Comparison of foot-prints of FFRPs on promoters designed for autoregulation: FL10 (pot0377090, LrpA), FL11 (pot0434017), and Ss/Sa-Lrp

Suzuki, Masashi

doi:10.2183/pjab.81.403

Cited by 5 publications

(2 citation statements)

References 32 publications

(21 reference statements)

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“…FL10 is an ortholog of LrpA from P. furiosus , whose crystal structure was determined in the absence of DNA ( 24 ). LrpA represses transcription from the lrpA promoter ( 13 , 14 ), and consensus of two LrpA-binding sites in the lrpA promoter is GTCGA [AGA/TCT] TCGAC ( 25 ). Binding of FL11 to various promoters was characterized, and consensus of these binding sites is T TGAAA [AAT/ATT] TTTCA A ( 8 ).…”

Section: Introductionmentioning

confidence: 99%

The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

Yokoyama

Nogami

Kabasawa

et al. 2009

Nucleic Acids Research

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The DNA-binding mode of archaeal feast/famine-regulatory proteins (FFRPs), i.e. paralogs of the Esherichia coli leucine-responsive regulatory protein (Lrp), was studied. Using the method of systematic evolution of ligands by exponential enrichment (SELEX), optimal DNA duplexes for interacting with TvFL3, FL10, FL11 and Ss-LrpB were identified as TACGA[AAT/ATT]TCGTA, GTTCGA[AAT/ATT]TCGAAC, CCGAAA[AAT/ATT]TTTCGG and TTGCAA[AAT/ATT]TTGCAA, respectively, all fitting into the form abcdeWWWedcba. Here W is A or T, and e.g. a and a are bases complementary to each other. Apparent equilibrium binding constants of the FFRPs and various DNA duplexes were determined, thereby confirming the DNA-binding specificities of the FFRPs. It is likely that these FFRPs recognize DNA in essentially the same way, since their DNA-binding specificities were all explained by the same pattern of relationship between amino-acid positions and base positions to form chemical interactions. As predicted from this relationship, when Gly36 of TvFL3 was replaced by Thr, the b base in the optimal DNA duplex changed from A to T, and, when Thr36 of FL10 was replaced by Ser, the b base changed from T to G/A. DNA-binding characteristics of other archaeal FFRPs, Ptr1, Ptr2, Ss-Lrp and LysM, are also consistent with the relationship.

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Section: Introductionmentioning

confidence: 99%

The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

Yokoyama

Nogami

Kabasawa

et al. 2009

Nucleic Acids Research

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“…4b). One of these sequences, TTCGAAAAATAAA, is closely related with another sequence identified as consensus of FL10-binding sites by analyzing foot-printing experiments, GTCGAAGATCGAC 2) : here bases the same in the two sequences are underlined. The eighteen 13 bp sequences can be grouped into four sets, in each of which entries share a core sequence.…”

Section: )40)mentioning

confidence: 99%

A SELEX study of the DNA-binding specificity of archaeal FFRPs: FL10 (pot0377090, LrpA)

Yokoyama¹,

Ihara²,

Ebihara³

et al. 2005

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

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Introduction.We have been studying the structure and function of a group of transcription factors, the feast/famine regulatory proteins (FFRPs), regulating many genes in archaea and eubacteria. and SELEX (systematic evolution of ligands by exponential environment) 28) experiments are carried out.The former can pinpoint a short binding site in a larger fragment chosen for the experiment. However, the chosen fragment might not be the most ideal target. While, the latter are able to select fragments containing ideal binding-sites, although it is not easy to identify a right one from many short sequences shared by larger fragments selected. Thus in order to obtain the best results, the two types of approaches need to be combined. In this paper, the results obtained by SELEX experiments are analyzed in order to determine the DNA-binding specificity of an FFRP, i.e. FL10, and compared with our re-interpretation Abstract: Using SELEX (systematic evolution of ligands by exponential environment) experiments, from a set of DNA fragments, ~150 bps, most of them originated in the genome of an archaeon, Pyrococcus furiosus, five fragments were selected as containing binding-sites of a transcription factor, FL10 (pot0377090, LrpA). The nucleotide sequences of these fragments were analyzed in the light of our previous finding that FFRPs in general recognize DNA sequences in the 5-3-5 arrangement:

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Feast/Famine Regulation by Transcription Factor FL11 for the Survival of the Hyperthermophilic Archaeon Pyrococcus OT3

et al. 2007

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Transcriptional repressor FL11 from the hyperthermophilic archaeon, Pyrococcus OT3, was crystallized in its dimer form in complex with a DNA duplex, TGAAAWWWTTTCA. Chemical contacting of FL11 to the terminal 5 bps, and DNA bending by propeller twisting at WWW confirmed specificity of the interaction. Dimer-binding sites were identified in promoters of approximately 200 transcription units coding, for example, H+-ATPase and NAD(P)H dehydrogenase. In the presence of lysine, four FL11 dimers were shown to assemble into an octamer, thereby covering the fl11 promoter. In the "feast" mode, when P. OT3 grows on amino acids, the FL11 octamer will terminate transcription of fl11, as was shown in vitro, thereby derepressing transcription of many metabolic genes. In the "famine" mode in the absence of lysine, approximately 6000 FL11 dimers present per cell will arrest growth. This regulation resembles global regulation by Escherichia coli leucine-responsive regulatory protein, and hints at a prototype of transcription regulations now highly diverged.

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Comparison of foot-prints of FFRPs on promoters designed for autoregulation: FL10 (pot0377090, LrpA), FL11 (pot0434017), and Ss/Sa-Lrp

Cited by 5 publications

References 32 publications

The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB

A SELEX study of the DNA-binding specificity of archaeal FFRPs: FL10 (pot0377090, LrpA)

Feast/Famine Regulation by Transcription Factor FL11 for the Survival of the Hyperthermophilic Archaeon Pyrococcus OT3

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