Optogenetics: 10 years of microbial opsins in neuroscience

Over the past 10 years, the development and convergence of microbial opsin engineering, modular genetic methods for cell-type targeting and optical strategies for guiding light through tissue have enabled versatile optical control of defined cells in living systems, defining modern optogenetics. Despite widespread recognition of the importance of spatiotemporally precise causal control over cellular signaling, for nearly the first half (2005-2009) of this 10-year period, as optogenetics was being created, there were difficulties in implementation, few publications and limited biological findings. In contrast, the ensuing years have witnessed a substantial acceleration in the application domain, with the publication of thousands of discoveries and insights into the function of nervous systems and beyond. This Historical Commentary reflects on the scientific landscape of this decade-long transition.

High overexpression and purification of optimized bacterio-opsin from Halobacterium Salinarum R1 in E. coli

The purple membrane of Halobacterium Salinarum carries out a protein, bacteriorhodopsin (bR), which is a model for structure-function studies of membrane proteins. The heterologous expression of integral membrane proteins (IMPS) is difficult. In this study, we reported the heterologous overexpression of bacterio-opsin (bO) in Escherichia coli BL21 (DE3). Bacterio-opsin expression is facilitated by using mistic, a membrane protein from Bacillus subtilis in E. coli BL21 (DE3) membranes. The optimized bO gene was cloned in fusion to the C-terminus of mistic in pET 30a (+) and contains an oct-histidine in C-terminal to facilitate purification. Different medium, temperature, and induction time were used to optimize protein overexpression. The highest expression was obtained from the Terrific Broth (TB) medium at 18 °C with an IPTG concentration of 0.1 mM. The final purified bR was 192 ± 1 mg/L which has an important value for the production of membrane proteins in E. coli.

Heterogeneity in Regeneration of Bacteriorhodopsin from Bacterio-Opsin and All-transRetinal at High Temperatures: Implications for Dynamic Structural Fluctuations

Measurements of regeneration kinetics were performed in order to investigate the regeneration mechanisms of bacteriorhodopsin (bR) from thermally unfolded bacterio-opsin (bO) and all-trans retinal. Regeneration kinetics data were successfully fitted to a single exponential function when regeneration was performed at 25 degrees C after incubation at high temperatures. Conversely, the process of regeneration after the addition of retinal to bO at high temperatures occurred at two different rate constants. These findings strongly suggest that the slower regeneration of bR at high temperatures occurs as a result of dynamic structural fluctuation of bO, whereas the faster process corresponds to regeneration from bO, which retains a native structure capable of retinal binding.

Isolation and characterization of unsaturated fatty acids during bacteriorhodopsin preparation from Halobacterium halobium

AIMS

Isolation and characterization of unsaturated fatty acids during bacteriorhodopsin preparation from Halobacterium halobium.

METHODS AND RESULTS

Halobacterium halobium was cultivated in a composite medium. Cells were collected by centrifugation followed by ultrasonic disruption, and the resulting suspension was subject to centrifugation for preparation of both pellet and supernatant. The pellet was saved in order to prepare bacteriorhodopsin, while the supernatant was used for the isolation of crude fatty acids by saponification and extraction. Crystallization then took place in acetone at -16 degrees C to remove fatty acids in which the carbon chain length was shorter than 13. The sample was obtained after purification and analysed by gas chromatography. The results demonstrated that Halobacterium halobium could synthesize multiple unsaturated fatty acids, particularly the three important polyunsaturated fatty acids arachidonic acid (1.12%), eicosapentaenoic acid (16.76%) and docosahexaenoic acid (9.38%).

CONCLUSION

Important unsaturated fatty acids were isolated and characterized from the waste, which was produced during the preparation of bacteriorhodopsin from Halobacterium halobium.

SIGNIFICANCE AND IMPACT OF THE STUDY

Halobacterium halobium has already been used for decades to prepare bacteriorhodopsin. We found that several important unsaturated fatty acids could be extracted from the bacterial waste, which extends its application scope and might bring additional benefits to humanity.

Translation initiation with GUC codon in the archaeon Halobacterium salinarum: implications for translation of leaderless mRNA and strict correlation between translation initiation and presence of mRNA

We have investigated whether anticodon sequence mutant of an archaeal initiator tRNA can initiate protein synthesis using reporter genes carrying mutations in the initiation codon. Halobacterium salinarum was used as the model organism and the bacterio-opsin gene (bop), which encodes the precursor of the protein component of the purple membrane protein bacterio-opsin (Bop), was chosen as the reporter. We demonstrate that a CAU to GAC anticodon sequence mutant of Haloferax volcanii initiator tRNA can initiate Bop protein synthesis using GUC as the initiation codon in H. salinarum. We generated four mutant bop genes, each carrying the AUG to GUC initiation codon mutation, with or without a compensatory mutation to maintain a predicted stem-loop structure at the 5'-end of the bop mRNA, and with or without mutations to test translation initiation at a site corresponding to the amino terminus of mature bacterio-opsin. H. salinarum chromosomal recombinants containing these mutant genes were phenotypically Pum- (purple membrane negative). Upon transformation with a plasmid carrying the mutant initiator tRNA gene, only strains designed to maintain the bop mRNA stem-loop structure produced Bop and were phenotypically Pum+ as indicated by purple colony colour, and immunoblotting and spectral analysis of cell extracts. Thus GUC can serve as an initiation codon in archaea and the stem-loop structure in the bop mRNA is important for translation. Interestingly, for the same mutant mRNA, only transformants that produce Bop protein contain bop mRNA. These results suggest either a strong coupling between translation and mRNA stability or strong transcriptional polarity in H. salinarum.

Downstream coding region determinants of bacterio-opsin, muscarinic acetylcholine receptor and adrenergic receptor expression in Halobacterium salinarum

The aim of this work is to develop a prokaryotic system capable of expressing membrane-bound receptors in quantities suitable for biochemical and biophysical studies. Our strategy exploits the endogenous high-level expression of the membrane protein bacteriorhodopsin (BR) in the Archaeon Halobacterium salinarum. We attempted to express the human muscarinic acetylcholine (M(1)) and adrenergic (a2b) receptors by fusing the coding region of the m1 and a2b genes to nucleotide sequences known to direct bacterio-opsin (bop) gene transcription. The fusions included downstream modifications to produce non-native carboxyl-terminal amino acids useful for protein identification and purification. bop mRNA and BR accumulation were found to be tightly coupled and the carboxyl-terminal coding region modifications perturbed both. m1 and a2b mRNA levels were low, and accumulation was sensitive to both the extent of the bop gene fusion and the specific carboxyl-terminal coding sequence modifications included. Functional a2b adrenergic receptor expression was observed to be dependent on the downstream coding region. This work demonstrates that a critical determinant of expression resides in the downstream coding region of the wild-type bop gene and manipulation of the downstream coding region of heterologous genes may affect their potential for expression in H. salinarum.

Identification of a lycopene beta-cyclase required for bacteriorhodopsin biogenesis in the archaeon Halobacterium salinarum

Biogenesis of the light-driven proton pump bacteriorhodopsin in the archaeon Halobacterium salinarum requires coordinate synthesis of the bacterioopsin apoprotein and carotenoid precursors of retinal, which serves as a covalently bound cofactor. As a step towards elucidating the mechanism and regulation of carotenoid metabolism during bacteriorhodopsin biogenesis, we have identified an H. salinarum gene required for conversion of lycopene to beta-carotene, a retinal precursor. The gene, designated crtY, is predicted to encode an integral membrane protein homologous to lycopene beta-cyclases identified in bacteria and fungi. To test crtY function, we constructed H. salinarum strains with in-frame deletions in the gene. In the deletion strains, bacteriorhodopsin, retinal, and beta-carotene were undetectable, whereas lycopene accumulated to high levels ( approximately 1.3 nmol/mg of total cell protein). Heterologous expression of H. salinarum crtY in a lycopene-producing Escherichia coli strain resulted in beta-carotene production. These results indicate that H. salinarum crtY encodes a functional lycopene beta-cyclase required for bacteriorhodopsin biogenesis. Comparative sequence analysis yields a topological model of the protein and provides a plausible evolutionary connection between heterodimeric lycopene cyclases in bacteria and bifunctional lycopene cyclase-phytoene synthases in fungi.

brp and blh are required for synthesis of the retinal cofactor of bacteriorhodopsin in Halobacterium salinarum

Bacteriorhodopsin, the light-driven proton pump of Halobacterium salinarum, consists of the membrane apoprotein bacterioopsin and a covalently bound retinal cofactor. The mechanism by which retinal is synthesized and bound to bacterioopsin in vivo is unknown. As a step toward identifying cellular factors involved in this process, we constructed an in-frame deletion of brp, a gene implicated in bacteriorhodopsin biogenesis. In the Deltabrp strain, bacteriorhodopsin levels are decreased approximately 4.0-fold compared with wild type, whereas bacterioopsin levels are normal. The probable precursor of retinal, beta-carotene, is increased approximately 3.8-fold, whereas retinal is decreased by approximately 3.7-fold. These results suggest that brp is involved in retinal synthesis. Additional cellular factors may substitute for brp function in the Deltabrp strain because retinal production is not abolished. The in-frame deletion of blh, a brp paralog identified by analysis of the Halobacterium sp. NRC-1 genome, reduced bacteriorhodopsin accumulation on solid medium but not in liquid. However, deletion of both brp and blh abolished bacteriorhodopsin and retinal production in liquid medium, again without affecting bacterioopsin accumulation. The level of beta-carotene increased approximately 5.3-fold. The simplest interpretation of these results is that brp and blh encode similar proteins that catalyze or regulate the conversion of beta-carotene to retinal.

Bacterioopsin-triggered retinal biosynthesis is inhibited by bacteriorhodopsin formation in Halobacterium salinarium

Factors regulating retinal biosynthesis in halobacteria are not clearly understood. In halobacteria, events leading to the biosynthesis of bacteriorhodopsin have been proposed to participate in stringent regulation of retinal biosynthesis. The present study describes a novel approach of in vivo introductions of mRNA and membrane proteins via liposome fusion to test their role in cellular metabolism. Both the bacterioopsin-encoding mRNA and the liposome-encapsulated bacterioopsin (apoprotein) are independently introduced in spheroplasts of the purple membrane-negative strain Halobacterium salinarium that initially contain neither bacterioopsin nor retinal. Isoprenoid analyses of these cells indicate that the expression/presence of bacterioopsin triggers retinal biosynthesis from lycopene, and its subsequent binding to opsin generates bacteriorhodopsin. When bacteriorhodopsin and excess retinal were independently introduced into spheroplasts of purple membrane-negative cells, the introduction of bacteriorhodopsin resulted in an accumulation of lycopene, indicating an inhibition of retinal biosynthesis. These results provide direct evidence that the formation of bacterioopsin acts as a trigger for lycopene conversion to beta-carotene in retinal biosynthesis. The trigger for this event does not lie with either transcription or translation of the bop gene. It is clearly associated with the folded and the membrane-integrated state of bacterioopsin. On the other hand, the trigger signaling inhibition of retinal biosynthesis does not lie with the presence of excess retinal but with the correctly folded, retinal-bound form, bacteriorhodopsin.

Role of helix-helix interactions in assembly of the bacteriorhodopsin lattice

The purple membrane of Halobacterium salinarium is a two-dimensional lattice of lipids and the integral membrane protein bacteriorhodopsin (BR). To determine whether helix-helix interactions within the membrane core stabilize this complex, we substituted amino acid residues at the helix-helix interface between BR monomers and examined the assembly of the protein into the lattice. Lattice assembly was demonstrated to fit a cooperative self-assembly model that exhibits a critical concentration in vivo. Using this model as the basis for a quantitative assay of lattice stability, bulky substitutions at the helix-helix interface between BR monomers within the membrane core were shown to be destabilizing, probably due to steric clash. Ala substitutions of two residues at the helix-helix interface also reduced stability, suggesting that the side chains of these residues participate in favorable van der Waals packing interactions. However, the stabilizing interactions were restricted to a small region of the interface, and most of the substitutions had little effect. Thus, the contribution of helix-helix interactions to lattice stability appears limited, and favorable interactions between other regions of neighboring BR monomers or between BR and lipid molecules must also contribute.

Purification of histidine tagged bacteriorhodopsin, pharaonis halorhodopsin and pharaonis sensory rhodopsin II functionally expressed in Escherichia coli

Bacteriorhodopsin (BR) from Halobacterium salinarum as well as halorhodopsin (pHR) and sensory rhodopsin II (pSRII) from Natronobacterium pharaonis were functionally expressed in E. coli using the method of Shimono et al. IFEBS Lett. (1997) 420, 54-56]. The histidine tagged proteins were purified with yields up to 1.0 mg/l cell culture and characterized by ESI mass spectrometry and their photocycle. The pSRII and pHR photocycles were indistinguishable from the wild type proteins. The BR photocycle was considerably prolonged. pSOII is located in the cytoplasmic membrane and the C-terminus is oriented towards the cytoplasm as determined by immunogold labelling.

Primary structure of the novel bacterial rhodopsin from extremely halophilic archaeon Haloarcula japonica strain TR-1

A novel bacterial rhodopsin was identified in Haloarcula japonica strain TR-1. The gene encoding the bacterial rhodopsin was cloned and sequenced. The structural gene consisted of an open reading frame of 750 nucleotides encoding 250 amino acids. The deduced amino acid sequence of the Ha. japonica bacterial rhodopsin showed the highest homology to those of cruxrhodopsins.

Voltage dependence of proton pumping by bacteriorhodopsin is regulated by the voltage-sensitive ratio of M1 to M2

The voltage dependence of light-induced proton pumping was studied with bacteriorhodopsin (bR) from Halobacterium salinarum, expressed in the plasma membrane of oocytes from Xenopus laevis in the range -160 mV to +60 mV at different light intensities. Depending on the applied field, the quenching effect by blue light, which bypasses the normal photo and transport cycle, is drastically increased at inhibiting (negative) potentials, and is diminished at pump current increasing (positive) potentials. At any potential, two processes with different time constants for the M --> bR decay of approximately 5 ms (tau1) and approximately 20 ms (tau2) are obtained. At pump-inhibiting potentials, a third, long-lasting process with tau3 approximately 300 ms at neutral pH is observed. The fast processes (tau1, tau2) can be assigned to the decay of M2 in the normal pump cycle, i.e., to the reprotonation of the Schiff base via the cytoplasmic side, whereas tau3 is due to the decay of M1 without net pumping, i.e., the reprotonation of the Schiff base via the extracellular side. The results are supported by determination of photocurrents induced by bR on planar lipid films. The pH dependence of the slow decay of M1 is fully in agreement with the interpretation that the reprotonation of the Schiff base occurs from the extracellular side. The results give strong evidence that an externally applied electrical field changes the ratio of the M1 and the M2 intermediate. As a consequence, the transport cycle branches into a nontransporting cycle at negative potentials. This interpretation explains the current-voltage behavior of bR on a new basis, but agrees with the isomerisation, switch, transfer model for vectorial transport.

Temperature-dependent conformational change of bacteriorhodopsin as studied by solid-state 13C NMR

Cross-polarization and dipolar-decoupled magic-angle spinning 13C-NMR spectra of [3-13C]Ala-labelled bacteriorhodopsin were obtained for hydrated purple membrane in the temperatures range 23 degrees C to -110 degrees C. Well-resolved 13C-NMR signals were observed either at ambient temperature or at -20 degrees C but were broadened considerably at lower temperature below -40 degrees C. This situation was interpreted in terms of the presence of exchange processes with a rate constant of 10(2) s-1 at ambient temperature among several conformations slightly different from each other. We found that such an exchange process was strongly influenced by the manner of organization of the lipid bilayers depending upon the presence or absence of cations responsible for electric shielding of negative charge at the polar head groups. The manner of organization of the lipid bilayers was conveniently characterized by a characteristic temperature at which the methyl peaks of fatty acyl groups of lipids in the purple membrane were suppressed due to interference of motional frequency with the decoupling frequency (10-100 kHz) for preparations containing 10 mM NaCl or CaCl2. No such spectral change in the absence of these cations was noted even if a preparation was cooled to -110 degrees C. The secondary structures of [3-13C]Ala-labelled bacteriorhodopsin was not always identical at temperatures between ambient and low temperatures, since the 13C chemical shifts and relative peak intensities for purple membrane preparations containing these salts changed with temperature in the range -110 degrees C to 23 degrees C. In particular, we found that some residues involving Ala residues at the alpha II-helix and loop region were converted at temperatures below -60 degrees C to a conformation involving alpha 1-helix. In other words, some portion of the alpha-helical conformation of bacteriorhodopsin proposed from results obtained by cryo-electron microscopy, at very low temperatures, is not always retained at ambient temperature.

Influence exercised by histidine-95 on chloride transport and the photocycle in halorhodopsin

The anion pumping mechanism of halorhodopsin was studied using site-directed mutagenesis. Comparison of the amino acid sequence revealed that the B-C interhelix loop segment was highly homologous in all known halorhodopsins. Especially a basic residue, histidine-95, was conserved in all halorhodopsins. Using the expression-vector plasmid carrying the bop promoter, two His-95 mutants (H95R, H95A) were successfully expressed in Halobacterium salinarium. The expression levels of these halorhodopsin mutants were slightly lower than that for the wild-type halorhodopsin. In addition, these mutants were unstable under illumination compared with the wild-type. It suggested that His-95 is probably important for stabilizing the structure of halorhodopsin. The absorption maxima of these mutants are approximately 15 nm blue-shifted compared with the wild-type, suggesting that His-95 interacts with the retinal Schiff base. At low chloride concentrations, the light-induced chloride pumping activity of these mutants was more than 20 times lower than that for the wild-type. Only under physiological conditions, the chloride pumping activity was detected. Even at a high chloride concentration (1 M NaCl), the HR520 intermediate could not be detected for these mutants. These results clearly indicate that His-95 has a crucial role in the chloride transport of halorhodopsin.

Over-expression of a new photo-active halorhodopsin in Halobacterium salinarium

The gene of haloopsin (hop) from halobacterial strain shark was cloned and its nucleotide sequence was determined. The deduced amino acid sequence of shark halorhodopsin (HR) showed that its homology with halobium HR was 62%. The gene product seems to be HR having several positively charged residues that are conserved in all known HRs. The gene encoding shark hop as well as that encoding halobium hop were successfully expressed in Halobacterium salinarium (halobium) by using a plasmid shuttle vector containing the bacterioopsin (bop) promoter. The expression level of shark HR is almost the same as that for halobium HR with the same shuttle vector containing the bop promoter. Under the physiological conditions, the anion pumping activity of the shark HR expressed in H. salinarium was almost the same as that for halobium HR; however, the anion selectivity and half-maximal anion transport were different. Furthermore, its absorption maximum in the absence of chloride shifted to approx. 596 nm in contrast to that for halobium HR. The half-lifetimes of HR520 formation for shark HR and halobium HR were almost the same; however, the half-lifetime of its decay was approx. 6-times faster for shark HR than it was for halobium HR at a high chloride concentration (1000 mM). Even at a low chloride concentration (50 mM), HR520 and HR640 intermediates could be detected for shark HR, and the half-lifetime of HR640 decay was found to be approx. 25 ms. In the presence of nitrate, the half-lifetime of HR565 recovery for shark HR was approx. 10-times slower than that for halobium HR. Some of amino acid substitutions between shark HR and halobium HR may affect the anion selectivity and the photoreaction of HR.

The role of the leader sequence coding region in expression and assembly of bacteriorhodopsin

Bacterio-opsin is made as a precursor in Halobacterium halobium, which has 13 additional residues at the amino terminus. The codons for these residues have been proposed to form a hairpin structure in the mRNA and play a role in ribosome binding; the leader peptide sequence also has been proposed to have a role in membrane insertion of bacteriorhodopsin (BR). We have made mutations in the bop gene region coding for the leader sequence and expressed the mutant genes in an H. halobium mutant lacking wild-type BR. The leader sequence coding region was found to be important for the stability of the mRNA and for its efficient translation. Single base substitutions in this region that did not affect the amino acid sequence caused significant reductions in protein expression. Deletion of the leader region resulted in unstable mRNA and almost no BR production. Introduction of a new ribosome-binding sequence within the coding region of the mature protein restored mRNA stability and some protein expression. Protein made without the leader peptide was properly assembled in the membrane.

Site-directed isotope labeling and FTIR spectroscopy: assignment of tyrosine bands in the bR-->M difference spectrum of bacteriorhodopsin

Fourier transform infrared difference spectroscopy has been used extensively to probe structural changes in bacteriorthodopsin and other retinal proteins. However, the absence of a general method to assign bands to individual chemical groups in a protein has limited the application of this technique. While site-directed mutagenesis has been successful in special cases for such assignments, in general, this approach induces perturbations in the structure and function of the protein, thereby preventing unambiguous band assignments. A new approach has recently been reported (Sonar et al., Nature Struct. Biol. 1 (1994) 512-517) which involves cell-free expression of bacteriorhodopsin and site-directed isotope labeling (SDIL). We have now used this method to re-examine bands assigned in the bR-->M difference spectrum to tyrosine residues. Our results show that out of 11 tyrosines in bR, only Tyr 185 is structurally active. This work further demonstrates the power of SDIL and FTIR to probe conformational changes at the level of individual amino acid residues in proteins.

Anion selectivity and pumping mechanism of halorhodopsin

Comparison of the amino acid sequences in the A-B and B-C interhelical loop segments in all bacteriorhodopsins and halorhodopsins has shed light on the anion selectivity and pumping mechanism of halorhodopsin. The nucleotide sequences of two haloopsins from two new halobacterial strains, shark and port, have been determined, and shark halorhodopsin was functionally overexpressed in Halobacterium halobium. Although a series of six amino acid residues (EMPAGH) in the B-C interhelical loop segment was substituted by QMPPGH, all putative charged residues were conserved. It was also shown that His-95 mutants had lower pumping activity in low chloride concentrations. These results further support the hypothesis that His-95 is important in the halorhodopsin function.

The primary structure of sensory rhodopsin II: a member of an additional retinal protein subgroup is coexpressed with its transducer, the halobacterial transducer of rhodopsin II

The blue-light receptor genes (sopII) of sensory rhodopsin (SR) II were cloned from two species, the halophilic bacteria Haloarcula vallismortis (vSR-II) and Natronobacterium pharaonis (pSR-II). Upstream of both sopII gene loci, sequences corresponding to the halobacterial transducer of rhodopsin (Htr) II were recognized. In N. pharaonis, psopII and phtrII are transcribed as a single transcript. Comparison of the amino acid sequences of vHtr-II and pHtr-II with Htr-I and the chemotactic methyl-accepting proteins from Escherichia coli revealed considerable identities in the signal domain and methyl-accepting sites. Similarities with Htr-I in Halobacterium salinarium suggest a common principle in the phototaxis of extreme halophiles. Alignment of all known retinal protein sequences from Archaea identifies both SR-IIs as an additional subgroup of the family. Positions defining the retinal binding site are usually identical with the exception of Met-118 (numbering is according to the bacteriorhodopsin sequence), which might explain the typical blue color shift of SR-II to approximately 490 nm. In archaeal retinal proteins, the function can be deduced from amino acids in positions 85 and 96. Proton pumps are characterized by Asp-85 and Asp-96; chloride pumps by Thr-85 and Ala-96; and sensors by Asp-85 and Tyr-96 or Phe-96.

Two-chain bacteriorhodopsin synthesized by Schizosaccharomyces pombe

Bacteriorhodopsin (BR), the light-driven proton pump of Halobacterium salinarium purple membrane, was produced in functional form as a two-chain protein by simultaneous expression in the fission yeast Schizosaccharomyces pombe of two separate structural genes, one coding for an aminoterminal BR fragment encompassing the first two transmembrane helices of BR, the other coding for the remainder of the protein. The fragments assemble spontaneously in vivo to yield functional BR which can be purified by immobilized metal ion affinity chromatography.

Photoactive mitochondria: in vivo transfer of a light-driven proton pump into the inner mitochondrial membrane of Schizosaccharomyces pombe

The light-driven proton pump bacteriorhodopsin (bR) from Halobacterium salinarium has been genetically transferred into the inner mitochondrial membrane (IM) of the eukaryotic cell Schizosaccharomyces pombe, where the archaebacterial proton pump replaces or increases the proton gradient usually formed by the respiratory chain. For targeting and integration, as well as for the correct orientation of bR in the IM, the bacterioopsin gene (bop) was fused to signal sequences of IM proteins. Northern and Western blot analysis proved that all hybrid gene constructs containing the bop gene and a mitochondrial signal sequence were expressed and processed to mature bR. Fast transient absorption spectroscopy showed photocycle activity of bR integrated in the IM by formation of the M intermediate. Experiments with the pH-sensitive fluorescence dye 2',7'-bis(2-carboxyethyl)-5 (and -6)-carboxyfluorescein revealed bR-mediated proton pumping from the mitochondrial matrix into the intermembrane space. Glucose uptake measurements under anaerobic conditions showed that yeast cells containing photoactive mitochondria need less sugar under illumination. In summary, our experiments demonstrate the functional genetic transfer of a light energy converter to a naturally nonphotoactive eukaryotic organism.

The archaebacterial membrane protein bacterio-opsin is expressed and N-terminally processed in the yeast Saccharomyces cerevisiae

The bop gene codes for the membrane protein bacterio-opsin (BO), which on binding all-trans-retinal, constitutes the light-driven proton pump bacteriorhodopsin (BR) in the archaebacterium Halobacterium salinarium. This gene was cloned in a yeast multi-copy vector and expressed in Saccharomyces cerevisiae under the control of the constitutive ADH1 promoter. Both the authentic gene and a modified form lacking the precursor sequence were expressed in yeast. Both proteins are incorporated into the membrane in S. cerevisiae. The presequence is thus not required for membrane targeting and insertion of the archaebacterial protein in budding yeast, or in the fission yeast Schizosaccharomyces pombe, as has been shown previously. However, in contrast to S. pombe transformants, which take on a reddish colour when all-trans-retinal is added to the culture medium as a result of the in vivo regeneration of the pigment, S. cerevisiae cells expressing BO do not take on a red colour. The precursor of BO is processed to a protein identical in size to the mature BO found in the purple membrane of Halobacterium. The efficiency of processing in S. cerevisiae is dependent on growth phase, as well as on the composition of the medium and on the strain used. The efficiency of processing of BR is reduced in S. pombe and in a retinal-deficient strain of H. salinarium, when retinal is present in the medium.

bop gene cluster expression in bacteriorhodopsin-overproducing mutants of Halobacterium halobium

mRNA levels from the bop (bacterio-opsin), brp (bacterio-opsin-related protein), and bat (bacterio-opsin activator) genes in wild-type Halobacterium halobium and two bacteriorhodopsin-overproducing mutants (ET1001 and II-7) were quantitated under conditions in which oxygen levels were steadily depleted and then cultures were either kept in the dark or exposed to light. All three strains showed similar responses to depleted oxygen tensions and the lack of light: bop gene cluster transcript levels first increased in response to steadily declining oxygen, and once oxygen was depleted, transcript levels decreased and became undetectable within 20 to 40 h. In contrast, each strain responded differently to conditions of depleted oxygen and the presence of light. In the wild-type strain, bop gene cluster transcript levels increased 2.4- to 9.2-fold above the highest levels obtained in the dark. In mutant ET1001, bop gene cluster transcript levels did not increase above the highest levels obtained in the dark. In mutant II-7, bop and brp transcript levels did not increase above the highest levels obtained in the dark, but bat transcript levels increased approximately 5.7-fold. This differing response to identical physiological conditions indicates that the mutations resulting in the bacteriorhodopsin-overproducing phenotype in these two mutants are different.

Cell-free synthesis, functional refolding, and spectroscopic characterization of bacteriorhodopsin, an integral membrane protein

Bacteriorhodopsin (bR) is an integral membrane protein which functions as a light-driven proton pump in Halobacterium halobium (also known as Halobacterium salinarium). The cell-free synthesis of bR in quantities sufficient for FTIR and NMR spectroscopy and the ability to selectively isotope label bR using aminoacylated suppressor tRNAs would provide a powerful approach for studying the role of specific amino acid residues. However, no integral membrane protein has yet been expressed in a cell-free system in quantities sufficient for such biophysical studies. We report the cell-free synthesis of bacterioopsin, its purification, its refolding in polar lipids from H. halobium, and its regeneration with all-trans-retinal to yield bacteriorhodopsin in a form functionally similar to bR in purple membrane. Importantly, the yields obtained from in vitro and in vivo expression are comparable. Functionality of the cell-free expressed bR is established using static and time-resolved absorption spectroscopy and FTIR difference spectroscopy.

Projection structure of halorhodopsin from Halobacterium halobium at 6 A resolution obtained by electron cryo-microscopy

Two-dimensional crystals of halorhodopsin (HR), in space group p42(1)2 (a = 102 A) have been obtained using the overexpressing Halobacterium halobium strain D2. An HR membrane fraction with the same buoyant density as purple membrane (HR-PM) was obtained by homogenization and sucrose gradient purification and used for electron cryomicroscopic analysis. Electron micrographs and electron diffraction patterns of HR-PM were recorded at liquid nitrogen temperatures. The micrographs showed significant diffraction out to 9 A resolution optically and to 6 A after computer processing. By combining data from electron micrographs and electron diffraction patterns, a projection map of HR was calculated. The crystal form of the isolated HR consists of one membrane in which alternating halorhodopsin tetramers are oriented in opposite directions across the membrane. It is not known whether this occurs by misinsertion of some of the molecules in vivo, or by adventitious fusion at some point during isolation. The projected structure of the HR molecule to a resolution of 6A is almost identical to that found for bacteriorhodopsin (BR). This physical structural similarity thus complements the known sequence relatedness to BR.

Removal of the transducer protein from sensory rhodopsin I exposes sites of proton release and uptake during the receptor photocycle

The phototaxis receptor sensory rhodopsin-I (SR-I) was genetically truncated in the COOH terminus which leads to overexpression in Halobacterium salinarium and was expressed in the presence and absence of its transducer, HtrI. Pyranine (8-hydroxyl-1,3,6-pyrene-trisulfonate) was used as a pH probe to show that proton release to the bulk phase results from the SR-I587 to S373 photoconversion, but only in the absence of transducer. The stoichiometry is 1 proton/S373 molecule formed. When SR-I is overexpressed in the presence of HtrI, the kinetics of the thermal return of S373 to SR-I587 is biphasic. A kinetic dissection indicates that overexpressed SR-I is present in two pools: one pool which generates an SR-I molecule possessing a normal (i.e., transducer-interacting) pH-independent rate of S373 decay, and a second pool which shows the pH-dependent kinetics of transducer-free S373 decay. The truncated SR-I receptor functions normally based on the following criteria: (i) Truncated SR-I restores phototaxis (attractant and repellent responses) when expressed in a strain lacking native SR-I, but containing HtrI. (ii) The absorption spectrum and the flash-induced absorption difference spectrum are indistinguishable from those of native SR-I. (iii) The rate of decay of S373 is pH-dependent in the absence of HtrI but not in the presence of HtrI. The data presented here indicate that a proton-conducting path exists between the protonated Schiff base nitrogen and the extramembranous environment in the transducer-free receptor, and transducer binding blocks this path.

Properties of bacteriorhodopsin derivatives constructed by insertion of an exogenous epitope into extra-membrane loops

Bacteriorhodopsin (BR) is folded into a bundle of seven alpha-helices which is embedded in the cellular membrane of Halobacterium salinarium; these helices are connected by short extra-membrane loops, three on the cytoplasmic side and three on the outside. Oligonucleotide-directed insertion or replacement mutagenesis was used to integrate the C-terminal sequence (13 amino acids long) of Sendai virus L-protein individually into each of the six helix-connecting loops. The altered gene products were obtained by expression of the mutant genes in either Escherichia coli or Schizosaccharomyces pombe and were used to reconstitute BR in proteoliposomes. In four cases (altered loops B/C, C/D, D/E or E/F), the mutant BRs were found to be fully functional as judged by light-driven proton pumping and photocycle kinetics. Within the four functional BR variants, recognition of the viral epitope by a monoclonal antibody is restricted to modified loops B/C and E/F. Immunogold staining of S.pombe cells producing either of the two latter BR variants shows that the protein is distributed among various cellular membranes but is not present in mitochondrial membranes. Sequence alteration of loop A/B or F/G resulted in loss of function, most plausibly due to a folding defect of the respective proteins. These results on the one hand document differences in structural importance of the various BR extra-membrane loops and on the other hand open the door to the construction of multifunctional membrane proteins via loop replacement mutagenesis of BR.

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.

Localisation of methionine residues in bacteriorhodopsin by carbonyl 13C-NMR with sequence-specific assignments

High-resolution 13C-NMR experiments have been performed on bacteriorhodopsin biosynthetically labeled with carbonyl-13C amino acids and solubilized in the detergent dodecylmaltoside. 13C-NMR spectra showing good resolution were obtained in the case of labeled amino acids moderately represented in the BR sequence. For BR labeled with [13C]carbonyl methionine, several sequence-specific assignment could be performed by co-labeling with 15N amino acids or proteolysis. These assignments were used to obtain structural data on BR. Water-exposure of methionine side chains in the protein was assessed by studying, using NMR, their oxidation by hydrogen peroxide. Local secondary structure at the level of methionine residues was monitored through the effect of 1H-2H exchange on NMR spectra. It was concluded that Met32, Met68 and Met163 are peripheral while all 6 other methionine residues are deeply embedded within hydrophobic alpha-helices. These results confirm the current model of the BR folding and secondary structure.

Homologous overexpression of a light-driven anion pump in an archaebacterium

The retinal protein halorhodopsin (HR), a light-driven chloride pump from Halobacterium halobium, was homologously overexpressed in this archaebacterium. Two DNA expression systems differing in their promoter region were investigated. The halopsin, hop, promoter coupled to the hop gene gave an increased level of HR synthesis. However, the extent of expression was driven by the copy number of the shuttle vector and did not reach the magnitude of the bacterio-opsin, bop, promoter system. Employing a gene fusion approach, the promoter for the bop gene was used to drive expression of the hop gene. A shuttle vector containing a bop-hop-cartridge was transformed into a HR-deficient strain and blueish-coloured transformants were obtained. The bop promoter expressed HR to an extent where a specific membrane fraction resembled the crystalline purple membrane of BR in terms of the lipid to protein ratio. HR could, therefore, be easily isolated in a natural membrane-bound state. This allows for direct use in biophysical studies without the application of detergents. This was the first successful overexpression of a 7-helical transmembrane protein and may be extended to other proteins of this family.

Biosynthetic incorporation of m-fluorotyrosine into bacteriorhodopsin

Halobacterium halobium, grown in a defined medium where tyrosine had been largely replaced with m-fluorotyrosine, biosynthetically produced purple membrane. Analysis of this membrane by high pressure liquid chromatography of phenylthiocarbamyl derivatized amino acids of membrane acid hydrolysates revealed that up to 50% of the tyrosine was present as the m-fluorotyrosine form. Yields of the purple membrane decreased as the level of incorporation increased. The experimental purple membrane showed a single 19F NMR resonance at -61.983 ppm (relative to trifluoroacetic acid). The bacteriorhodopsin (bR) in the purple membrane was normal as assayed by gel electrophoresis, isoelectric focusing, circular dichroic spectra, and UV-visible spectra. However, the fluorinated tyrosine bacteriorhodopsins at near neutral pH exhibited slightly slower rates of proton uptake and a slower M-state decay with biphasic kinetics reminiscent of alkaline solutions of bR (pH > 9). These results imply that the tyrosines in bacteriorhodopsin may play a role in the photoactivated proton translocation process of this pigment.

The essential role of specific Halobacterium halobium polar lipids in 2D-array formation of bacteriorhodopsin

The mechanism whereby bacteriorhodopsin (BR), the light driven proton pump from the purple membrane of Halobacterium halobium, arranges in a 2D-hexagonal array, has been studied in bilayers containing the protein, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and various fractions of H. halobium membrane lipids, by freeze fracture electron microscopy and examination of optical diffractograms of the micrographs obtained. Electron micrographs of BR/DMPC complexes containing the entire polar lipid component of H. halobium cell membranes or the total lipid component of the purple membrane, with a protein-to-total lipid molar ratio of less than 1:50 and to which 4 M NaCl had been added, revealed that trimers of BR formed into an hexagonal 2D-array similar to that found in the native purple membrane, suggesting that one or more types of the purple membrane polar lipids are required for array formation. To support this suggestion, bacteriorhodopsin was purified free of endogenous purple membrane lipids and reconstituted into lipid bilayer complexes by detergent dialysis. The lipids used to form these complexes are 1,2-dimyristoyl-sn-glycerol-phosphocholine (DMPC) as the major lipid and, separately, each of the individual lipid types from the H. halobium cell membranes, namely 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-phosphate (DPhPGP), 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-sulphate (DPhPGS), 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol (DPhPG) and 2,3-di-O-phytanyl-1-O-[beta-D-Galp-3-sulphate-(1----6)-alpha-D- Manp-(1----2)-alpha-D-Glcp]-sn-glycerol (DPhGLS). When examined by freeze-fracture electron microscopy, only the complexes containing 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol- 1'-phosphate or 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol-1'-sulphate, at high protein density (less than 1:50, bacteriorhodopsin/phospholipid, molar ratio) and to which 4 M NaCl had been added, showed well defined 2D hexagonal arrays of bacteriorhodopsin trimers similar to those observed in the purple membrane of H. halobium.

Expression of the bop gene cluster of Halobacterium halobium is induced by low oxygen tension and by light

The bop gene cluster consists of at least three genes: bop (bacterio-opsin), brp (bacterio-opsin-related protein), and bat (bacterio-opsin activator). We have quantitated transcript levels from these genes in a wild-type and bacterioruberin-deficient mutant of Halobacterium halobium under conditions which affect purple membrane synthesis. In wild-type cultures grown under high oxygen tension in the dark, bop and bat transcript levels were low during steady-state growth and then increased approximately 29- and approximately 45-fold, respectively, upon entry into stationary phase. brp gene transcription remained very low and essentially unchanged under these conditions. In addition, exposure of wild-type cultures growing under high oxygen tension to 30,000 lx of light stimulated expression of all three genes, especially brp. In contrast to the wild-type, transcription from all three genes in the bacterioruberin mutant was very high during steady-state growth under high oxygen tension in the dark. Cultures of the bacterioruberin mutant were shifted at early stationary phase to low oxygen tension to determine whether oxygen concentrations lower than those present in stationary phase would induce transcription of the bop gene cluster in this strain. Indeed, transcription was induced, suggesting that the bop gene cluster is not completely uncoupled from regulation by oxygen tension in the bacterioruberin mutant. From these data, we propose a regulatory model involving two different mechanisms: (i) bat gene expression is induced under conditions of low oxygen tension and the bat gene product activates bop gene expression and (ii) light induces brp transcription, which stimulates or modulates bat transcription.

Transcriptional induction of purple membrane and gas vesicle synthesis in the archaebacterium Halobacterium halobium is blocked by a DNA gyrase inhibitor

We have investigated the expression of the bacteriorhodopsin gene (bop) and the gas vesicle protein gene (gvpA) in the extremely halophilic archaebacterium Halobacterium halobium, using primer-directed reverse transcription of RNA to quantify message levels. The level of gvpA gene transcript was found to increase about 5-fold from early to mid-logarithmic growth phase, while the level of bop gene transcript increased about 20-fold from mid-logarithmic to stationary phase. Transcriptional induction of both the gvpA and bop genes was significantly reduced by aeration and almost completely blocked by the DNA gyrase inhibitor novobiocin.

An efficient system for the synthesis of bacteriorhodopsin in Halobacterium halobium

The mechanism by which bacteriorhodopsin (BR) transports protons across the cell membrane of Halobacterium halobium is actively studied in many laboratories. Currently available systems for the synthesis of mutant proteins obtained by site-directed mutagenesis of the gene encoding BR (bop) require reconstitution of the denatured polypeptide after its synthesis Escherichia coli or yeast; this approach is technically difficult and labor intensive, and raises questions about possible differences between in vivo and in vitro folding. Using a newly described transformation system and a halobacterial plasmid vector, we show that it is possible to reintroduce the bop gene into BR- strains of H. halobium. The bop-carrying plasmid expresses native BR in amounts similar to those obtained in several wild type strains. This system allows facile site-directed mutagenesis in halophilic archaebacteria.

Genetic transfer of the pigment bacteriorhodopsin into the eukaryote Schizosaccharomyces pombe

The gene encoding for bacterio-opsin (bop gene) from Halobacterium halobium has been introduced in a yeast expression vector. After transformation in Schizosaccharomyces pombe, bacterio-opsin (BO) is expressed and was detected by antisera. The precursor protein of BO (pre-BO) is processed by cleavage of amino acids at the N-terminal end as in H. halobium. Addition of the chromophore, retinal, to the culture medium results in a slight purple colour of the yeast cells indicating the in vivo regeneration of BO to bacteriorhodopsin (BR) and its incorporation into membranes. Therefore, in contrast to the expression in E. coli, isolation of the membrane protein and reconstitution in lipid vesicles is not necessary for functional analysis. The kinetics of the ground state signal of the photocycle BR in protoplasts is demonstrated by flash spectroscopy and is comparable to that of the natural system. The present investigation shows for the first time the transfer of an energy converting protein from archaebacteria to eukaryotes by genetic techniques. This is a basis for further studies on membrane biogenesis, genetics, and bioenergetics by analysis of in vivo active mutants.

[Expressing plasmid vectors on the basis of Escherichia coli beta-galactosidase gene fragments]

With the use of synthetic DNA fragments, a set of new plasmid vectors has been obtained. The vectors provided high level expression of peptides and small proteins in E. coli as fusions with fragments of beta-galactosidase of various length. These vectors were used to achieve expression of a synthetic gene for a functionally active fragment of bacteriorhodopsin. The yields of hybrid proteins consisting of beta-galactosidase and bacteriorhodopsin fragments were in the range of 5-30% from the total amount of cellular protein.

Induction of the photosynthetic membranes of Rhodopseudomonas sphaeroides: biochemical and morphological studies

Cells of Rhodopseudomonas sphaeroides grown in a 25% O2 atmosphere were rapidly subjected to total anaerobiosis in the presence of light to study the progression of events associated with the de novo synthesis of the inducible intracytoplasmic membrane (ICM). This abrupt change in physiological conditions resulted in the immediate cessation of cell growth and whole cell protein, DNA, and phospholipid accumulation. Detectable cell growth and whole cell protein accumulation resumed ca. 12 h later. Bulk phospholipid accumulation paralleled cell growth, but the synthesis of individual phospholipid species during the adaptation period suggested the existence of a specific regulatory site in phospholipid synthesis at the level of the phosphatidylethanolamine methyltransferase system. Freeze-fracture electron microscopy showed that aerobic cells contain small indentations within the cell membrane that appear to be converted into discrete ICM invaginations within 1 h after the imposition of anaerobiosis. Microscopic examination also revealed a series of morphological changes in ICM structure and organization during the lag period before the initiation of photosynthetic growth. Bacteriochlorophyll synthesis and the formation of the two light-harvesting bacteriochlorophyll-protein complexes of R. sphaeroides (B800-850 and B875) occurred coordinately within 2 h after the shift to anaerobic conditions. Using antibodies prepared against various ICM-specific polypeptides, the synthesis of reaction center proteins and the polypeptides associated with the B800-850 complex was monitored. The reaction center H polypeptide was immunochemically detected at low levels in the cell membrane of aerobic cells, which contained no detectable ICM or bacteriochlorophyll. The results are discussed in terms of the oxygen-dependent regulation of gene expression in R. sphaeroides and the possible role of the reaction center H polypeptide and the cell membrane indentations in the site-specific assembly of ICM pigment-protein complexes during the de novo synthesis of the ICM.

Phototrophic growth of halobacteria and its use for isolation of photosynthetically-deficient mutants

Phototrophic growth conditions for halobacteria in complex and synthetic media have been established, demonstrating the photosynthetic capacity of this class of archaebacteria. Mutagenesis, 5-bromo-2'-deoxyuridine selection and screening techniques are described which are useful tools in the elucidation of the structure-function relationship of retinal proteins in halobacteria.

Genetic and biochemical resolution of the chromophoric polypeptide of halorhodopsin

Retinal-binding proteins in bacteriorhodopsin-deficient membranes of Halobacterium halobium have been separated on polyacrylamide gels after labeling with (3H)retinal. Four labeled polypeptides are observed: one at an Mr of 19,000, two distinct bands near 25,000, and one at 94,000. Comparing halorhodopsin-containing and halorhodopsin-deficient mutants and using ion translocation measurements and flash spectroscopy to test for the photoactive retinal pigments, we show that the lower of the two radiolabeled bands at 25,000 is the retinal-binding polypeptide of halorhodopsin. The identities of the other three polypeptides are not known, but one of them, probably the upper of the two 25,000 bands, is likely to be s-rhodopsin.

Bacteriorhodopsin is an inside-out protein

Neutron scattering is particulary useful when parts of a structure can be deuterated. From Halobacterium halobium we have obtained, by biosynthetic incorporation, purple membranes in which all of the valines or all of the phenylalanines are present in deuterated form. Difference Fourier techniques permit a general assessment of the distribution of valine and phenylalanine in projections of the purple membrane structure. These show that valine is distributed toward the periphery of a single bacteriorhodopsin molecule, whereas phenylalanine is distributed toward its center. We use the facts that the amino acid sequence is known and that much of it can be assigned to the alpha helices of the bacteriorhodopsin structure to interpret our results. Comparison of our maps with the distribution of valine and phenylalanine around alpha-helical perimetrs establishes the distribution of other amino acids and leads to the conclusion that the charged and polar groups of the bacteriorhodopsin molecule tend to lie at the molecular interior, away from contact with lipid, while the nonpolar surfaces are directed outward, making contact with the lipid regions. Thus, the protein is "inside-out" compared with the organization of soluble proteins.

Studies on the biosynthesis of bacterio-opsin. Demonstration of the existence of protein species structurally related to bacterio-opsin

1. The kinetics of processing newly synthesized bacterio-opsin from the non-crystalline state within the brown membrane to the crystalline state within the purple membrane was followed by pulse-chase experiments. 2. Biosynthesis of bacterio-opsin was found to be highly resistant to RNA-synthesis inhibitors like rifampicin and ethidium bromide. In the presence of ethidium bromide, only five protein species continue to be synthesized in halobacteria, one of them being bacterio-opsin. 3. In spheroplasts, synthesis of bacterio-opsin is found to be selectively disturbed. The purple membrane isolated from spheroplasts contains new, additional protein species with apparent molecular weights of 19 000, 23 000 and 29 000. These proteins share common amino acid sequences with bacterio-opsin. 4. In the halobacterial cell membrane, two membrane proteins with apparent molecular weights of 30 000 and 36 000 were detected which are structurally related to bacterio-opsin. 5. Bacterio-opsin as well as the 30 000 Mr and 36 000-Mr proteins contain covalently bound sulphate.