Biosynthesis of the two halobacterial light sensors P480 and sensory rhodopsin and variation in gain of their signal transduction chains

Microbial rhodopsins of Halorubrum species isolated from Ejinoor salt lake in Inner Mongolia of China

Microbial rhodopsins are photoactive proteins that use a retinal molecule as the photoactive center. Because of structural simplicity and functional diversity, microbial rhodopsins have been an excellent model system for structural biology. In this study, a halophilic archaea that has three microbial rhodopsin-type genes in its genome was isolated from Ejinoor salt lake in Inner Mongolia of China. A sequence of 16S rRNA showed that the strain belongs to Halorubrum genus and named Halorubrum sp. ejinoor (He). The translated amino acid sequences of its microbial rhodopsin-type genes suggest that they are homologs of archaerhodopsin (HeAR), halorhodopsin (HeHR) and sensory rhodopsin II (HeSRII). The mRNAs of three types of genes were detected by RT-PCR and their amounts were investigated by Real-Time RT-PCR. The amount of mRNA of HeSRII was the smallest and the amounts of of HeAR and HeHR were 30 times and 10 times greater than that of HeSRII. The results of light-induced pH changes suggested the presence of a light-driven proton pump and a light-driven chloride ion pump in the membrane vesicles of He. Flash induced absorbance changes of the He membrane fraction indicated that HeAR and HeHR are photoactive and undergo their own photocycles. This study revealed that three microbial rhodopsin-type genes are all expressed in the strain and at least two of them, HeAR and HeHR, are photochemically and physiologically active like BR and HR of Halobacterium salinarum, respectively. To our knowledge, this is the first report of physiological activity of HR-homolog of Halorubrum species.

A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis

Background

Photo- and chemotaxis of the archaeon Halobacterium salinarum is based on the control of flagellar motor switching through stimulus-specific methyl-accepting transducer proteins that relay the sensory input signal to a two-component system. Certain members of the transducer family function as receptor proteins by directly sensing specific chemical or physical stimuli. Others interact with specific receptor proteins like the phototaxis photoreceptors sensory rhodopsin I and II, or require specific binding proteins as for example some chemotaxis transducers. Receptor activation by light or a change in receptor occupancy by chemical stimuli results in reversible methylation of glutamate residues of the transducer proteins. Both, methylation and demethylation reactions are involved in sensory adaptation and are modulated by the response regulator CheY.

Results

By mathematical modeling we infer the kinetic mechanisms of stimulus-induced transducer methylation and adaptation. The model (deterministic and in the form of ordinary differential equations) correctly predicts experimentally observed transducer demethylation (as detected by released methanol) in response to attractant and repellent stimuli of wildtype cells, a cheY deletion mutant, and a mutant in which the stimulated transducer species is methylation-deficient.

Conclusions

We provide a kinetic model for signal processing in photo- and chemotaxis in the archaeon H. salinarum suggesting an essential role of receptor cooperativity, antagonistic reversible methylation, and a CheY-dependent feedback on transducer demethylation.

Translational diffusion and interaction of a photoreceptor and its cognate transducer observed in giant unilamellar vesicles by using dual-focus FCS

In order to monitor membrane-protein binding in lipid bilayers at physiological protein concentrations, we employed the recently developed dual-focus fluorescence correlation spectroscopy (2fFCS) technique. In a case study on a photoreceptor consisting of seven transmembrane helices and its cognate transducer (two transmembrane helices), the lateral diffusion for these integral membrane proteins was analyzed in giant unilamellar vesicles (GUVs). The two-dimensional diffusion coefficients of both separately diffusing proteins differ significantly, with D = 2.2 x 10(-8) cm2 s(-1) for the photoreceptor and with D = 4.1 x 10(-8) cm2 s(-1) for the transducer. In GUVs with both membrane proteins present together, we observed significantly smaller diffusion coefficients for labelled transducer molecules; this indicates the presence of larger diffusing units and therefore intermolecular protein binding. Based on the phenomenological dependence of diffusion coefficients on the molecule's cylindrical radius, we are able to estimate the degree of membrane protein binding on a quantitative level.

Automatic reconstruction of molecular and genetic networks from discrete time series data

We apply a mathematical algorithm which processes discrete time series data to generate a complete list of Petri net structures containing the minimal number of nodes required to reproduce the data set. The completeness of the list as guaranteed by a mathematical proof allows to define a minimal set of experiments required to discriminate between alternative network structures. This in principle allows to prove all possible minimal network structures by disproving all alternative candidate structures. The dynamic behaviour of the networks in terms of a switching rule for the transitions of the Petri net is part of the result. In addition to network reconstruction, the algorithm can be used to determine how many yet undetected components at least must be involved in a certain process. The algorithm also reveals all alternative structural modifications of a network that are required to generate a predefined behaviour.

Direct observation of different surface structures on high-resolution images of native halorhodopsin

Halorhodopsin (HR) was investigated with atomic force microscopic techniques (AFM) in aqueous solution. Two-dimensional (2D) crystals of HR were obtained by purifying an HR membrane fraction with the same buoyant density as the purple membrane (HR-PM) from the overexpressing strain Halobacterium salinarum D2. The membrane patches of HR were immobilized on mica. Images with a resolution up to 14 A were recorded. Crystals showed an orthogonal structure and the orientation of the molecules showed p42(1)2 symmetry; thus, alternate tetramers are inverted in the membrane. The crystal surface was found to display different structures depending on the imaging force used, indicating that some parts of the HR molecule are more rigid but others more compressible. From samples with single tetramers missing in the crystalline patches dimensions of the unit cell could be determined. Helix-connecting loops in single molecules of halorhodopsin were assigned. The images indicate that the large extracellular BC loop covers the whole molecule and is very flexible.

Competition-integration of blue and orange stimuli in Halobacterium salinarum cannot occur solely in SRI photoreceptor

Experiments on the integration of blue and orange stimuli in Halobacterium salinarum were performed by using different combinations of blue and orange steps. The results show that the prevalence of the blue stimulus over the orange one depends on both the blue and the orange light intensities. A quantitative analysis of the current hypotheses on the phototransduction of orange and UV-blue light stimuli is presented, showing that the balancing between the two antagonistic stimuli should depend only on the intensity of the blue stimulus and not on that of the orange one, provided that the combination of the two stimuli occurs linearly at the photoreceptor stage. We conclude that blue and orange stimuli elicit distinct intracellular signals whose integration occurs downstream of the photoreceptor.

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.

Damped oscillations in photosensory transduction of Halobacterium salinarium induced by repellent light stimuli

Halobacteria usually respond to repellent light stimuli by reversing their swimming direction. However, cells seem to be in a refractory state when stimulated immediately after performance of a reversal. I found that in this case, a special type of response is exhibited rather than spontaneous behavior. A strong stimulus induced a rhythmic pattern of successive reversals. On stimulation immediately after a reversal of swimming direction, the first of these reversals was skipped without influence on the rhythm. The results suggest that the stimulus evokes an oscillating signal which alters reversal probability but which is itself independent of the state of the motor apparatus. The oscillation has a period length of about 5 s and is damped out within a few cycles. It does not depend on the special sensory photosystem through which the stimulus is applied. The consequences of these findings for the model description of swimming behavior control in halobacteria are discussed.

Isolation of photochemically active archaebacterial photoreceptor, pharaonis phoborhodopsin from Natronobacterium pharaonis

A photoreceptor, pharaonis phoborhodopsin for the negative phototaxis of extremely halophilic and alkalophilic archaebacterium, Natronobacterium pharaonis was isolated in a photochemically active state. A detailed examination of the chromatographic separation made it possible to separate contaminating proteins, such as cytochromes. The procedure resulted in a 2938-fold enrichment with a yield of 15.5%. The isolated pharaonis phoborhodopsin had an absorption maximum at 498 nm, an A280/A498 ratio of 1.27 and a single band near 24 kDa on the SDS-polyacrylamide gels. The isolated pharaonis phoborhodopsin underwent a photochemical reaction after flash excitation. The photocyclic reaction closely resembled that of the membrane-bound pharaonis phoborhodopsin.

Sensitivity of Halobacterium salinarium to attractant light stimuli does not change periodically

Halobacterium salinarium swims alternately in both directions of its cell axis. The average time between two reversals of the swimming direction is modulated by light stimuli. It is a matter of dispute whether the sensitivity to attractant stimuli depends on the time of stimulation during an interval. This question is crucial for model descriptions of the system. I have confirmed constancy of responsiveness with cells adapted to constant conditions and have reconstructed contradicting results. These are shown to be based on inadequate experimental and evaluative methods. The assumption of self-sustained oscillations which modulate sensitivity can not be justified from the attractant response.

The photoactive yellow protein from Ectothiorhodospira halophila as studied with a highly specific polyclonal antiserum: (intra)cellular localization, regulation of expression, and taxonomic distribution of cross-reacting proteins

A rabbit antiserum was raised against the photoactive yellow protein (PYP) from Ectothiorhodospira halophila and purified by adsorption experiments to obtain a highly specific polyclonal antiserum. This antiserum was used to obtain the following results. (i) In E. halophila, PYP can be isolated from the fraction of soluble proteins. In the intact cell, however, PYP appeared to be associated with (intra)cytoplasmic membranes, as was concluded from analysis of immunogold-labelled thin sections of the organism. (ii) The regulation of expression of PYP was studied by using dot blot assays, Western blotting (immunoblotting), and rocket immunoelectrophoresis. Under all conditions investigated (light color, salt concentration, and growth phase), PYP was expressed constitutively in E. halophila. However, when Rhodospirillum salexigens was grown aerobically, the expression of PYP was suppressed. (iii) A large number of prokaryotic microorganisms contained a single protein, with an apparent size of approximately 15 kDa, that cross-reacted with the antiserum. Among the positively reacting organisms were both phototrophic and chemotrophic, as well as motile and nonmotile, organisms. After separation of cellular proteins into a membrane fraction and soluble proteins, it was established that organisms adapted to growth at higher salt concentrations tended to have the cross-reacting protein in the soluble fraction. In the cases of R. salexigens and Chromatium salexigens, we have shown that the cross-reacting protein involved is strongly homologous to PYP from E. halophila.

Sensory rhodopsin-controlled release of the switch factor fumarate in Halobacterium salinarium

Halobacterium salinarium responds to blue light by reversing its swimming direction. Fumarate has been proposed as one of the molecular components of this sensory system and is involved in the switching process of the flagellar motor. In order to obtain chemical proof for this role of fumarate, cells were stimulated with a pulse of blue light and lysed by rapid mixing with distilled water. The lysate contained fumarate in free and bound form, which were separated by ultrafiltration. The fumarate concentration in the low-molecular-mass fraction (< 5 kDa) of the lysate was assayed enzymatically and a light-induced increase was observed. Additionally, the total cellular fumarate content decreased in response to light, indicating that fumarate was released from a cellular pool rather than being formed by de novo synthesis. The light-induced release was not detected in a mutant defective in sensory rhodopsin-I and -II. Therefore it is concluded that photoreceptor activation rather than a direct effect of light on the activity of metabolic enzymes causes fumarate release. For each photoactivated sensory rhodopsin-II molecule at least 350 molecules of fumarate were liberated demonstrating efficient amplification. The rate of light-induced fumarate release is at least 10-times faster than the fumarate turnover number of the citric acid cycle which was estimated as approximately 4300 per cell and second. Therefore this metabolic process is not expected to be part of the signal transduction chain in the halobacterial cell.

A C-terminal truncation results in high-level expression of the functional photoreceptor sensory rhodopsin I in the archaeon Halobacterium salinarium

Expression of the gene encoding the halobacterial photoreceptor sensory rhodopsin I (SRI), sopI, was studied by means of homologous gene targeting. A sopI- Halobacterium salinarium mutant strain was constructed by homologous replacement of sopI with a novobiocin-resistant gyrB from Haloferax Aa 2.2. Cells bearing gyrB were resistant to novobiocin, indicating that the Haloferax gene is functional in H. salinarium. Complementation of this deletion strain with sopI fused to the bacterio-opsin promoter resulted in the recovery of all phenotypical attributes of SRI. This establishes the first direct correlation between sopI and the function of its gene product. In the complemented deletion strain, functional expression of sopI occurred from the bop locus, where sopI had integrated by homologous recombination. This shows that cotranscription of sopI and the gene encoding the SRI signal transducer, htrI, which is found in the wild type, is not a prerequisite for photosensory activity. Deletion of the last 43 bp at the 3' end of sopI resulted in a 10-fold increase in the amount of SRI, without affecting the activity of the pigment. The mRNA level of the truncated gene was not affected as compared to that of the wild type. We propose that regulation occurs at the protein level, probably through a negative determinant of protein stability located in the C-terminus of SRI. Replacement of the last 28 amino acids of bacteriorhodopsin by the last 29 amino acids of SRI results in a decrease of the bacteriorhodopsin, supporting our observations. The C-terminus of SRI is the first domain with a downregulating influence on protein levels thus far identified in H. salinarium. The system for SRI overexpression we present here greatly facilitates biochemical and biophysical studies on the photoreceptor and allows investigation of the molecular interactions underlying the signal transduction chain of halobacterial phototaxis.

The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein

The motile, alkalophilic, and extremely halophilic purple sulfur bacterium Ectothiorhodospira halophila is positively photophobotactic. This response results in the accumulation of bacteria in light spots (E. Hustede, M. Liebergesell, and H. G. Schlegel, Photochem. Photobiol. 50:809-815, 1989; D. E. McRee, J. A. Tainer, T. E. Meyer, J. Van Beeumen, M. A. Cusanovich, and E. D. Getzoff, Proc. Natl. Acad. Sci. USA 86:6533-6537, 1989; also, this work). In this study, we demonstrated that E. halophila is also negatively phototactic. Video analysis of free-swimming bacteria and the formation of cell distribution patterns as a result of light-color boundaries in an anaerobic suspension of cells revealed the existence of a repellent response toward intense (but nondamaging) blue light. In the presence of saturating background photosynthetic light, an increase in the intensity of blue light induced directional switches, whereas a decrease in intense blue light gave rise to suppression of these reversals. To our knowledge, this is the first report of a true repellent response to light in a free-swimming eubacterium, since the blue light response in Escherichia coli and Salmonella typhimurium (B. L. Taylor and D. E. Koshland, Jr., J. Bacteriol. 123:557-569, 1975), which requires an extremely high light intensity, is unlikely to be a sensory process. The wavelength dependence of this negative photoresponse was determined with narrow band pass interference filters. It showed similarity to the absorption spectrum of the photoactive yellow protein from E. halophila.

Sensitivity increase in the photophobic response of Halobacterium halobium reconstituted with retinal analogs: a novel interpretation for the fluence-response relationship and a kinetic modeling

Phoborhodopsin (also called sensory rhodopsin II) is a photoreceptor protein which mediates photophobic responses of Halobacterium halobium to blue-green light. Under conditions where the synthesis of the chromophore retinal is inhibited, the photophobic system is reconstituted in vivo by incorporation of all-trans retinal or retinal analogs into the apoprotein of phoborhodopsin. Retinal analogs which retard the cyclic photoreaction kinetics of phoborhodopsin increase significantly the sensitivity of the photophobic response. This supports the previously reported hypothesis that signal amplification occurs during the lifetime of intermediate states of the photocycle. The sensitivity increase caused by the chromophore substitution is observed in cells at several different growth stages, i.e. the naturally occurring chromophore (all-trans retinal) does not produce maximal sensitivity at any stage of the culture growth. These results are difficult to interpret in terms of the proposal by Marwan et al. (J. Mol. Biol. 199, 663-664, 1988) that only a single photon is sufficient to cause the photobehavioral response in cells containing native phoborhodopsin. A new interpretation for the fluence-response curves is described based in part on their Poisson statistical analysis. Further, a kinetic model which relates the receptor photochemical reaction cycle to the behavioral response is developed, which accounts for both the sensitivity increase and the shape of the fluence-response curves.

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.

Rotation and switching of the flagellar motor assembly in Halobacterium halobium

Halobacterium halobium swims with a polarly inserted motor-driven flagellar bundle. The swimming direction of the cell can be reserved by switching the rotational sense of the bundle. The switch is under the control of photoreceptor and chemoreceptor proteins that act through a branched signal chain. The swimming behavior of the cells and the switching process of the flagellar bundle were investigated with a computer-assisted motion analysis system. The cells were shown to swim faster by clockwise than by counterclockwise rotation of the flagellar bundle. From the small magnitude of speed fluctuations, it is concluded that the majority, if not all, of the individual flagellar motors of a cell rotate in the same direction at any given time. After stimulation with light (blue light pulse or orange light step-down), the cells continued swimming with almost constant speed but then slowed before they reversed direction. The cells passed through a pausing state during the change of the rotational sense of the flagellar bundle and then exhibited a transient acceleration. Both the average length of the pausing period and the transient acceleration were independent of the stimulus size and thus represent intrinsic properties of the flagellar motor assembly. The average length of the pausing period of individual cells, however, was not constant. The time course of the probability for spontaneous motor switching was calculated from frequency distribution and shown to be independent of the rotational sense. The time course further characterizes spontaneous switching as a stochastic rather than an oscillator-triggered event.

Quantitation of photochromism of sensory rhodopsin-I by computerized tracking of Halobacterium halobium cells

The swimming behavior of Halobacterium halobium is controlled by light which acts through retinal photoreceptor proteins. The sensing of near-ultraviolet (u.v.) was proposed to be mediated by the thermally metastable intermediate SR-I373 that is formed upon orange light absorption by sensory rhodopsin-I (SR-I). In order to test the validity of this proposal, we analyzed the photochromic behavior of the functional near-u.v. receptor in situ by use of an automated cell tracking system. The system was specifically designed for detection of swimming reversals in individual cells and calibrated with a straight-swimming mutant of H. halobium. Quantitative analysis of the response of the cells to near-u.v. revealed that orange background light increased the number of active near-u.v. receptor molecules. The intensity-dependence of this effect fitted into the kinetic scheme of a photochromic receptor pigment. The half-life of the functional near-u.v. receptor species was determined under continuous orange background light and found to be similar to that of the SR-I373 intermediate of sensory rhodopsin-I in intact cells. These results clearly support the assignment of the near-u.v. receptor to SR-I373. The kind of kinetic analysis described here, might be a useful tool in assigning spectroscopic data of pigments to photoreceptor function also in other organisms.

Characterization of Halobacterium halobium mutants defective in taxis

Mutant derivatives of Halobacterium halobium previously isolated by using a procedure that selected for defective phototactic response to white light were examined for an array of phenotypic characteristics related to phototaxis and chemotaxis. The properties tested were unstimulated swimming behavior, behaviorial responses to temporal gradients of light and spatial gradients of chemoattractants, content of photoreceptor pigments, methylation of methyl-accepting taxis proteins, and transient increases in rate of release of volatile methyl groups induced by tactic stimulation. Several distinct phenotypes were identified, corresponding to a mutant missing photoreceptors, a mutant defective in the methyltransferase, a mutant altered in control of the methylesterase, and mutants apparently defective in intracellular signaling. All except the photoreceptor mutant were defective in both chemotaxis and phototaxis.