Leucine-regulated self-association of leucine-responsive regulatory protein (Lrp) from Escherichia coli 1 1Edited by M. F. Moody

Chen, Shaolin; Rosner, Michele H.; Calvo, Joseph M.

doi:10.1006/jmbi.2001.4955

Cited by 69 publications

(88 citation statements)

References 36 publications

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“…This appears to occur as a result of diminished PapI homologue-dependent binding of Lrp to GATC dist and increased binding of Lrp to GATC prox , locking cells in the OFFphase transcription state. Lrp has a binding site for aliphatic amino acids, which appears to modulate the multimeric state of Lrp between dimeric, octameric, and hexadecameric states (57,59). If Lrp binding sites are phased such that they occur on the same DNA face, then an octameric Lrp could engage up to four sites, contributing to binding cooperativity.…”

Section: Pap-related Systemsmentioning

confidence: 99%

Epigenetic Gene Regulation in the Bacterial World

Casadesús

Low

2006

Microbiol Mol Biol Rev

543

562

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SUMMARY Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.

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Section: Pap-related Systemsmentioning

confidence: 99%

Epigenetic Gene Regulation in the Bacterial World

Casadesús

Low

2006

Microbiol Mol Biol Rev

543

562

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“…increased compaction) or the formation of a novel complex, dependent on the presence of lysine. For E. coli Lrp, it has been shown recently that its ligand, leucine, induces dissociation of the Lrp hexadecameric form to the octameric form (29), which may alter the affinity for sites within its different target operons. Using chemical cross-linking of LysM we analyzed its oligomeric state (not shown).…”

Section: Identification Of the Lysine Biosynthesis Gene Cluster-inmentioning

confidence: 99%

The Sulfolobus solfataricus Lrp-like Protein LysM Regulates Lysine Biosynthesis in Response to Lysine Availability

Brinkman¹,

Bell²,

Lebbink³

et al. 2002

Journal of Biological Chemistry

104

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Although the archaeal transcription apparatus resembles the eukaryal RNA polymerase II system, many bacterial-like regulators can be found in archaea. Particularly, all archaeal genomes sequenced to date contain genes encoding homologues of Lrp (leucine-responsive regulatory protein). Whereas Lrp-like proteins in bacteria are involved in regulation of amino acid metabolism, their physiological role in archaea is unknown. Although several archaeal Lrp-like proteins have been characterized recently, no target genes apart from their own coding genes have been discovered yet, and no ligands for these regulators have been identified so far. In this study, we show that the Lrp-like protein LysM from Sulfolobus solfataricus is involved in the regulation of lysine and possibly also arginine biosynthesis, encoded by the lys gene cluster. Exogenous lysine is the regulatory signal for lys gene expression and specifically serves as a ligand for LysM by altering its DNA binding affinity. LysM binds directly upstream of the TFB-responsive element of the intrinsically weak lysW promoter, and DNA binding is favored in the absence of lysine, when lysWXJK transcription is maximal. The combined in vivo and in vitro data are most compatible with a model in which the bacterial-like LysM activates the eukarya-like transcriptional machinery. As with transcriptional activation by Escherichia coli Lrp, activation by LysM is apparently dependent on a co-activator, which remains to be identified.Since the discovery of archaea as a distinct domain of life, many studies have focused on archaeal transcription. It has become clear that although archaea resemble bacteria with respect to their cellular and genetic organization, their transcriptional apparatus is fundamentally different from that of bacteria. Their RNA polymerase (RNAP) 1 is much more related to the eukaryal RNAPII system regarding subunit complexity and sequence homology (1). Thus, archaeal RNAP consists of at least 10 subunits in contrast to the five-subunit bacterial RNAP core enzyme. As in eukarya, archaeal transcription initiation is preceded by the binding of the TATA-binding protein (TBP) to a TATA-like sequence called the TATA-box and subsequent binding of transcription factor B (TFB). Archaeal TBP and TFB are highly homologous to the eukaryal TBP and TFIIB, respectively. However, archaeal TBP is not complexed with TBP-associated factors as in eukarya (2), and there is no evidence that archaeal genomes encode TBP-associated factor homologues. The archaeal TATA-box is 8 bp in length and is located ϳ25 bp upstream of the start of transcription. Directly upstream of the TATA-box, a purine-rich sequence is present, called the TFB-responsive element (BRE). The BRE was shown to be an important determinant in directionality of transcription and promoter strength through interaction with a C-terminal helix-turn-helix domain of TFB (3, 4). The TF(II)B-BRE interaction is a conserved feature between archaea and eukarya. Once TBP and TFB are bound to the promoter, RNAP is recruite...

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“…This mutual binding exclusion effect is reduced from 10-fold to only about 2-fold when unsupercoiled DNAs are used (unpublished data), showing a strong dependence on DNA topology. Because Lrp is known to form higher oligomers under certain conditions (19,20) and bend DNA (21), one possible mechanism is that the conformation of pap sites 4-6 might be altered as a result of a binding of Lrp at sites 1-3 located 102 bp away (measured from site 2 to site 5) (Fig. 1).…”

mentioning

confidence: 99%

Self-perpetuating epigenetic pili switches in bacteria

Hernday

Krabbe

Braaten

et al. 2002

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

132

204

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Cis-and Trans-Acting Pap Switch ComponentsB acteria have developed phase variation mechanisms to control cell surface pili-adhesin complexes between expression (phase ON) and nonexpression (phase OFF) states. Pili phase variation can occur by site specific (1, 2) and homologous recombination (3) mechanisms. In addition, a large group of pili operons including pyelonephritis-associated pili (pap) are regulated by an epigenetic switch directly controlled by DNA methylation pattern formation (4, 5). The focus of this paper is on the mechanisms by which the phase OFF and phase ON states are perpetuated, the transition between phase OFF and phase ON states, and the external inputs that control phase switching.

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Leucine-regulated self-association of leucine-responsive regulatory protein (Lrp) from Escherichia coli 1 1Edited by M. F. Moody

Cited by 69 publications

References 36 publications

Epigenetic Gene Regulation in the Bacterial World

Epigenetic Gene Regulation in the Bacterial World

The Sulfolobus solfataricus Lrp-like Protein LysM Regulates Lysine Biosynthesis in Response to Lysine Availability

Self-perpetuating epigenetic pili switches in bacteria

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