-binding domain and two homologous domains, PRD1 and PRD2. Based on structural studies of a BglG homologue, the two PRDs fold similarly, and the interactions within the dimer are PRD1-PRD1 and PRD2-PRD2. We have recently shown that the affinity between PRD1 and PRD2 of BglG is high, and a fraction of the BglG monomers folds in the cell into a compact conformation, in which PRD1 and PRD2 are in close proximity. We show here that both BglG forms, the compact and noncompact, bind to the active site-containing domain of BglF, IIB(bgl), in vitro. The interaction of BglG with IIB(bgl) or BglF is mediated by PRD2. Both BglG forms are detected as phosphorylated proteins after in vitro phosphorylation with IIB(bgl) and are dephosphorylated by BglF in vitro in the presence of beta-glucosides. Nevertheless, genetic evidence indicates that the interaction of IIB(bgl) and BglF with the compact form is seemingly less favorable. Using in vivo cross-linking, we show that BglF enhances folding of BglG into a compact conformation, whereas the addition of beta-glucosides reduces the amount of this form. Based on these results we suggest a model for the modulation of BglG conformation and activity by BglF.
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Affiliation(s)
- Liat Fux
- Department of Molecular Biology, The Hebrew University-Hadassah Medical School, P. O. Box 12272, Jerusalem 91120, Israel
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6
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Fux L, Nussbaum-Shochat A, Amster-Choder O. Interactions between the PTS regulation domains of the BglG transcriptional antiterminator from Escherichia coli. J Biol Chem 2003; 278:46203-9. [PMID: 12923168 DOI: 10.1074/jbc.m306506200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The E. coli BglG protein inhibits transcription termination within the bgl operon in the presence of beta-glucosides. BglG represents a family of transcriptional antiterminators that bind to RNA sequences, which partially overlap rho-independent terminators, and prevent termination by stabilizing an alternative structure of the transcript. The activity of BglG is determined by its dimeric state, which is modulated by reversible phosphorylation catalyzed by BglF, a PTS permease. Only the non-phosphorylated BglG dimer binds to RNA and allows read-through of transcription. BglG is composed of three domains: an RNA-binding domain followed by two domains, PRD1 and PRD2 (PTS regulation domains), which are similar in their sequence and folding. Based on the three-dimensional structure of dimeric LicT, a BglG homologue from Bacillus subtilis, the interactions within the dimer are PRD1-PRD1 and PRD2-PRD2. We have shown before that PRD2 mediates homodimerization very efficiently. Using genetic systems and in vitro techniques that assay and characterize protein-protein interactions, we show here that the PRD1 dimerizes very slowly, but once it does, the homodimers are stable. These results support our model that formation of BglG dimers initiates with PRD2 dimerization followed by zipping up of two BglG monomers to create the active RNA-binding domain. Moreover, our results demonstrate that PRD1 and PRD2 heterodimerize efficiently in vitro and in vivo. The affinity among the PRDs is in the following order: PRD2-PRD2 > PRD1-PRD2 > PRD1-PRD1. The interaction between PRD1 and PRD2 offers an explanation for the requirement of conserved residues in PRD1 for the phosphorylation of PRD2 by BglF.
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Affiliation(s)
- Liat Fux
- Department of Molecular Biology, The Hebrew University, Hadassah Medical School, P. O. Box 12272, Jerusalem 91120, Israel
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Görke B. Regulation of the Escherichia coli antiterminator protein BglG by phosphorylation at multiple sites and evidence for transfer of phosphoryl groups between monomers. J Biol Chem 2003; 278:46219-29. [PMID: 12963714 DOI: 10.1074/jbc.m308002200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activity of antiterminator protein BglG regulating the beta-glucoside operon in Escherichia coli is controlled by the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) in a dual manner. It requires HPr phosphorylation to be active, whereas phosphorylation by the beta-glucoside-specific transport protein EIIBgl inhibits its activity. BglG and its relatives carry two PTS regulation domains (PRD1 and PRD2), each containing two conserved histidines. For BglG, histidine 208 in PRD2 was reported to be the negative phosphorylation site. In contrast, other antiterminators of this family are negatively regulated by phosphorylation of the first histidine in PRD1, and presumably activated by phosphorylation of the histidines in PRD2. In this work, a screen for mutant BglG proteins that escape repression by EIIBgl yielded exchanges of nine residues within PRD1, including conserved histidines His-101 and His-160, and C-terminally truncated proteins. Genetic and phosphorylation analyses indicate that His-101 in PRD1 is phosphorylated by EIIBgl and that His-160 contributes to negative regulation. His-208 in PRD2 is essential for BglG activity, suggesting that it is phosphorylated by HPr. Surprisingly, phosphorylation by HPr is not fully abolished by exchanges of His-208. However, phosphorylation by HPr is inhibited by exchanges in PRD1 and the phosphorylation of these mutants is restored in the presence of wild-type BglG. These results suggest that the activating phosphoryl group is transiently donated from HPr to PRD1 and subsequently transferred to His-208 of a second BglG monomer. The active His-208-phosphorylated BglG dimer can subsequently be inhibited in its activity by EIIBgl-catalyzed phosphorylation at His-101.
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Affiliation(s)
- Boris Görke
- Institut für Biologie III, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany.
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8
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Enz S, Brand H, Orellana C, Mahren S, Braun V. Sites of interaction between the FecA and FecR signal transduction proteins of ferric citrate transport in Escherichia coli K-12. J Bacteriol 2003; 185:3745-52. [PMID: 12813067 PMCID: PMC161571 DOI: 10.1128/jb.185.13.3745-3752.2003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of the fecABCDE ferric citrate transport genes of Escherichia coli K-12 is initiated by a signaling cascade from the cell surface into the cytoplasm. FecR receives the signal in the periplasm from the outer membrane protein FecA loaded with ferric citrate, transmits the signal across the cytoplasmic membrane, and converts FecI in the cytoplasm to an active sigma factor. In this study, it was shown through the use of a bacterial two-hybrid system that, in the periplasm, the C-terminal FecR(237-317) fragment interacts with the N-terminal FecA(1-79) fragment. In the same C-terminal region, amino acid residues important for the interaction of FecR with FecA were identified by random and site-directed mutagenesis. They were preferentially located in and around a leucine motif (residues 247 to 268) which was found to be highly conserved in FecR-like proteins. The degree of residual binding of FecR mutant proteins to FecA was correlated with the degree of transcription initiation in response to ferric citrate in the culture medium. Three randomly generated inactive FecR mutants, FecR(L254E), FecR(L269G), and FecR(F284L), were suppressed to different degrees by the mutants FecA(G39R) and FecR(D43E). One FecR mutant, FecR (D138E, V197A), induced fecA promoter-directed transcription constitutively in the absence of ferric citrate and bound more strongly than wild-type FecR to FecA. The data showed that FecR interacts in the periplasm with FecA to confer ferric citrate-induced transcription of the fec transport genes and identified sites in FecR and FecA that are important for signal transduction.
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Affiliation(s)
- Sabine Enz
- Mikrobiologie/Membranphysiologie, Universität Tübingen, D-72076 Tübingen, Germany
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9
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Glass PJ, Zeng CQ, Estes MK. Two nonoverlapping domains on the Norwalk virus open reading frame 3 (ORF3) protein are involved in the formation of the phosphorylated 35K protein and in ORF3-capsid protein interactions. J Virol 2003; 77:3569-77. [PMID: 12610132 PMCID: PMC149496 DOI: 10.1128/jvi.77.6.3569-3577.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Expression of the Norwalk virus open reading frame 3 (ORF3) in Spodoptera frugiperda (Sf9) cells yields two major forms, the predicted 23,000-molecular-weight (23K) form and a larger 35K form. The 23K form is able to interact with the ORF2 capsid protein and be incorporated into virus-like particles. In this paper, we provide mass spectrometry evidence that both the 23K and 35K forms are composed only of the ORF3 protein. Two-dimensional gel electrophoresis and phosphatase treatment showed that the 35K form results solely from phosphorylation and that the 35K band is composed of several different phosphorylated forms with distinct isoelectric points. Furthermore, we analyzed deletion and point mutants of the ORF3 protein. Mutants that lacked the C-terminal 33 amino acids (ORF3(1-179), ORF3(1-152), and ORF3(1-107)) no longer produced the 35K form. An N-terminal truncation mutant (ORF3(51-212)) and a site-directed mutant (ORF3(T201V)) were capable of producing the larger form, which was converted to the smaller form by treatment with protein phosphatase. These data suggest that the region between amino acids 180 and 212 is phosphorylated, and mass spectrometry showed that amino acids Arg196 to Arg211 are not phosphorylated; thus, phosphorylation of the serine-threonine-rich region from Thr181 to Ser193 must be involved in the generation of the 35K form. Studies of the interaction between the ORF2 protein and full-length and mutated ORF3 proteins showed that the full-length ORF3 protein (ORF3(FL)), ORF3(1-179), ORF3(1-152), and ORF3(51-212) interacted with the ORF2 protein, while an ORF3(1-107) protein did not. These results indicate that the region of the ORF3 protein between amino acids 108 and 152 is responsible for interaction with the ORF2 protein.
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Affiliation(s)
- Pamela J Glass
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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10
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Greenberg DB, Stülke J, Saier MH. Domain analysis of transcriptional regulators bearing PTS regulatory domains. Res Microbiol 2002; 153:519-26. [PMID: 12437213 DOI: 10.1016/s0923-2508(02)01362-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Multidomain transcriptional activators and antiterminators that include PTS regulatory domains (PRDs) were subjected to sequence analyses. All of these transcriptional regulators exhibit one or more N-terminal nucleic acid binding site(s) and two PRD regions. Additionally, we show that the activators contain C-terminal PTS IIB and IIA domains with fully conserved phosphorylation sites (cysteine and histidine, respectively). One activator, LevR has a different domain order than all other activators with a truncated IIA domain preceding (rather than following) the IIB domain, and it has a C-terminal PRD, rather than two adjacent PRDs. Our analyses suggest that the activators and antiterminators arose early, and that domain shuffling either within or between proteins has occurred rarely. The results allow us to propose an evolutionary pathway for the appearance of these transcription factors and to suggest functional significance for these domains and specific residues within them.
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Affiliation(s)
- David B Greenberg
- Division of Biology, University of California at San Diego, La Jolla 92093-0116, USA
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11
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Abstract
In this review, we describe a variety of mechanisms that bacteria use to regulate transcription elongation in order to control gene expression in response to changes in their environment. Together, these mechanisms are known as attenuation and antitermination, and both involve controlling the formation of a transcription terminator structure in the RNA transcript prior to a structural gene or operon. We examine attenuation and antitermination from the point of view of the different biomolecules that are used to influence the RNA structure. Attenuation of many amino acid biosynthetic operons, particularly in enteric bacteria, is controlled by ribosomes translating leader peptides. RNA-binding proteins regulate attenuation, particularly in gram-positive bacteria such as Bacillus subtilis. Transfer RNA is also used to bind to leader RNAs and influence transcription antitermination in a large number of amino acyl tRNA synthetase genes and several biosynthetic genes in gram-positive bacteria. Finally, antisense RNA is involved in mediating transcription attenuation to control copy number of several plasmids.
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Affiliation(s)
- Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA.
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12
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Beloin C, McKenna S, Dorman CJ. Molecular dissection of VirB, a key regulator of the virulence cascade of Shigella flexneri. J Biol Chem 2002; 277:15333-44. [PMID: 11850420 DOI: 10.1074/jbc.m111429200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The VirB protein is a key regulator of virulence gene expression in the facultative enteroinvasive pathogen Shigella flexneri. While genetic evidence has shown that it is required for activation of transcription of virulence genes located on a 230-kb plasmid in this bacterium, hitherto, evidence that VirB is a DNA-binding protein has been lacking. Although VirB shows extensive homology to proteins involved in plasmid partitioning, it does not resemble any known conventional transcription factor. Here we show for the first time that VirB binds to the promoter regions of the virulence genes in vivo. We also show that VirB forms dimeric and higher oligomeric structures both in vivo and in vitro and that this property is independent of DNA binding. The oligomerization activity of VirB is distributed over two domains: a leucine zipper-like motif and a carboxyl-terminal domain likely to form triple coiled structures. VirB possesses a helix-turn-helix motif, which is required for DNA binding. The amino-terminal domain of the protein is also required for DNA binding and virulence gene activation. The possibility that VirB requires a co-factor for specific interaction with target promoters in vivo is discussed.
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Affiliation(s)
- Christophe Beloin
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Republic of Ireland
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Gosalbes MAJ, Esteban CD, Pérez-Martı Nez G. In vivo effect of mutations in the antiterminator LacT in Lactobacillus casei. MICROBIOLOGY (READING, ENGLAND) 2002; 148:695-702. [PMID: 11882703 DOI: 10.1099/00221287-148-3-695] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The antiterminator LacT regulates the expression of the lactose operon in Lactobacillus casei and its activity is controlled by EII(Lac) and common PTS elements. LacT shows the two conserved domains (PRD-I and PRD-II) characteristic of the BglG antiterminator family that are implicated in the regulation of their activity, possibly by phosphorylation of conserved histidines. By site-directed mutagenesis of LacT, four histidines (His-101, His-159 in PRD-I and His-210, His-273 in PRD-II) were replaced by alanine or aspartate, mimicking non-phosphorylated and phosphorylated forms, respectively. These constructions were used to complement DeltalacT and DeltaccpA mutants. L. casei strains (DeltalacT) carrying the replacement of His-101 or His-159 by Ala showed phospho-beta-galactosidase activity in absence of the inducer (lactose), indicating that these amino acids, located in PRD-I, are essential for EII-dependent induction of the lac operon, possibly by dephosphorylation. Interestingly, these mutations rendered LacT thermosensitive. Moreover, expression of H210A and H273A (PRD-II) mutations in L. casei DeltaccpA showed that these two histidyl residues could have a role in LacT-dependent carbon catabolite repression (CCR) of this system. Overexpression of LacT in a ccpA background rendered the lac operon insensitive to CCR, but it was still sensitive to lactose induction. This suggests that the transfer of phosphate groups from PTS elements, which controls these two regulatory processes (CCR and substrate induction), could have different affinity for PRD-I and PRD-II histidines.
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Affiliation(s)
- Marı A J Gosalbes
- Departamento de Biotecnologı́a, Instituto de Agroquı́mica y Tecnologı́a de Alimentos (CSIC), Polı́gono de la Coma s/n, Apartado de correos (PO Box) 73, 46100-Burjassot, Valencia, Spain1
| | - Carlos D Esteban
- Departamento de Biotecnologı́a, Instituto de Agroquı́mica y Tecnologı́a de Alimentos (CSIC), Polı́gono de la Coma s/n, Apartado de correos (PO Box) 73, 46100-Burjassot, Valencia, Spain1
| | - Gaspar Pérez-Martı Nez
- Departamento de Biotecnologı́a, Instituto de Agroquı́mica y Tecnologı́a de Alimentos (CSIC), Polı́gono de la Coma s/n, Apartado de correos (PO Box) 73, 46100-Burjassot, Valencia, Spain1
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14
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Declerck N, Dutartre H, Receveur V, Dubois V, Royer C, Aymerich S, van Tilbeurgh H. Dimer stabilization upon activation of the transcriptional antiterminator LicT. J Mol Biol 2001; 314:671-81. [PMID: 11733988 DOI: 10.1006/jmbi.2001.5185] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
LicT belongs to the BglG/SacY family of transcriptional antiterminators that induce the expression of sugar metabolizing operons in Gram positive and Gram negative bacteria. These proteins contain a N-terminal RNA-binding domain and a regulatory domain called PRD which is phosphorylated on conserved histidine residues by components of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). Although it is now well established that phosphorylation of PRD-containing transcriptional regulators tunes their functional response, the molecular and structural basis of the regulation mechanism remain largely unknown.A constitutively active LicT variant has been obtained by introducing aspartic acid in replacement of His207 and His269, the two phosphorylatable residues of the PRD2 regulatory sub-domain. Here, the functional and structural consequences of these activating mutations have been evaluated in vitro using various techniques including surface plasmon resonance, limited proteolysis, analytical centrifugation and X-ray scattering. Comparison with the native, unphosphorylated form shows that the activating mutations enhance the RNA-binding activity and induce tertiary and quaternary structural changes. Both mutant and native LicT form dimers in solution but the native dimer exhibits a less stable and more open conformation than the activated mutant form. Examination of the recently determined crystal structure of mutant LicT regulatory domain suggests that dimer stabilization is accomplished through salt-bridge formation at the PRD2:PRD2 interface, resulting in domain motion and dimer closure propagating the stabilizing effect from the protein C-terminal end to the N-terminal effector domain. These results suggest that LicT activation arises from a conformational switch inducing long range rearrangement of the dimer interaction surface, rather than from an oligomerization switch converting an inactive monomer into an active dimer.
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Affiliation(s)
- N Declerck
- Génétique Moléculaire et Cellulaire, INRA-UMR216 CNRS-URA1925, and INAPG, Thiverval-Grignon, F-78850, France.
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15
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van Tilbeurgh H, Le Coq D, Declerck N. Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator. EMBO J 2001; 20:3789-99. [PMID: 11447120 PMCID: PMC125546 DOI: 10.1093/emboj/20.14.3789] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transcriptional antiterminator protein LicT regulates the expression of Bacillus subtilis operons involved in beta-glucoside metabolism. It belongs to a newly characterized family of bacterial regulators whose activity is controlled by the phosphoenolpyruvate:sugar phosphotransferase system (PTS). LicT contains an N-terminal RNA-binding domain (56 residues), and a PTS regulation domain (PRD, 221 residues) that is phosphorylated on conserved histidines in response to substrate availability. Replacement of both His207 and His269 with a negatively charged residue (aspartic acid) led to a highly active LicT variant that no longer responds to either induction or catabolite repression signals from the PTS. In contrast to wild type, the activated mutant form of the LicT regulatory domain crystallized easily and provided the first structure of a PRD, determined at 1.55 A resolution. The structure is a homodimer, each monomer containing two analogous alpha-helical domains. The phosphorylation sites are totally buried at the dimer interface and hence inaccessible to phosphorylating partners. The structure suggests important tertiary and quaternary rearrangements upon LicT activation, which could be communicated from the protein C-terminal end up to the RNA-binding domain.
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Affiliation(s)
- Herman van Tilbeurgh
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 du CNRS, Université d’Aix-Marseille, I et II, ESIL-GBMA, 163 Avenue de Luminy Case 925, 13288 Marseille Cedex 9 and Laboratoire de Génétique des Microorganismes, INRA-CNRS, URA1925, 78850 Thiverval-Grignon, France Present address: Centre de Biochimie Structurale, UMR 9955 du CNRS, Université de Montpellier I, INSERM U414, 29 rue de Navacelles, 34090 Montpellier, France Corresponding author e-mail:
| | - Dominique Le Coq
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 du CNRS, Université d’Aix-Marseille, I et II, ESIL-GBMA, 163 Avenue de Luminy Case 925, 13288 Marseille Cedex 9 and Laboratoire de Génétique des Microorganismes, INRA-CNRS, URA1925, 78850 Thiverval-Grignon, France Present address: Centre de Biochimie Structurale, UMR 9955 du CNRS, Université de Montpellier I, INSERM U414, 29 rue de Navacelles, 34090 Montpellier, France Corresponding author e-mail:
| | - Nathalie Declerck
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 du CNRS, Université d’Aix-Marseille, I et II, ESIL-GBMA, 163 Avenue de Luminy Case 925, 13288 Marseille Cedex 9 and Laboratoire de Génétique des Microorganismes, INRA-CNRS, URA1925, 78850 Thiverval-Grignon, France Present address: Centre de Biochimie Structurale, UMR 9955 du CNRS, Université de Montpellier I, INSERM U414, 29 rue de Navacelles, 34090 Montpellier, France Corresponding author e-mail:
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Bae T, Dunny GM. Dominant-negative mutants of prgX: evidence for a role for PrgX dimerization in negative regulation of pheromone-inducible conjugation. Mol Microbiol 2001; 39:1307-20. [PMID: 11251846 DOI: 10.1111/j.1365-2958.2001.02319.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PrgX negatively regulates prgQ transcriptional readthrough in the pheromone-inducible enterococcal conjugative plasmid pCF10. We isolated and characterized 13 dominant-negative prgX mutants, all of which mapped in either the N- or the C-terminus of PrgX. In all mutants, the in vivo level of Qa RNA, an antisense RNA to prgQ RNA, was greatly reduced. When oligomerization of PrgX was tested with a phage lambda cI repressor fusion system, the oligomerization domain was found to be between amino acid residues 78 and 280. When histidine-tagged PrgX (His-PrgX) was purified by nickel column chromatography from a strain also expressing PrgX, PrgX was co-purified with His-PrgX. Although PrgX was expressed at a much higher level than His-PrgX, an approximately equal amount of PrgX was co-purified. Pheromone induction greatly decreased the co-purification of PrgX. Based on these data, we propose that both the N- and the C-terminal domains of PrgX are required for PrgX positive autoregulation and for the repression of prgQ transcription readthrough. In vivo, PrgX exists as a dimer, and dimerization is mediated by the central region of PrgX.
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Affiliation(s)
- T Bae
- Department of Microbiology, 1460 Mayo Memorial Bldg., University of Minnesota, Minneapolis 55455, USA
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Abstract
We present a summary of recent progress in understanding Escherichia coli K-12 gene and protein functions. New information has come both from classical biological experimentation and from using the analytical tools of functional genomics. The content of the E. coli genome can clearly be seen to contain elements acquired by horizontal transfer. Nevertheless, there is probably a large, stable core of >3500 genes that are shared among all E. coli strains. The gene-enzyme relationship is examined, and, in many cases, it exhibits complexity beyond a simple one-to-one relationship. Also, the E. coli genome can now be seen to contain many multiple enzymes that carry out the same or closely similar reactions. Some are similar in sequence and may share common ancestry; some are not. We discuss the concept of a minimal genome as being variable among organisms and obligatorily linked to their life styles and defined environmental conditions. We also address classification of functions of gene products and avenues of insight into the history of protein evolution.
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Affiliation(s)
- M Riley
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA. ,
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Kotrba P, Inui M, Yukawa H. Bacterial phosphotransferase system (PTS) in carbohydrate uptake and control of carbon metabolism. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80308-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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19
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Knezevic I, Bachem S, Sickmann A, Meyer HE, Stülke J, Hengstenberg W. Regulation of the glucose-specific phosphotransferase system (PTS) of Staphylococcus carnosus by the antiterminator protein GlcT. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 9):2333-2342. [PMID: 10974121 DOI: 10.1099/00221287-146-9-2333] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ptsG operon of Staphylococcus carnosus consists of two adjacent genes, glcA and glcB, encoding glucose- and glucoside-specific enzymes II, respectively, the sugar permeases of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The expression of the ptsG operon is glucose-inducible. Putative RAT (ribonucleic antiterminator) and terminator sequences localized in the promoter region of glcA suggest regulation via antitermination. The glcT gene was cloned and the putative antiterminator protein GlcT was purified. Activity of this protein was demonstrated in vivo in Escherichia coli and Bacillus subtilis. In vitro studies led to the assumption that phosphoenolpyruvate-dependent phosphorylation of residue His105 via the general PTS components enzyme I and HPr facilitates dimerization of GlcT and consequently activation. Because of the high similarity of the two ptsG-RAT sequences of B. subtilis and S. carnosus, in vivo studies were performed in B. subtilis. These indicated that GlcT of S. carnosus is able to recognize ptsG-RAT sequences of B. subtilis and to cause antitermination. The specific interaction between B. subtilis ptsG-RAT and S. carnosus GlcT demonstrated by surface plasmon resonance suggests that only the dimer of GlcT binds to the RAT sequence. HPr-dependent phosphorylation of GlcT facilitates dimer formation and may be a control device for the proper function of the general PTS components enzyme I and HPr necessary for glucose uptake and phosphorylation by the corresponding enzyme II.
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Affiliation(s)
- Igor Knezevic
- AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, ND 06/744, Universitätsstr. 150, D-44780 Bochum, Germany1
| | - Steffi Bachem
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik der Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany2
| | - Albert Sickmann
- Institut für Immunologie, Abteilung Proteinstrukturlabor, MA 2/143, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany3
| | - Helmut E Meyer
- Institut für Immunologie, Abteilung Proteinstrukturlabor, MA 2/143, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany3
| | - Jörg Stülke
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik der Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany2
| | - Wolfgang Hengstenberg
- AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, ND 06/744, Universitätsstr. 150, D-44780 Bochum, Germany1
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20
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Marasco R, Salatiello I, De Felice M, Sacco M. A physical and functional analysis of the newly-identified bglGPT operon of Lactobacillus plantarum. FEMS Microbiol Lett 2000; 186:269-73. [PMID: 10802183 DOI: 10.1111/j.1574-6968.2000.tb09116.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A newly-identified bglGPT operon of Lactobacillus plantarum was isolated and expressed in Escherichia coli. The sequence analysis of the cloned DNA fragment showed three open reading frames encoding (i) a 237-amino acid protein (BglG), (ii) a 577-amino acid protein (BglP) and (iii) a 486-amino acid protein (BglT). BglG, BglP and BglT were shown to be homologous to the BglG family of transcriptional antiterminators, to permeases of the phosphoenolpyruvate-dependent phosphotransferase system and to beta-glucosidases, respectively. Complementation of E. coli mutant strains showed that BglP and BglT are a permease and a beta-glucosidase active on the beta-glucosides, 5-bromo-4-chloro-3-indolyl-beta-D-glucopyranoside and p-nitrophenyl-beta-D-glucoside, respectively. BglG was also shown to promote expression of a bglG-lacZ gene fusion in an E. coli bglG(-) background. A ribonucleic antiterminator sequence, the antiterminator-responsive cis-element and a 'catabolite responsive element', were found downstream of the transcriptional start point. Transcription of the operon was repressed 10-fold in L. plantarum cells grown on glucose as compared to ribose.
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Affiliation(s)
- R Marasco
- Facoltà di Scienze MM, FF e NN, Università degli Studi del Sannio, via Caio Ponzio Telesino 11, 82100, Benevento, Italy
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Abstract
Transcription termination is a dynamic process and is subject to control at a number of levels. New information about the molecular mechanisms of transcription elongation and termination, as well as new insights into protein-RNA interactions, are providing a framework for increased understanding of the molecular details of transcription termination control.
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Affiliation(s)
- T M Henkin
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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22
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Langbein I, Bachem S, Stülke J. Specific interaction of the RNA-binding domain of the bacillus subtilis transcriptional antiterminator GlcT with its RNA target, RAT. J Mol Biol 1999; 293:795-805. [PMID: 10543968 DOI: 10.1006/jmbi.1999.3176] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expression of the Bacillus subtilis ptsGHI operon is controlled by transcriptional antitermination mediated by the antiterminator protein GlcT. The antiterminator is inactivated in the absence of glucose, presumably by phosphorylation. A conditional terminator in the ptsG mRNA leader region has been identified. Mutations in this terminator resulted in constitutive expression of the operon. The terminator is overlapped by an inverted repeat (called ribonucleic-antiterminator, RAT) which is thought to form a stem-loop structure upon binding of the antiterminator protein GlcT. The N-terminal 60 amino acid residues of GlcT are able to bind to the RAT and prevent transcriptional termination in vivo. Sequence-specific interaction between the RNA-binding domain and the RAT was demonstrated by surface plasmon resonance analysis. Mutations affecting the RNA-binding domain were isolated and will be discussed with respect to their consequences for dimerization and RNA binding.
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Affiliation(s)
- I Langbein
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie Biochemie und Genetik der Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, Erlangen, D-91058, Germany
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Caguiat JJ, Watson AL, Summers AO. Cd(II)-responsive and constitutive mutants implicate a novel domain in MerR. J Bacteriol 1999; 181:3462-71. [PMID: 10348859 PMCID: PMC93814 DOI: 10.1128/jb.181.11.3462-3471.1999] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of the Tn21 mercury resistance (mer) operon is controlled by a metal-sensing repressor-activator, MerR. When present, MerR always binds to the same position on the DNA (the operator merO), repressing transcription of the structural genes merTPCAD in the absence of Hg(II) and inducing their transcription in the presence of Hg(II). Although it has two potential binding sites, the purified MerR homodimer binds only one Hg(II) ion, employing Cys82 from one monomer and Cys117 and Cys126 from the other. When MerR binds Hg(II), it changes allosterically and also distorts the merO DNA to facilitate transcriptional initiation by sigma70 RNA polymerase. Wild-type MerR is highly specific for Hg(II) and is 100- and 1, 000-fold less responsive to the chemically related group 12 metals, Cd(II) and Zn(II), respectively. We sought merR mutants that respond to Cd(II) and obtained 11 Cd(II)-responsive and 5 constitutive mutants. The Cd(II)-responsive mutants, most of which had only single-residue replacements, were also repression deficient and still Hg(II) responsive but, like the wild type, were completely unresponsive to Zn(II). None of the Cd(II)-responsive mutations occurred in the DNA binding domain or replaced any of the key Cys residues. Five Cd(II)-responsive single mutations lie in the antiparallel coiled-coil domain between Cys82 and Cys117 which constitutes the dimer interface. These mutations identify 10 new positions whose alteration significantly affect MerR's metal responsiveness or its repressor function. They give rise to specific predictions for how MerR distinguishes group 12 metals, and they refine our model of the novel domain structure of MerR. Secondary-structure predictions suggest that certain elements of this model also apply to other MerR family regulators.
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Affiliation(s)
- J J Caguiat
- Department of Microbiology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2605, USA
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