Transcription Regulation by Feast/Famine Regulatory Proteins, FFRPs, in Archaea and Eubacteria

Kawashima, Tomokazu; Aramaki, Hironori; Oyamada, Tomoya; Makino, Kozo; Yamada, Michihiro; Okamura, Hideyasu; Yokoyama, Katsushi; Ishijima, Sanae A.; Suzuki, Masashi

doi:10.1248/bpb.31.173

Cited by 23 publications

(35 citation statements)

References 69 publications

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“…The present structure where a single point mutation of a residue in the ligand-binding loop results in a stable, open quaternary association suggests that ligand binding at the distal C-terminal domain can also induce symmetry deviations as opposed to the substrateinduced structural change observed in the E. coli Lrp-DNA complex. Indeed, in a recent review, 21 the authors mention that an analogous deviation from the closed octameric structure was observed in the Pyrococcus FL11 Lrp crystallized in the presence of Arg, although the report is yet to be published.…”

Section: Discussionmentioning

confidence: 89%

“…Surprisingly, density was observed in the case of Lys where, analogous to the experiments with Arg, we expected no binding. Lys was earlier reportedly known to bind only to some of the archaeal Lrp regulators, 21 and we report the structure of its complex with MtbLrp here. We also report the crystal structures of a couple of mutants of the protein.…”

Section: Introductionmentioning

confidence: 82%

“…This information is expected to give functional insights especially since the regulatory roles performed by these proteins are generally thought to involve an interplay between gross quaternary structural changes and finer changes in the tertiary structure. 21 Since the functional unit of the protein is a dimer, we compared the dimers across the respective crystal structures to identify conformationally invariant regions using the program ESCET. The program uses a parameter σ that defines the positional uncertainties in the coordinates of individual atoms while calculating an error-scaled difference distance matrix, to divide protein subunits into relatively rigid and flexible regions.…”

Section: Identification Of Relatively Rigid and Flexible Regionsmentioning

confidence: 99%

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Ligand-Induced Structural Transitions, Mutational Analysis, and ‘Open’ Quaternary Structure of the M. tuberculosis Feast/Famine Regulatory Protein (Rv3291c)

Shrivastava¹,

Dey²,

Ramachandran³

2009

Journal of Molecular Biology

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Section: Discussionmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 82%

Section: Identification Of Relatively Rigid and Flexible Regionsmentioning

confidence: 99%

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Ligand-Induced Structural Transitions, Mutational Analysis, and ‘Open’ Quaternary Structure of the M. tuberculosis Feast/Famine Regulatory Protein (Rv3291c)

Shrivastava¹,

Dey²,

Ramachandran³

2009

Journal of Molecular Biology

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“…Typically, an Lrp monomer has a molecular mass of about 15 kDa and consists of two domains: an amino-terminal DNA-binding domain with a helix-turn-helix (HTH) motif and a carboxy-terminal domain, named Regulation of Amino acid Metabolism (RAM) [20], which is responsible for protein multimerization and cofactor binding [8]. This RAM domain forms an αβ sandwich fold having an antiparallel β sheet composed of four strands “sandwiched” between two α helices.…”

Section: Introductionmentioning

confidence: 99%

The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

et al. 2013

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BackgroundGene regulatory processes are largely resulting from binding of transcription factors to specific genomic targets. Leucine-responsive Regulatory Protein (Lrp) is a prevalent transcription factor family in prokaryotes, however, little information is available on biological functions of these proteins in archaea. Here, we study genome-wide binding of the Lrp-like transcription factor Ss-LrpB from Sulfolobus solfataricus.ResultsChromatin immunoprecipitation in combination with DNA microarray analysis (ChIP-chip) has revealed that Ss-LrpB interacts with 36 additional loci besides the four previously identified local targets. Only a subset of the newly identified binding targets, concentrated in a highly variable IS-dense genomic region, is also bound in vitro by pure Ss-LrpB. There is no clear relationship between the in vitro measured DNA-binding specificity of Ss-LrpB and the in vivo association suggesting a limited permissivity of the crenarchaeal chromatin for transcription factor binding. Of 37 identified binding regions, 29 are co-bound by LysM, another Lrp-like transcription factor in S. solfataricus. Comparative gene expression analysis in an Ss-lrpB mutant strain shows no significant Ss-LrpB-mediated regulation for most targeted genes, with exception of the CRISPR B cluster, which is activated by Ss-LrpB through binding to a specific motif in the leader region.ConclusionsThe genome-wide binding profile presented here implies that Ss-LrpB is associated at additional genomic binding sites besides the local gene targets, but acts as a specific transcription regulator in the tested growth conditions. Moreover, we have provided evidence that two Lrp-like transcription factors in S. solfataricus, Ss-LrpB and LysM, interact in vivo.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-828) contains supplementary material, which is available to authorized users.

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“…In a Pyrococcus furiosus cell-free transcription system, LrpA exerts negative autoregulation of its own transcription [19] by interfering with the recruitment of RNA polymerase [28]. Crystal structures determined for several bacterial and archaeal Lrp-like proteins (for an overview, see [29] show that they contain a N-terminal helix-turn-helix DNA-binding domain (HTH). A flexible hinge connects this domain with the C-terminal oligomerization and effector binding domain [30-32].…”

Section: Introductionmentioning

confidence: 99%

Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1

et al. 2010

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BackgroundArchaea combine bacterial-as well as eukaryotic-like features to regulate cellular processes. Halobacterium salinarum R1 encodes eight leucine-responsive regulatory protein (Lrp)-homologues. The function of two of them, Irp (OE3923F) and lrpA1 (OE2621R), were analyzed by gene deletion and overexpression, including genome scale impacts using microarrays.ResultsIt was shown that Lrp affects the transcription of multiple target genes, including those encoding enzymes involved in amino acid synthesis, central metabolism, transport processes and other regulators of transcription. In contrast, LrpA1 regulates transcription in a more specific manner. The aspB3 gene, coding for an aspartate transaminase, was repressed by LrpA1 in the presence of L-aspartate. Analytical DNA-affinity chromatography was adapted to high salt, and demonstrated binding of LrpA1 to its own promoter, as well as L-aspartate dependent binding to the aspB3 promoter.ConclusionThe gene expression profiles of two archaeal Lrp-homologues report in detail their role in H. salinarum R1. LrpA1 and Lrp show similar functions to those already described in bacteria, but in addition they play a key role in regulatory networks, such as controlling the transcription of other regulators. In a more detailed analysis ligand dependent binding of LrpA1 was demonstrated to its target gene aspB3.

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Transcription Regulation by Feast/Famine Regulatory Proteins, FFRPs, in Archaea and Eubacteria

Cited by 23 publications

References 69 publications

Ligand-Induced Structural Transitions, Mutational Analysis, and ‘Open’ Quaternary Structure of the M. tuberculosis Feast/Famine Regulatory Protein (Rv3291c)

Ligand-Induced Structural Transitions, Mutational Analysis, and ‘Open’ Quaternary Structure of the M. tuberculosis Feast/Famine Regulatory Protein (Rv3291c)

The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1

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