Influence of a Joining Helix on the BLUF Domain of the YcgF Photoreceptor from <i>Escherichia coli</i>

Schroeder, Claudia; Werner, Karla; Otten, H.; Krätzig, Steffen; Schwalbe, Harald; Essen, Lars‐Oliver

doi:10.1002/cbic.200800280

Cited by 26 publications

(36 citation statements)

References 90 publications

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“…These data suggest high affinities and low off-rates of the interaction reactions involved. This is also consistent with no rebinding of YcgE to ycgZ p DNA, when samples treated as in Figure 3A were kept in the dark for 60 min before running them on the gel (data not shown), and the slow reversion to the ground state in the photocycle of YcgF (Schroeder et al 2008). In the absence of blue-light irradiation, even a relatively large excess of YcgF did not release YcgE from its operator.…”

Section: Identification Of Target Genes Of the Merr-like Regulator Ycgesupporting

confidence: 75%

“…We noted that low temperature induction of ycgF expression is clearly stronger than that of ycgE (;30-fold and sevenfold, respectively, when cells were shifted from 37°C to 16°C). Blue light promotes a conformational change of YcgF (Hasegawa et al 2006;Nakasone et al 2007;Schroeder et al 2008) that probably increases YcgF affinity for YcgE and allows it to release YcgE from its operator site (as discussed above). Yet, by simple mass action, the cold-induced increase in the YcgF:YcgE stoichiometry also could have similar consequences; i.e., generate enough active YcgF to sequester YcgE and therefore induce the YcgE regulon.…”

Section: Discussionmentioning

confidence: 99%

“…Yet, by simple mass action, the cold-induced increase in the YcgF:YcgE stoichiometry also could have similar consequences; i.e., generate enough active YcgF to sequester YcgE and therefore induce the YcgE regulon. Interestingly, the recovery of the dark ground state of YcgF also is strongly delayed at lower temperature (Schroeder et al 2008). Therefore, blue light and low temperature can act in an additive manner on target gene expression.…”

Section: Discussionmentioning

confidence: 99%

“…In biophysical studies, conformational changes upon bluelight irradiation have been observed in the BLUF domain as well as in the entire YcgF protein, and the protein is believed to dimerize upon photo-excitation (Rajagopal et al 2004;Hasegawa et al 2006;Nakasone et al 2007;Schroeder et al 2008). However, the molecular output function controlled by the BLUF domain as well as the physiological context, where all this plays a role for E. coli, have remained elusive.…”

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confidence: 99%

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The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli

Tschowri¹,

Busse²,

Hengge³

2009

Genes Dev.

172

215

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The blue light using FAD (BLUF)-EAL protein YcgF is a known blue-light sensor of Escherichia coli, but its direct regulatory output and physiological function have remained unknown. Here, we demonstrate that unlike other EAL domain proteins, YcgF does not degrade the signaling molecule c-di-GMP, but directly binds to and releases the MerR-like repressor YcgE from its operator DNA upon blue-light irradiation. As a consequence, a distinct regulon of eight small proteins (of 71-126 amino acids) is strongly induced. These include YmgA and YmgB, which, via the RcsC/RcsD/RcsB two-component phosphorelay system, activate production of the biofilm matrix substance colanic acid as well as acid resistance genes and the biofilm-associated bdm gene and down-regulate adhesive curli fimbriae. Thus, small proteins under YcgF/YcgE control seem to act as ''connectors'' that provide additional signal input into a two-component signaling pathway. Moreover, we found ycgF and ycgE expression to be strongly activated at low temperature, and we elucidate how blue light, cold, and starvation signals are integrated in the expression and activity of the YcgF/YcgE/small protein signaling pathway. In conclusion, this pathway may modulate biofilm formation via the two-component network when E. coli has to survive in an extrahost aquatic environment.[Keywords: Biofilm; connectors; cyclic-di-GMP; GGDEF; RcsB; RpoS] Supplemental material is available at http://www.genesdev.org.

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Section: Identification Of Target Genes Of the Merr-like Regulator Ycgesupporting

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli

Tschowri¹,

Busse²,

Hengge³

2009

Genes Dev.

172

215

View full text Add to dashboard Cite

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“…A direct inhibitory effect of the uncomplexed PAS-like domain appears unlikely, because it is rather remote from the ␤5-␣5 loop. For the same reason, direct transmission of the information by the domain linking helix seems unlikely, although light-induced structural changes in the joining helix have been seen for a fragment of the BLUF-EAL protein YcgF by NMR (52). However, impact of the state of the PAS domain on the quaternary arrangement of YkuI (possibly transmitted by the linking helix) appears possible.…”

Section: C-di-gmp-specific Phosphodiesterasementioning

confidence: 99%

Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains

Minasov

Padavattan

Shuvalova

et al. 2009

Journal of Biological Chemistry

121

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Cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of cell surface-associated traits and the persistence of infections. Omnipresent GGDEF and EAL domains, which occur in various combinations with regulatory domains, catalyze c-di-GMP synthesis and degradation, respectively. The crystal structure of full-length YkuI from Bacillus subtilis, composed of an EAL domain and a C-terminal PAS-like domain, has been determined in its native form and in complex with c-di-GMP and Ca 2؉. The EAL domain exhibits a triose-phosphate isomerase-barrel fold with one antiparallel ␤-strand. The complex with c-di-GMP-Ca 2؉ defines the active site of the putative phosphodiesterase located at the C-terminal end of the ␤-barrel. The EAL motif is part of the active site with Glu-33 of the motif being involved in cation coordination. The structure of the complex allows the proposal of a phosphodiesterase mechanism, in which the divalent cation and the general base Glu-209 activate a catalytic water molecule for nucleophilic in-line attack on the phosphorus. The C-terminal domain closely resembles the PASfold. Its pocket-like structure could accommodate a yet unknown ligand. YkuI forms a tight dimer via EAL-EAL and trans EAL-PASlike domain association. The possible regulatory significance of the EAL-EAL interface and a mechanism for signal transduction between sensory and catalytic domains of c-di-GMP-specific phosphodiesterases are discussed.

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Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1

et al. 2010

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The first biochemical and structural characterization of the full-length active photoreceptor BlrP1 from Klebsiella pneumoniae was recently reported by Barends et al. [Nature 459:1015-1018, (2009)]. The light-regulated catalytic function of its C-terminal c-di-guanosine monophosphate phosphodiesterase, the EAL (Glu-Ala-Leu) domain, is activated by the N-terminal sensor of blue light using the flavin adenine dinucleotide (BLUF) domain. We performed molecular dynamics simulations on the dimeric BlrP1 protein in order to examine the coupling regions that are presumably involved in transmitting light-induced structural changes which occur in the BLUF domain to the EAL domain. According to the results of simulations and an analysis of the hydrogen bonding between the respective polypeptide chains, the region containing the site on the α3α4 loop of BLUF is responsible for communication between the photosensing and catalytic domains in the dimeric BlrP1 protein.

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Influence of a Joining Helix on the BLUF Domain of the YcgF Photoreceptor from Escherichia coli

Cited by 26 publications

References 90 publications

The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli

The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli

Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains

Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1

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