The arginine repressor of Escherichia coli K-12 makes direct contacts to minor and major groove determinants of the operators 1 1Edited by M. Yaniv

Wang, Haifeng; Glansdorff, Nicolas; Charlier, Daniël

doi:10.1006/jmbi.1998.1632

Cited by 61 publications

(53 citation statements)

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“…An earlier study on ArgR/ ARG box interaction has pointed to the importance of a T base at the seventh position (T7), with minor groove occupancy, which is highly conserved in DNA sequences of all ARG boxes, mediating contact with ArgR (36). Furthermore, in all ARG box sequences there is absence of a guanine base at the T7 position (36). Another study has shown that replacement of T7 with G led to loss of ArgR repression at the promoter of hisJ (37).…”

Section: Resultsmentioning

confidence: 99%

Distinct Paths for Basic Amino Acid Export in Escherichia coli: YbjE (LysO) Mediates Export of l -Lysine

Pathania

Sardesai

2015

J Bacteriol

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In Escherichia coli, argO encodes an exporter for L-arginine (Arg) and its toxic analogue canavanine (CAN), and its transcriptional activation and repression, by Arg and L-lysine (Lys), respectively, are mediated by the regulator ArgP. Accordingly argO and argP mutants are CAN supersensitive (CAN ss IMPORTANCEThis work ascribes a lysine export function to the product of the ybjE gene of Escherichia coli, leading to a physiological scenario wherein two proteins, ArgO and YbjE, perform the task of separately exporting arginine and lysine, respectively, which is distinct from that seen for Corynebacterium glutamicum, where the ortholog of ArgO, LysE, mediates export of both arginine and lysine. Repression of argO transcription by lysine is thought to effect this separation. Accordingly, ArgO mediates lysine export when repression of its transcription by lysine is bypassed. Repression of ybjE transcription by arginine via the ArgR repressor, together with the lysine repression of argO effected by ArgP, is indicative of a mechanism of maintenance of arginine/lysine balance in E. coli. Bacteria possess membrane exporters for a variety of compounds. Their activities to a large extent are thought to play an adaptive role in mitigating the detrimental effects on bacterial growth caused by the presence of biotic stresses, such as those imposed by antibiotics, heavy metals, and other toxic compounds, in their natural environments. While it is easy to come to terms with the existence of proteins that mediate export of compounds described above, the presence of specific export systems for cellular metabolites such as sugars and amino acids appears somewhat enigmatic. For example, Escherichia coli encodes multiple proteins for the export of sugars, such as glucose and lactose (1), and for arabinose (2, 3). In addition, the occurrence of proteins mediating export of amino acids, such as alanine (4), arginine (5), aromatic amino acids (6), cysteine (7, 8), leucine (9), threonine (10, 11) and valine (12), in E. coli has been reported. While the physiological basis for the existence of amino acid exporters is not clear, their occurrence is relatively widespread in bacteria (13,14). It is thought that an amino acid exporter may serve to contribute to the fitness of an organism during conditions of metabolic imbalance resulting from excessive levels of its amino acid substrate in the cytoplasm (13,14). An alternative view could be that export of the amino acid occurs by chance, with the cognate substrate being a naturally occurring structurally related antimetabolite present in the environment. As an example of the latter, one mechanism contributing to the resistance of E. coli to the plant-derived antimetabolite canavanine (CAN), an L-arginine analogue, involves its export by ArgO, the ortholog of the basic amino acid exporter LysE of Corynebacterium glutamicum, following its uptake (5). Harnessing the amino acid export potential of a given bacterium has found widespread application in the commercial production of amin...

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Section: Resultsmentioning

confidence: 99%

Distinct Paths for Basic Amino Acid Export in Escherichia coli: YbjE (LysO) Mediates Export of l -Lysine

Pathania

Sardesai

2015

J Bacteriol

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“…5) (15, 133). The molecular details of the ArgR-operator interactions have been described (22,167). Initiation at promoter P1, the more upstream promoter, is negatively regulated by pyrimidines and to a lesser extent by purines, with the latter occurring by PurRmediated repression (15,101,133).…”

Section: Regulation Of Carab Expression In E Colimentioning

confidence: 99%

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

Turnbough

Switzer

2008

Microbiol Mol Biol Rev

164

172

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SUMMARY DNA-binding repressor proteins that govern transcription initiation in response to end products generally regulate bacterial biosynthetic genes, but this is rarely true for the pyrimidine biosynthetic (pyr) genes. Instead, bacterial pyr gene regulation generally involves mechanisms that rely only on regulatory sequences embedded in the leader region of the operon, which cause premature transcription termination or translation inhibition in response to nucleotide signals. Studies with Escherichia coli and Bacillus subtilis pyr genes reveal a variety of regulatory mechanisms. Transcription attenuation via UTP-sensitive coupled transcription and translation regulates expression of the pyrBI and pyrE operons in enteric bacteria, whereas nucleotide effects on binding of the PyrR protein to pyr mRNA attenuation sites control pyr operon expression in most gram-positive bacteria. Nucleotide-sensitive reiterative transcription underlies regulation of other pyr genes. With the E. coli pyrBI, carAB, codBA, and upp-uraA operons, UTP-sensitive reiterative transcription within the initially transcribed region (ITR) leads to nonproductive transcription initiation. CTP-sensitive reiterative transcription in the pyrG ITRs of gram-positive bacteria, which involves the addition of G residues, results in the formation of an antiterminator RNA hairpin and suppression of transcription attenuation. Some mechanisms involve regulation of translation rather than transcription. Expression of the pyrC and pyrD operons of enteric bacteria is controlled by nucleotide-sensitive transcription start switching that produces transcripts with different potentials for translation. In Mycobacterium smegmatis and other bacteria, PyrR modulates translation of pyr genes by binding to their ribosome binding site. Evidence supporting these conclusions, generalizations for other bacteria, and prospects for future research are presented.

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“…Furthermore, arginine binding to distinct amino acids (four of the six residues involved are conserved in the oligomerization domain of both ArgR proteins; Fig. 1) leads to allosteric changes in both hexameric repressors (28,41,45), thereby increasing their arg operator DNA-binding affinity (5,6,8,10,21,42,43,46). It has been shown that binding six arginine molecules, in addition to reinforcing interactions between monomers within a trimer FIG.…”

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confidence: 98%

“…The ArgR protein consists of N-terminal DNA-binding and C-terminal oligomerization domains connected by a short protease-sensitive linker (15), and a three-dimensional structure has been separately resolved for each domain (41,45). A winged helixturn-helix (wHTH) motif of the DNA-binding domain (41) recognizes a 40-bp sequence which comprises two adjacent imperfect 18-bp palindromes, known as Arg boxes, that are separated by a 3-bp spacer in the majority of cognate operators or by a 2-bp spacer in the argR operator (6,44,46). ArgR monomers associate spontaneously to form trimers, and arginine, as a ligand, binds distinct amino acids located within the oligomerization domain and provides the transition of two identical apo-trimers to a holohexameric molecule (45).…”

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Arginine Operator Binding by Heterologous and Chimeric ArgR Repressors fromEscherichia coliandBacillus stearothermophilus

et al. 2002

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Bacillus stearothermophilus ArgR binds efficiently to the Escherichia coli carAB operator, whereas the E. coli repressor binds very poorly to the argCo operator of B. stearothermophilus. In order to elucidate this contradictory behavior between ArgRs, we constructed chimeric proteins by swapping N-terminal DNA-binding and C-terminal oligomerization domains or by exchanging the linker peptide. Chimeras carrying the E. coli DNA-binding domain and the B. stearothermophilus oligomerization domain showed sequence-nonspecific rather than sequence-specific interactions with arg operators. Chimeras carrying the B. stearothermophilus DNA-binding domain and E. coli oligomerization domain exhibited a high DNA-binding affinity for the B. stearothermophilus argCo and E. coli carAB operators and repressed the reporter-gene transcription from the B. stearothermophilus PargCo control region in vitro; arginine had no effect on, and indeed even decreased, their DNA-binding affinity. With the protein array method, we showed that the wild-type B. stearothermophilus ArgR and derivatives of it containing only the exchanged linker from E. coli ArgR or carrying the B. stearothermophilus DNA-binding domain along with the linker and the ␣4 regions were able to bind argCo containing the single Arg box. This binding was weaker than binding to the two-box operator but was no longer arginine dependent. Several lines of observations indicate that the ␣4 helix in the oligomerization domain and the linker peptide can contribute to the recognition of single or double Arg boxes and therefore to the operator DNA-binding specificity in similar but not identical ArgR repressors from two distant bacteria.Recent genome comparative analysis has revealed a global vision of arg genes transcription regulation in microorganisms (3,23,26,30). However, experimental studies on distant organisms are required to elucidate the molecular mechanisms and to understand the evolutionary principles established for arginine regulatory systems in various microbes.A substantial amount of functional and structural information regarding transcription regulation has accumulated for the Escherichia coli arginine repressor, ArgR (14,22,40). In this organism, the repressor, in cooperation with L-arginine, governs expression of the arginine biosynthesis genes (arg) and carAB genes, coding for carbamoylphosphate synthetase (EC 6.3.5.5), providing the carbamoylphosphate required for the synthesis of both arginine and pyrimidine residues. The ArgR protein consists of N-terminal DNA-binding and C-terminal oligomerization domains connected by a short protease-sensitive linker (15), and a three-dimensional structure has been separately resolved for each domain (41,45). A winged helixturn-helix (wHTH) motif of the DNA-binding domain (41) recognizes a 40-bp sequence which comprises two adjacent imperfect 18-bp palindromes, known as Arg boxes, that are separated by a 3-bp spacer in the majority of cognate operators or by a 2-bp spacer in the argR operator (6,44,46). ArgR monomers associ...

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The arginine repressor of Escherichia coli K-12 makes direct contacts to minor and major groove determinants of the operators 1 1Edited by M. Yaniv

Cited by 61 publications

References 65 publications

Distinct Paths for Basic Amino Acid Export in Escherichia coli: YbjE (LysO) Mediates Export of l -Lysine

Distinct Paths for Basic Amino Acid Export in Escherichia coli: YbjE (LysO) Mediates Export of l -Lysine

Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors

Arginine Operator Binding by Heterologous and Chimeric ArgR Repressors fromEscherichia coliandBacillus stearothermophilus

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