Photo-dynamics and thermal behavior of the BLUF domain containing adenylate cyclase NgPAC2 from the amoeboflagellate Naegleria gruberi NEG-M strain

doi:10.1016/j.chemphys.2012.12.015

Chemical Physics

Volume 412, 1 February 2013, Pages 96-108

https://doi.org/10.1016/j.chemphys.2012.12.015 Get rights and content

Abstract

The absorption and emission spectroscopic behavior of the photo-activated adenylate cyclase NgPAC2 from the amoeboflagellate Naegleria gruberi NEG-M strain was studied in the dark, during blue-light exposure and after blue-light exposure. The typical BLUF domain (BLUF = Blue Light sensor Using Flavin) flavin cofactor absorption and fluorescence photo-cycle dynamics was observed. For fresh samples a reversible concentration dependent protein oligomerization occurred showing up in free flavin binding and protein color center formation with increasing protein concentration. Thermal and temporal irreversible protein unfolding with loss of BLUF domain activity was investigated. Temperature dependent protein melting times and the apparent protein melting temperature were determined. The photodynamic behavior of the NgPAC2 is compared with the behavior of the previously investigated photo-activated cyclase NgPAC1 (nPAC) from the same N. gruberi NEG-M strain.

Graphical abstract

Highlights

► Photo-activated adenylyl cyclase NgPAC2 from Naegleria gruberi NEG-M was expressed. ► Photo-cycle dynamics of BLUF domain in NgPAC2 protein was studied. ► Photo-excitation of Flavin in signaling state caused main conversion to lumichrome. ► Concentration dependent protein aggregation and color center formation observed. ► Melting temperature and melting times at fixed temperatures were determined.

Introduction

Naegleria gruberi is a widespread free-living soil and freshwater amoeboflagellate [1], [2], [3], [4]. Different strains of N. gruberi exist in the nature. The genome of the N. gruberi NEG-M strain (ATCC 30224) was sequenced [5] and gives unique insights into core eukaryotic cell biology [6]. The genome contains at least 108 cyclase encoding genes. Four of them are photo-activated cyclases (PACs) which have potential to catalyze light-controlled chemical reactions to form cyclic compounds (cAMP and cGMP). The photo-activated cyclases consist of a BLUF protein domain (BLUF = Blue Light sensor Using Flavin) and a cyclase homology domain (CHD). One of these PACs named nPAC and now renamed to NgPAC1 (GenBank accession XP_002674372 and JF928492) was expressed [7] and characterized by optical spectroscopic methods (photo-cycle dynamics of its BLUF domain [7], protein color-center emission of nano-clusters [8], and thermal protein unfolding [9]). The typical BLUF domain photoreceptor photo-cycle dynamics [10], [11], [12], [13] was observed (flavin S₀ − S₁ absorption red shift in light adapted state due to hydrogen bond restructuring, and enhanced flavin fluorescence quenching in light adapted state due to increased photo-induced tyrosine to flavin electron transfer).

Here, we report on another BLUF domain containing photo-activated cyclase, called NgPAC2 (GeneBank Accession number JX967006), from N. gruberi NEG-M strain which was expressed heterologously in Escherichia coli and its photo-dynamics in aqueous pH 7.5 phosphate buffer was studied using spectroscopic methods. Like nPAC (NgPAC1), NgPAC2 shows the typical BLUF domain photo-cycle characteristics. Differences are found in the efficiency of signaling state formation and secondary photo-dynamics in the signaling state, the flavin binding strength to the BLUF domain binding pocket, the concentration dependent protein oligomerization with protein color center formation, and the thermal protein stability (temperature dependent protein melting time and apparent protein melting temperature).

Section snippets

Sample preparation

Nucleotide and protein sequence were fetched from N. gruberi genome database at JGI portal. Synthesis of the codon-adapted gene for expression in E. coli was done with commercial service (Mr. Gene GmbH, Regensburg, Germany). The amino acid sequence is shown in Fig. 1a together with the amino acid sequence of NgPAC1 (nPAC). The multiple sequence alignment structure is displayed [14], [15], [16]. Identical residues are marked in white letters on dark gray background. Similar residues in chemical

Flavin composition and cofactor loading of NgPAC2

The flavin composition was determined by HPLC analysis using the same procedure as described in [7] for NgPAC1. FMN with a mole-fraction of about 80% and FAD with a mole-fraction of about 20% were found to be present.

For cofactor loading calculation the flavin cofactor concentration and the apo-protein concentration of NgPAC2 were determined from the absorption coefficient spectrum α_a(λ) of the dashed curve in Fig. 2 and the known absorption cross-section spectra, σ_a,i(λ), of FMN, FAD, Trp, and

Discussion

The second of four photo-activated cyclases (PACs), i.e. NgPAC2, from the amoeboflagellate N. gruberi NEG-M strain was characterized here by optical spectroscopic methods. The first photo-activated cyclase NgPAC1 was investigated in [7], [8], [9] (there called nPAC). Characterization of NgPAC3 is in progress. Fourth PAC of N. gruberi has not yet been checked for expression.

Conclusions

The second photo-activated cyclase NgPAC2 from the amoeboflagellate N. gruberi NEG-M strain was investigated by optical spectroscopic methods and compared with the first photo-activated cyclase NgPAC1 from the same amoeboflagellate. The BLUF domains of both PACs exhibited photo-cycling activity, but the parameters of quantum efficiency of signaling state formation, signaling state recovery, time constants of Tyr–flavin electron transfer and charge recombination turned out to be different. At

Acknowledgments

A.P. thanks Prof. F.J. Gießibl for his kind hospitality. We are thankful to BMBF, Germany, and DBT, India, for financial support of the joint Indo-German project.

References (64)

C. Fulton
Exp. Cell Res.
(1974)
L.K. Fritz-Laylin et al.
Res. Microbiol.
(2011)
L.K. Fritz-Laylin et al.
Cell
(2010)
A. Penzkofer et al.
Chem. Phys.
(2011)
A. Penzkofer et al.
Chem. Phys.
(2012)
A. Penzkofer et al.
J. Photochem. Photobiol. A Chem.
(2011)
S. Masuda et al.
Cell
(2002)
P. Zirak et al.
J. Photochem. Photobiol. B Biol.
(2006)
J.U. Linder et al.
Cell. Signal.
(2003)
J. Garnier et al.
Methods Enzymol.
(1996)

W. Holzer et al.

Chem. Phys.

(1999)

A. Penzkofer

Chem. Phys.

(2012)

D. Fujimoto

Comp. Biochem. Physiol.

(1975)

D.A. Malencik et al.

Biochem. Biophys. Res. Commun.

(1991)

D.A. Malencik et al.

Analyt. Biochem.

(1996)

L.A. Marquez et al.

J. Biol. Chem.

(1995)

Y.P. Tsentalovich et al.

J. Photochem. Photobiol. A Chem.

(2004)

W. Holzer et al.

Chem. Phys.

(2005)

P.L. Privalov

Adv. Protein Chem.

(1979)

J. Walters et al.

Methods Enzymol.

(2009)

L.M. Gloss

Methods Enzymol.

(2009)

P. Zirak et al.

Chem. Phys.

(2007)

A. Tyagi et al.

Chem. Phys.

(2008)

P. Drössler et al.

Chem. Phys.

(2002)

S.-H. Song et al.

J. Photochem. Photobiol. B Biol.

(2007)

M. Stierl et al.

J. Biol. Chem.

(2011)

J. Götze et al.

J. Photochem. Photobiol. B: Biol.

(2009)

J.F. De Jonckheere

Acta Protozool.

(2002)

C. Fulton et al.

PNAS

(1984)

C. Fulton et al.

Microbiol.

(1983)

B.D. Zoltowski et al.

Biochem.

(2011)

W. Laan et al.

Biochem.

(2006)

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Absorption and emission spectroscopic characterization of photo-dynamics of photoactivated adenylyl cyclase mutant bPAC-Y7F of Beggiatoa sp.
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Citation Excerpt :
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The absorption and emission spectroscopic behavior of the photo-activated adenylyl cyclase NgPAC3 from the amoeboflagellate Naegleria gruberi NEG-M strain was studied. The flavin cofactor was found to be partly fully oxidized and partly fully reduced. The typical BLUF domain (BLUF = Blue Light sensor Using Flavin) oxidized flavin absorption photo-cycle dynamics with about 14 nm flavin absorption red-shift in the signaling state was observed. The quantum efficiency of signaling state formation was determined to be ϕ_s = 0.66 ± 0.03. A bi-exponential signaling state recovery to the dark-adapted receptor state was observed with the time constants τ_rec,f = 275 s and τ_rec,sl = 45 min. The thermal irreversible protein unfolding was studied and an apparent protein melting temperature of ϑ_m ≈ 50 °C was found. The photodynamic behavior of NgPAC3 is compared with the behavior of the previously investigated photo-activated cyclases NgPAC1 (nPAC) and NgPAC2 from the same N. gruberi NEG-M strain. Purified recombinant NgPAC3 showed light-gated adenylate cyclase activity upon illumination with blue light. Its cyclase activity is compared with those of NgPAC1 and NgPAC2.
Photo-dynamics of the lyophilized photo-activated adenylate cyclase NgPAC2 from the amoeboflagellate Naegleria gruberi NEG-M strain
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Citation Excerpt :
This indicates that the flavin – amino acid interaction in the BLUF domain flavin binding pocket is different for snap-frozen and lyophilized NgPAC2. In snap-frozen NgPAC2 the adjacent location of the amino acids Ala(9) and Glu(102) were reported to be responsible for the red-shift of the S0–S1 flavin absorption band [10,56,57]. The BLUF-type photo-cycling of snap-frozen NgPAC2 showing up in photo-induced flavin S0–S1 absorption band red-shift was lost for lyophilized NgPAC2.
The absorption and emission spectroscopic behavior of lyophilized photo-activated adenylate cyclase NgPAC2 from the amoeboflagellate Naegleria gruberi NEG-M strain consisting of a BLUF domain (BLUF = Blue Light sensor Using Flavin) and a cyclase homology domain was studied in the dark, during blue-light exposure and after blue-light exposure at a temperature of 4 °C. The BLUF domain photo-cycle dynamics observed for snap-frozen NgPAC2 was lost by lyophilization (no signaling state formation with flavin absorption red-shift). Instead, blue-light photo-excitation of lyophilized NgPAC2 caused sterically restricted Tyr–Tyr cross-linking (o,o′-ditysosine formation) and partial flavin cofactor reduction.

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Photo-dynamics and thermal behavior of the BLUF domain containing adenylate cyclase NgPAC2 from the amoeboflagellate Naegleria gruberi NEG-M strain

Abstract

Graphical abstract

Highlights

Introduction

Section snippets

Sample preparation

Flavin composition and cofactor loading of NgPAC2

Discussion

Conclusions

Acknowledgments

Exp. Cell Res.

Res. Microbiol.

Cell

Chem. Phys.

Chem. Phys.

J. Photochem. Photobiol. A Chem.

Cell

J. Photochem. Photobiol. B Biol.

Cell. Signal.

Methods Enzymol.

Chem. Phys.

Chem. Phys.

Comp. Biochem. Physiol.

Biochem. Biophys. Res. Commun.

Analyt. Biochem.

J. Biol. Chem.

J. Photochem. Photobiol. A Chem.

Chem. Phys.

Adv. Protein Chem.

Methods Enzymol.

Methods Enzymol.

Chem. Phys.

Chem. Phys.

Chem. Phys.

J. Photochem. Photobiol. B Biol.

J. Biol. Chem.

J. Photochem. Photobiol. B: Biol.

Acta Protozool.

PNAS

Microbiol.

Biochem.

Biochem.