Feast/famine regulatory proteins (FFRPs):<i>Escherichia coli</i>Lrp, AsnC and related archaeal transcription factors

Yokoyama, Katsushi; Ishijima, Sanae A.; Clowney, Lester; Koike, Hideaki; Aramaki, Hironori; Tanaka, Chikako; Makino, Kozo; Suzuki, Masashi

doi:10.1111/j.1574-6976.2005.00005.x

Cited by 110 publications

(113 citation statements)

References 92 publications

(200 reference statements)

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“…Little is known at present about the transition between the regulatory modes in the feedback loop motifs for global TFs in bacteria. One such transcription factor is the leucineresponsive protein (Lrp), which is a global transcription regulator widely distributed throughout the bacteria including Escherichia coli (2)(3)(4). The Lrp regulon includes genes involved in amino acid biosynthesis and degradation, small molecule transport, pili synthesis, and other cellular functions including 1-carbon metabolism (2,(4)(5)(6).…”

mentioning

confidence: 99%

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

Cho

Barrett

Knight

et al. 2008

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

165

225

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Broad-acting transcription factors (TFs) in bacteria form regulons. Here, we present a 4-step method to fully reconstruct the leucineresponsive protein (Lrp) regulon in Escherichia coli K-12 MG 1655 that regulates nitrogen metabolism.Step 1 is composed of obtaining high-resolution ChIP-chip data for Lrp, the RNA polymerase and expression profiles under multiple environmental conditions. We identified 138 unique and reproducible Lrp-binding regions and classified their binding state under different conditions. In the second step, the analysis of these data revealed 6 distinct regulatory modes for individual ORFs. In the third step, we used the functional assignment of the regulated ORFs to reconstruct 4 types of regulatory network motifs around the metabolites that are affected by the corresponding gene products. In the fourth step, we determined how leucine, as a signaling molecule, shifts the regulatory motifs for particular metabolites. The physiological structure that emerges shows the regulatory motifs for different amino acid fall into the traditional classification of amino acid families, thus elucidating the structure and physiological functions of the Lrp-regulon. The same procedure can be applied to other broad-acting TFs, opening the way to full bottom-up reconstruction of the transcriptional regulatory network in bacterial cells. ChIP-chip ͉ transcription factorT ranscriptional regulatory systems often regulate the formation rates and the concentration of small molecules by 2 feedback loops that regulate the transporters and metabolic enzymes. In many cases, these 2 feedback loops are connected by a common transcription factor (TF) that senses the concentration of the small molecule (1). Little is known at present about the transition between the regulatory modes in the feedback loop motifs for global TFs in bacteria. One such transcription factor is the leucineresponsive protein (Lrp), which is a global transcription regulator widely distributed throughout the bacteria including Escherichia coli (2-4). The Lrp regulon includes genes involved in amino acid biosynthesis and degradation, small molecule transport, pili synthesis, and other cellular functions including 1-carbon metabolism (2, 4-6). The regulatory action of Lrp on target genes is often modulated by the binding of the small effector molecule leucine and in effect endows Lrp with the ability to affect transcriptional regulation in all possible ways. That is, upon addition of leucine to the environment, the activity of Lrp can be enhanced, reversed, or unaffected (2, 4, 7). Little is known about in vivo Lrp-binding events at the genome scale in the presence or absence of leucine and the extent to which the different modes of regulation are used for different metabolites. Such information is needed to reconstruct the Lrp regulon and the understanding of nitrogen metabolism.In this study, we applied a systems approach by integrating genome-scale data from chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip) for Lrp and...

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mentioning

confidence: 99%

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

Cho

Barrett

Knight

et al. 2008

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

165

225

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“…They are members of a larger conserved family of transcriptional regulators known as the feast/famine regulatory proteins. These regulators contribute to nutrient adaptation by sensing various environmental signals and eliciting an adaptive global change in gene expression (66). In X. nematophila, Lrp is a global regulator that controls numerous genes with predicted roles in host interactions, motility, nutrient adaptation, and the production of small molecules (67,68).…”

Section: Phenotypic Variation In X Nematophilamentioning

confidence: 99%

Ready or Not: Microbial Adaptive Responses in Dynamic Symbiosis Environments

Cao

Goodrich‐Blair

2017

J Bacteriol

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In mutually beneficial and pathogenic symbiotic associations, microbes must adapt to the host environment for optimal fitness. Both within an individual host and during transmission between hosts, microbes are exposed to temporal and spatial variation in environmental conditions. The phenomenon of phenotypic variation, in which different subpopulations of cells express distinctive and potentially adaptive characteristics, can contribute to microbial adaptation to a lifestyle that includes rapidly changing environments. The environments experienced by a symbiotic microbe during its life history can be erratic or predictable, and each can impact the evolution of adaptive responses. In particular, the predictability of a rhythmic or cyclical series of environments may promote the evolution of signal transduction cascades that allow preadaptive responses to environments that are likely to be encountered in the future, a phenomenon known as adaptive prediction. In this review, we summarize environmental variations known to occur in some well-studied models of symbiosis and how these may contribute to the evolution of microbial population heterogeneity and anticipatory behavior. We provide details about the symbiosis between Xenorhabdus bacteria and Steinernema nematodes as a model to investigate the concept of environmental adaptation and adaptive prediction in a microbial symbiosis.

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“…Factors, FFRPs, have two different modes for regulating transcription of genes. 60) When binding downstream of the TATA-box, these repress transcription. When binding immediately upstream of the TATA-box, as is the case for the Dam promoter (Fig.…”

Section: )-67)mentioning

confidence: 99%

GATC Methylation by Dam methylase in archaea: its roles and possible transcription regulation by an FFRP

Koike

Yokoyama

Kawashima

et al. 2005

Proceedings of the Japan Academy. Ser. B: Physical and Biologic

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Methylation of pairs of adenines at their N6 positions in GATC sites (GATC methylation) in archaeal genomic DNAs has been studied. Genomic DNAs in cells of three archaeal species were found as fully methylated, while those of four other archaeal species were free of such methylation. Consistently with this pattern of the presence or absence of GATC methylation, homologues of E. coli Dam methylase was found present or absent, but various other types of DNA methylases were not. A Dam homologue from Pyrococcus sp. OT3 was expressed and its expected function of methylating GATC was confirmed. By methylation of each adenine the DNA duplex was destabilized by 0.56 ± 0.10 Kcal/mol, and this effect was additive. For some archaea, transcription regulation of Dam methylase gene appears to be needed upon cell replication, and in regions upstream of three Dam methylase genes, nucleotide sequences close to TTTTC-TTTGAAAA were present. This arrangement, five bases each at the ends, which are complementary to each other, sandwiching three T bases at the center, fits into a pattern the same as those recognized by dimers of transcription factors, feast/famine regulatory proteins (FFRPs).

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Feast/famine regulatory proteins (FFRPs):Escherichia coliLrp, AsnC and related archaeal transcription factors

Cited by 110 publications

References 92 publications

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

Ready or Not: Microbial Adaptive Responses in Dynamic Symbiosis Environments

GATC Methylation by Dam methylase in archaea: its roles and possible transcription regulation by an FFRP

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