Low-temperature spectrophotometry of phoborhodopsin

Key determinants for signaling in the sensory rhodopsin II/transducer complex are different between Halobacterium salinarum and Natronomonas pharaonis

The cell membrane of Halobacterium salinarum contains a retinal-binding photoreceptor, sensory rhodopsin II (HsSRII), coupled with its cognate transducer (HsHtrII), allowing repellent phototaxis behavior for shorter wavelength light. Previous studies on SRII from Natronomonas pharaonis (NpSRII) pointed out the importance of the hydrogen bonding interaction between Thr204NpSRII and Tyr174NpSRII in signal transfer from SRII to HtrII. Here, we investigated the effect on phototactic function by replacing residues in HsSRII corresponding to Thr204NpSRII and Tyr174NpSRII . Whereas replacement of either residue altered the photocycle kinetics, introduction of any mutations at Ser201HsSRII and Tyr171HsSRII did not eliminate negative phototaxis function. These observations imply the possibility of the presence of an unidentified molecular mechanism for photophobic signal transduction differing from NpSRII-NpHtrII.

Molecular and evolutionary aspects of microbial sensory rhodopsins

Retinal proteins (~rhodopsins) are photochemically reactive membrane-embedded proteins, with seven transmembrane α-helices which bind the chromophore retinal (vitamin A aldehyde). They are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. Light absorption by the retinal proteins triggers a photoisomerization of the chromophore, leading to the biological function, light-energy conversion or light-signal transduction. This article reviews molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors and their related proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

An amino acid residue (S201) in the retinal binding pocket regulates the photoreaction pathway of phoborhodopsin

Phoborhodopsin from Halobacterium salinarum (salinarum phoborhodopsin, spR also called HsSR II) is a photoreceptor for the negative phototaxis of the bacterium. A unique feature of spR is the formation of a shorter wavelength photoproduct, P480, observed at liquid nitrogen temperature beside the K intermediate. Formation of similar photoproduct has not been reported in the other microbial rhodopsins. This photoproduct showed its maximum absorbance wavelength (λ(max)) at 482 nm and can thermally revert back to spR above -160 °C. It was revealed that P480 is a photoproduct of K intermediate by combination of an irradiation and warming experiment. Fourier transform infrared (FTIR) difference spectrum of P480 from spR in C-C stretching vibration region showed similar features with that of K intermediate, suggesting that P480 has a 13-cis-retinal chromophore. The appearance of a broad positive band at 1214 cm(-1) in the P480-spR spectrum suggested that configuration around C9═C10 likely be different between P480 and K intermediate. Vibrational bands in HOOP region (1035 to 900 cm(-1)) suggested that the chromophore distortion in K intermediate was largely relaxed in P480. The amount of P480 formed by the irradiation was greatly decreased by amino acid replacement of S201 with T, suggesting S201 was involved in the formation of P480. According to the crystal structure of pharaonis phoborhodopsin (ppR), a homologue of spR found in Natronomonas pharaonis, S201 should locate near the C14 of retinal chromophore. Thus, the interaction between S201 and C14 might be the main factor affecting formation of P480.

The photochemical reaction cycle and photoinduced proton transfer of sensory rhodopsin II (Phoborhodopsin) from Halobacterium salinarum

Sensory rhodopsin II (HsSRII, also called phoborhodopsin) is a negative phototaxis receptor of Halobacterium salinarum, a bacterium that avoids blue-green light. In this study, we expressed the protein in Escherichia coli cells, and reconstituted the purified protein with phosphatidylcholine. The reconstituted HsSRII was stable. We examined the photocycle by flash-photolysis spectroscopy in the time range of milliseconds to seconds, and measured proton uptake/release using a transparent indium-tin oxide electrode. The pKa of the counterion of the Schiff base, Asp(73), was 3.0. Below pH 3, the depleted band was observed on flash illumination, but the positive band in the difference spectra was not found. Above pH 3, the basic photocycle was HsSRII (490) --> M (350) --> O (520) --> Y (490) --> HsSRII, where the numbers in parentheses are the maximum wavelengths. The decay rate of O-intermediate and Y-intermediate were pH-independent, whereas the M-intermediate decay was pH-dependent. For 3 < pH < 4.5, the M-decay was one phase, and the rate decreased with an increase in pH. For 4.5 < pH < 6.5, the decay was one phase with pH-independent rates, and azide markedly accelerated the M-decay. These findings suggest the existence of a protonated amino acid residue (X-H) that may serve as a proton relay to reprotonate the Schiff base. Above pH 6.5, the M-decay showed two phases. The fast M-decay was pH-independent and originated from the molecule having a protonated X-H, and the slow M-decay originated from the molecule having a deprotonated X, in which the proton came directly from the outside. The analysis yielded a value of 7.5 for the pKa of X-H. The proton uptake and release occurred during M-decay and O-decay, respectively.

Structural changes of pharaonis phoborhodopsin upon photoisomerization of the retinal chromophore: infrared spectral comparison with bacteriorhodopsin

Archaeal rhodopsins possess a retinal molecule as their chromophores, and their light energy and light signal conversions are triggered by all-trans to 13-cis isomerization of the retinal chromophore. Relaxation through structural changes of the protein then leads to functional processes, proton pump in bacteriorhodopsin and transducer activation in sensory rhodopsins. In the present paper, low-temperature Fourier transform infrared spectroscopy is applied to phoborhodopsin from Natronobacterium pharaonis (ppR), a photoreceptor for the negative phototaxis of the bacteria, and infrared spectral changes before and after photoisomerization are compared with those of bacteriorhodopsin (BR) at 77 K. Spectral comparison of the C--C stretching vibrations of the retinal chromophore shows that chromophore conformation of the polyene chain is similar between ppR and BR. This fact implies that the unique chromophore-protein interaction in ppR, such as the blue-shifted absorption spectrum with vibrational fine structure, originates from both ends, the beta-ionone ring and the Schiff base regions. In fact, less planer ring structure and stronger hydrogen bond of the Schiff base were suggested for ppR. Similar frequency changes upon photoisomerization are observed for the C==N stretch of the retinal Schiff base and the stretch of the neighboring threonine side chain (Thr79 in ppR and Thr89 in BR), suggesting that photoisomerization in ppR is driven by the motion of the Schiff base like BR. Nevertheless, the structure of the K state after photoisomerization is different between ppR and BR. In BR, chromophore distortion is localized in the Schiff base region, as shown in its hydrogen out-of-plane vibrations. In contrast, more extended structural changes take place in ppR in view of chromophore distortion and protein structural changes. Such structure of the K intermediate of ppR is probably correlated with its high thermal stability. In fact, almost identical infrared spectra are obtained between 77 and 170 K in ppR. Unique chromophore-protein interaction and photoisomerization processes in ppR are discussed on the basis of the present infrared spectral comparison with BR.

The photophobic receptor from Natronobacterium pharaonis: temperature and pH dependencies of the photocycle of sensory rhodopsin II

The photocycle of the photophobic receptor sensory rhodopsin II from N. pharaonis was analyzed by varying measuring wavelengths, temperature, and pH, and by exchanging H2O with D2O. The data can be satisfactorily modeled by eight exponents over the whole range of modified parameters. The kinetic data support a model similar to that of bacteriorhodopsin (BR) if a scheme of irreversible first-order reactions is assumed. Eight kinetically distinct protein states can then be identified. These states are formed from five spectrally distinct species. The chromophore states Si correspond in their spectral properties to those of the BR photocycle, namely pSRII510 (K), pSRII495 (L), pSRII400 (M), pSRII485 (N), and pSRII535 (O). In comparison to BR, pSRII400 is formed approximately 10 times faster than the M state; however, the back-reaction is almost 100 times slower. Comparison of the temperature dependence of the rate constants with those from the BR photocycle suggests that the differences are caused by changes of DeltaS. The rate constants of the pSRII photocycle are almost insensitive to the pH variation from 9.0 to 5.5, and show only a small H2O/D2O effect. This analysis supports the idea that the conformational dynamics of pSRII controls the kinetics of the photocycle of pSRII.

Molecular mechanism of photosignaling by archaeal sensory rhodopsins

Two sensory rhodopsins (SRI and SRII) mediate color-sensitive phototaxis responses in halobacteria. These seven-helix receptor proteins, structurally and functionally similar to animal visual pigments, couple retinal photoisomerization to receptor activation and are complexed with membrane-embedded transducer proteins (HtrI and HtrII) that modulate a cytoplasmic phosphorylation cascade controlling the flagellar motor. The Htr proteins resemble the chemotaxis transducers from Escherichia coli. The SR-Htr signaling complexes allow studies of the biophysical chemistry of signal generation and relay, from the photobiophysics of initial excitation of the receptors to the final output at the level of the flagellar motor switch, revealing fundamental principles of sensory transduction and more broadly the nature of dynamic interactions between membrane proteins. We review here recent advances that have led to new insights into the molecular mechanism of signaling by these membrane complexes.

Divergent pathways in photobleaching of 7,9-dicis-rhodopsin and 9,11-dicis-12-fluororhodopsin: one-photon-two-bond and one-photon-one-bond isomerization

Through low-temperature photochemistry, UV/vis spectroscopy, and chromophore extraction experiments, we have established that 7,9-dicis-rhodopsin undergoes one-photon-two-bond photoisomerization to a batho intermediate (its absorption maximum is slightly blue shifted from that of bathorhodopsin) containing the all-trans geometry, while 9,11-dicis-12-fluororhodopsin undergoes one-photon-one-bond isomerization to the corresponding 9-cis isomer and then the all-trans batho intermediate. The difference in the photochemical properties of the two dicis pigment analogs was rationalized by possible local protein perturbation, lability of the 11-cis geometry, and photochemical properties of the chromophores.

Biochemical and photochemical properties of the photophobic receptors from Halobacterium halobium and Natronobacterium pharaonis

The phototaxis of Halobacterium halobium is initiated by two photoreceptors, the sensory rhodopsins sR-I and sR-II. An sR-II-like pigment has also been described in Natronobacterium pharaonis. In this work it was shown that N. pharaonis cells are repelled by light with a wavelength of 500 nm. A further comparison of membrane preparations from H. halobium (mutant D1) containing only sR-II and from N. pharaonis [strain SP1(28)] with a chromophoric protein (psR-II) resembling sR-II revealed substantial similarities. The biochemical and photochemical properties of the pigments are quite similar, with psR-II being more stable to external conditions such as pH and ionic strength of the buffer. Both pigments are bleached by low concentrations of hydroxylamine and can be reconstituted by the addition of all-trans-retinal. The absorption spectrum of psR-II is quite similar to sR-II including the shoulder on the short-wavelength side. After light excitation sR-II and psR-II undergo photocycles with at least three intermediates. The earliest intermediate has an absorption maximum above 520 nm and decays to a species which has a characteristic absorption (approximately 380 nm) of a deprotonated Schiff base. The final step is the regeneration of the original ground state via a red-shifted intermediate absorbing around 540 nm. From this cumulative evidence it can be concluded that, not only sR-II, but also the pigment from N. pharaonis is a photophobic photoreceptor.

Identification of signaling states of a sensory receptor by modulation of lifetimes of stimulus-induced conformations: the case of sensory rhodopsin II

Lifetimes of stimulus-induced conformations of the phototaxis receptor sensory rhodopsin II (SR-II) from Halobacterium halobium are modulated with seven receptor analogues. By monitoring the receptor dynamics in vitro and physiological responses of the cell in vivo, we observe receptor signaling efficiency increases with decreasing cycling frequency (turnover number) of the receptor. The results demonstrate that modulating lifetimes of protein conformations at the SR-II photoactivation site with chromophore analogues alters the lifetime of the active conformation at the signaling site. We further explore the relationship between photocycle intermediates and the signaling efficiency by analyzing the time-averaged concentrations of the two long-lived spectral intermediates of the SR-II photocycle: S-II350 and S-II530. The results are consistent with the signaling site being activated during formation of S-II350, but not reset by the transition of S-II350 into S-II530; rather deactivation appears to require subsequent decay of S-II530. The results indicate the structural changes at the photoactivation site in the S-II350----S-II530 transition do not reset the signaling site. The procedure used here, applicable in principle to any photoactivated or ligand-activated receptor, provides an initial approach to identify structural alterations key to the receptor activation process.

Photoreaction cycle of phoborhodopsin studied by low-temperature spectrophotometry

The photochemical and subsequent thermal reactions of phoborhodopsin (pR490), which mediates the negative phototaxis (phobic reaction) of Halobacterium halobium, were investigated by low-temperature spectrophotometry. At room temperature, the absorption spectrum of pR490 displayed vibrational structure with a maximum at 490 nm and a shoulder at 460 nm, which were remarkably sharpened by cooling, resulting in the appearance of two well-separated peaks. On irradiation of pR490 at -170 degrees C, a photo-steady-state mixture composed of pR490 and two photoproducts, P520 and P480, was formed. P480 had an absorption maximum at 480 nm and thermally converted to pR490 above -160 degrees C, while P520 had an absorption maximum at 515 nm and thermally converted to P350, the next intermediate, above -60 degrees C. Above -30 degrees C, P350 was converted to P530, and then reverted to pR490. P520, P350, and P530 may correspond to K, M, and O intermediates of bacteriorhodopsin, respectively, on the basis of their absorption spectra, but the intermediates corresponding to L and N intermediates were not observed. On the basis of these results, a new scheme of the photoreaction cycle of pR490 was presented.