Alternative secondary structures of leader RNAs and the regulation of the trp, phe, his, thr, and leu operons.

Keller, Elizabeth B.; Calvo, Joseph M.

doi:10.1073/pnas.76.12.6186

Cited by 88 publications

(34 citation statements)

References 30 publications

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“…In the regulatory regions of these latter operons, three pairing regions are arranged in an overlapping fashion such that formation of one prevents formation of its downstream neighbor. In the absence of protein factors, transcription terminates at the terminator because the first stem (the protector) forms efficiently and protects the terminator by preventing the antiterminator from forming (8,10).…”

Section: Resultsmentioning

confidence: 99%

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

et al. 1993

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The ilv-ku operon ofBacillus subtilis is regulated in part by transcription attenuation. The cis-acting elements required for regulation by leucine lie within a 683-bp fragment of DNA from the region upstream of ilvB, the first gene of the operon. This fragment contains the ilv-ku promoter and 482 bp of the ilv-ku leader region. Spontaneous mutations that lead to increased expression of the operon were shown to lie in an imperfect inverted repeat encoding the terminator stem within the leader region. Mutations within the inverted repeat of the terminator destroyed most of the leucine-mediated repression. The remaining leucine-mediated repression probably resulted from a decrease in transcription initiation. A systematic analysis of other deletions within the ilv-ku leader region identified a 40-bp region required for the derepression that occurred during leucine limitation. This region lies within a potential RNA stem-and-loop structure that is probably required for leucine-dependent control. Deletion analysis also suggested that alternate secondary structures proximal to the terminator are involved in allowing transcription to proceed beyond the terminator. Additional experiments suggested that attenuation of the ilv-ku operon is not dependent on coupling translation to transcription of the leader region. Our data support a model proposed by Grundy and Henkin (F. J. Grundy and T. M. Henkin, Cell 74:475-482, 1993) in which uncharged tRNA acts as a positive regulatory factor to increase gene expression during amino acid limitation.The ilv-leu operon of Bacillus subtilis contains seven genes encoding enzymes for the biosynthesis of isoleucine, valine, and leucine ( Fig. 1). Transcription of this operon is repressed by leucine but not by isoleucine or valine (21). In work published previously we showed that transcription is initiated 482 bp upstream of the start codon for ilvB, the first gene in the operon (4).In vitro transcription studies defined a strong transcription termination site at position +405, immediately downstream from an extended inverted repeat. Ninety percent of transcripts initiated at the promoter in vitro were terminated at this site. Analysis of mRNA levels in vivo suggested that repression by leucine occurs by attenuation of transcription within the 482-bp leader region and that the transcription terminator within the ilv-leu leader region is involved in the mechanism of leucine control (4).The ilv and leu genes in enteric bacteria are regulated mostly by translation-dependent attenuation, which relies on translation of a short open reading frame (ORF) within the leader RNA upstream of the structural genes. In the case of the leu operon, limitation for leucine results in stalling of the ribosome at leucine control codons within the leader. Stalling at these sites prevents formation of a terminator stem and loop by promoting formation of an antiterminator stem, leading to readthrough (10). When leucine is in excess, the ribosome does not stall and formation of the terminator is favored because...

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Section: Resultsmentioning

confidence: 99%

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

et al. 1993

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“…The general model of attenuation requires that the ribosome synthesizing the leader peptide be in close proximity to the transcribing RNA polymer ase molecule (29,45,79). If for any reason translation initiation were delayed, the transcribing RNA polymerase molecule would not have the opportunity to sense secondary structures that would indicate whether the translating ribosome had or had not stalled at the relevant codons.…”

Section: Other Features Of Attenuationmentioning

confidence: 99%

Attenuation in Amino Acid Biosynthetic Operons

1982

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“…Expression ofthe high-affinity histidine transport operon of Salmonella typhimurium seems to be regulated independently from the histidine biosynthetic operon (unpublished observations). Thus, it seems that regulation of at least this amino acid transport operon involves regulatory mechanisms other than the transcription attenuation mechanism described in detail for several amino acid biosynthetic operons (1)(2)(3). On the other hand, it has been suggested that regulation of the leucine-isoleucine-valine-and the leucinespecific transport systems ofEscherichia coli might be regulated by such an attenuation mechanism (4).…”

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Regulatory regions of two transport operons under nitrogen control: nucleotide sequences.

Higgins¹,

Ames²

1982

Proc. Natl. Acad. Sci. U.S.A.

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We have determined the nucleotide sequences of the regulatory regions from two amino acid transport operons from SalmoneUa typhimurium: dhuA, which regulates the histidine transport operon, and argTr, which regulates argT, the gene encoding the lysine-arginine-ornithine-binding protein, LAO. The promoter for the histidine transport operon has been identified from the sequence change in the promoter-up mutation dhuAL. Neither regulatory region has any of the features typical of the regulatory regions of the amino acid biosynthetic operons, indicating that regulation of at least these transport genes does not involve a transcription attenuation mechanism. We have identified three interesting features, present in both ofthese sequences, which may be of importance in the regulation of these and other operons: a "stem-loop-foot" structure, a region of specific homology, and a mirror symmetry. The region of mirror symmetry may be a protein recognition site important in regulating expression ofthese and other operons in response to nitrogen availability. Mirror symmetry as a structure for DNA-protein interaction sites has not been proposed previously.Regulation of the active transport of amino acids in bacteria is poorly understood at a molecular level, despite many empirical observations that transport activity can vary markedly under different growth conditions. Expression ofthe high-affinity histidine transport operon of Salmonella typhimurium seems to be regulated independently from the histidine biosynthetic operon (unpublished observations). Thus, it seems that regulation of at least this amino acid transport operon involves regulatory mechanisms other than the transcription attenuation mechanism described in detail for several amino acid biosynthetic operons (1-3). On the other hand, it has been suggested that regulation of the leucine-isoleucine-valine-and the leucinespecific transport systems ofEscherichia coli might be regulated by such an attenuation mechanism (4). In order to clarify the mechanisms by which amino acid transport operons are regulated, we have studied two transport operons in detail: one encoding the histidine transport proteins, the other encoding the lysine-arginine-ornithine-binding protein (LAO).The high-affinity histidine transport system of S. typhimurium has been characterized in considerable detail. Four genes are required for transport, hisJ, hisQ, hisM, and hisP, which encode, respectively, a periplasmic histidine-binding protein, J. a membrane protein, Q, a protein ofas yet unknown location, M, and an inner membrane protein, P (refs. 5 and 6; unpublished data). Together with a genetically defined regulatory locus, dhuA, these genes form an operon located at 48.5 minutes on the recalibrated S. typhimurium chromosomal map (ref. 7; Fig. 1). The membrane-bound P protein and the periplasmic histidine-binding protein, J, interact with each other during transport (8). The P protein also interacts with another periplasmic binding protein, LAO (the lysine-arginine-ornithinebinding ...

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Alternative secondary structures of leader RNAs and the regulation of the trp, phe, his, thr, and leu operons.

Abstract: BiochemistryAlternative secondary structures of leader RNAs and the regulation of the trp, phe,-his, thr, and leu operons (attenuation/transcription termination/transcription read-through/enteric bacteria)

Cited by 88 publications

References 30 publications

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine

Attenuation in Amino Acid Biosynthetic Operons

Regulatory regions of two transport operons under nitrogen control: nucleotide sequences.

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