Primary structure of an archaebacterial transducer, a methyl-accepting protein associated with sensory rhodopsin I

Molecular Biology of Microbial Rhodopsins

Research on type 1 rhodopsins spans now a history of 50 years. Originally, just archaeal ion pumps and sensors have been discovered. However, with modern genetic techniques and gene sequencing tools, more and more proteins were identified in all kingdoms of life. Spectroscopic and other biophysical studies revealed quite diverse functions. Ion pumps, sensors, and channels are imprinted in the same seven-helix transmembrane protein scaffold carrying a retinal prosthetic group. In this review, molecular biology methods are described, which enabled the elucidation of their function and structure leading to optogenetic applications.

Taxis in archaea

Microorganisms can move towards favorable growth conditions as a response to environmental stimuli. This process requires a motility structure and a system to direct the movement. For swimming motility, archaea employ a rotating filament, the archaellum. This archaea-specific structure is functionally equivalent, but structurally different, from the bacterial flagellum. To control the directionality of movement, some archaea make use of the chemotaxis system, which is used for the same purpose by bacteria. Over the past decades, chemotaxis has been studied in detail in several model bacteria. In contrast, archaeal chemotaxis is much less explored and largely restricted to analyses in halophilic archaea. In this review, we summarize the available information on archaeal taxis. We conclude that archaeal chemotaxis proteins function similarly as their bacterial counterparts. However, because the motility structures are fundamentally different, an archaea-specific docking mechanism is required, for which initial experimental data have only recently been obtained.

Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers

Archaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two-component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the "U"-"V" transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55-58]. A model of cooperativity at the transmembrane level is discussed.

Microbial Rhodopsins: Diversity, Mechanisms, and Optogenetic Applications

Microbial rhodopsins are a family of photoactive retinylidene proteins widespread throughout the microbial world. They are notable for their diversity of function, using variations of a shared seven-transmembrane helix design and similar photochemical reactions to carry out distinctly different light-driven energy and sensory transduction processes. Their study has contributed to our understanding of how evolution modifies protein scaffolds to create new protein chemistry, and their use as tools to control membrane potential with light is fundamental to optogenetics for research and clinical applications. We review the currently known functions and present more in-depth assessment of three functionally and structurally distinct types discovered over the past two years: (a) anion channelrhodopsins (ACRs) from cryptophyte algae, which enable efficient optogenetic neural suppression; (b) cryptophyte cation channelrhodopsins (CCRs), structurally distinct from the green algae CCRs used extensively for neural activation and from cryptophyte ACRs; and

Surface-layer lattices as patterning element for multimeric extremozymes

A promising new approach for the production of biocatalysts comprises the use of surface-layer (S-layer) lattices that present functional multimeric enzymes on their surface, thereby guaranteeing most accurate spatial distribution and orientation, as well as maximal effectiveness and stability of these enzymes. For proof of concept, a tetrameric and a trimeric extremozyme are chosen for the construction of S-layer/extremozyme fusion proteins. By using a flexible peptide linker, either one monomer of the tetrameric xylose isomerase XylA from the thermophilic Thermoanaerobacterium strain JW/SL-YS 489 or, in another approach, one monomer of the trimeric carbonic anhydrase from the methanogenic archaeon Methanosarcina thermophila are genetically linked to one monomer of the S-layer protein SbpA of Lysinibacillus sphaericus CCM 2177. After isolation and purification, the self-assembly properties of both S-layer fusion proteins as well as the specific activity of the fused enzymes are confirmed, thus indicating that the S-layer protein moiety does not influence the nature of the multimeric enzymes and vice versa. By recrystallization of the S-layer/extremozyme fusion proteins on solid supports, the active enzyme multimers are exposed on the surface of the square S-layer lattice with 13.1 nm spacing.

Of ion pumps, sensors and channels - perspectives on microbial rhodopsins between science and history

We present a historical overview of research on microbial rhodopsins ranging from the 1960s to the present date. Bacteriorhodopsin (BR), the first identified microbial rhodopsin, was discovered in the context of cell and membrane biology and shown to be an outward directed proton transporter. In the 1970s, BR had a big impact on membrane structural research and bioenergetics, that made it to a model for membrane proteins and established it as a probe for the introduction of various biophysical techniques that are widely used today. Halorhodopsin (HR), which supports BR physiologically by transporting negatively charged Cl⁻ into the cell, is researched within the microbial rhodopsin community since the late 1970s. A few years earlier, the observation of phototactic responses in halobacteria initiated research on what are known today as sensory rhodopsins (SR). The discovery of the light-driven ion channel, channelrhodopsin (ChR), serving as photoreceptors for behavioral responses in green alga has complemented inquiries into this photoreceptor family. Comparing the discovery stories, we show that these followed quite different patterns, albeit the objects of research being very similar. The stories of microbial rhodopsins present a comprehensive perspective on what can nowadays be considered one of nature's paradigms for interactions between organisms and light. Moreover, they illustrate the unfolding of this paradigm within the broader conceptual and instrumental framework of the molecular life sciences. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

The protein interaction network of a taxis signal transduction system in a halophilic archaeon

Background

The taxis signaling system of the extreme halophilic archaeon Halobacterium (Hbt.) salinarum differs in several aspects from its model bacterial counterparts Escherichia coli and Bacillus subtilis. We studied the protein interactions in the Hbt. salinarum taxis signaling system to gain an understanding of its structure, to gain knowledge about its known components and to search for new members.

Results

The interaction analysis revealed that the core signaling proteins are involved in different protein complexes and our data provide evidence for dynamic interchanges between them. Fifteen of the eighteen taxis receptors (halobacterial transducers, Htrs) can be assigned to four different groups depending on their interactions with the core signaling proteins. Only one of these groups, which contains six of the eight Htrs with known signals, shows the composition expected for signaling complexes (receptor, kinase CheA, adaptor CheW, response regulator CheY). From the two Hbt. salinarum CheW proteins, only CheW1 is engaged in signaling complexes with Htrs and CheA, whereas CheW2 interacts with Htrs but not with CheA. CheY connects the core signaling structure to a subnetwork consisting of the two CheF proteins (which build a link to the flagellar apparatus), CheD (the hub of the subnetwork), two CheC complexes and the receptor methylesterase CheB.

Conclusions

Based on our findings, we propose two hypotheses. First, Hbt. salinarum might have the capability to dynamically adjust the impact of certain Htrs or Htr clusters depending on its current needs or environmental conditions. Secondly, we propose a hypothetical feedback loop from the response regulator to Htr methylation made from the CheC proteins, CheD and CheB, which might contribute to adaptation analogous to the CheC/CheD system of B. subtilis.

The signal transfer from the receptor NpSRII to the transducer NpHtrII is not hampered by the D75N mutation

Sensory rhodopsin II (NpSRII) is a phototaxis receptor of Natronomonas pharaonis that performs its function in complex with its cognate transducer (NpHtrII). Upon light activation NpSRII triggers by means of NpHtrII a signal transduction chain homologous to the two component system in eubacterial chemotaxis. The D75N mutant of NpSRII, which lacks the blue-shifted M intermediate and therefore exhibits a significantly faster photocycle compared to the wild-type, mediates normal phototaxis responses demonstrating that deprotonation of the Schiff base is not a prerequisite for transducer activation. Using site-directed spin labeling and time resolved electron paramagnetic-resonance spectroscopy, we show that the mechanism revealed for activation of the wild-type complex, namely an outward tilt motion of the cytoplasmic part of the receptor helix F and a concomitant rotation of the transmembrane transducer helix TM2, is also valid for the D75N variant. Apparently, the D75N mutation shifts the ground state conformation of NpSRII-D75N and its cognate transducer into the direction of the signaling state.

Attractant and repellent signaling conformers of sensory rhodopsin-transducer complexes

Attractant and repellent signaling conformers of the dual-signaling phototaxis receptor sensory rhodopsin I and its transducer subunit (SRI−HtrI) have recently been distinguished experimentally by the opposite connection of their retinylidene protonated Schiff bases to the outwardly located periplasmic side and inwardly located cytoplasmic side. Here we show that the pK_a of the outwardly located Asp76 counterion in the outwardly connected conformer is lowered by ∼1.5 units from that of the inwardly connected conformer. The pK_a difference enables quantitative determination of the relative amounts of the two conformers in wild-type cells and behavioral mutants prior to photoexcitation, comparison of their absorption spectra, and determination of their relative signaling efficiency. We have shown that the one-photon excitation of the SRI−HtrI attractant conformer causes a Schiff base connectivity switch from inwardly connected to outwardly connected states in the attractant signaling photoreaction. Conversely, a second near-UV photon drives the complex back to the inwardly connected conformer in the repellent signaling photoreaction. The results suggest a model of the color-discriminating dual-signaling mechanism in which phototaxis responses (his-kinase modulation) result from the photointerconversion of the two oppositely connected SRI−HtrI conformers by one-photon and two-photon activation. Furthermore, we find that the related repellent phototaxis SRII−HtrII receptor complex has an outwardly connected retinylidene Schiff base like the repellent signaling forms of the SRI−HtrI complex, indicating the general applicability of macro conformational changes, which can be detected by the connectivity switch, to phototaxis signaling by sensory rhodopsin−transducer complexes.

Bacterial energy taxis: a global strategy?

A functional energy metabolism is one of the most important requirements for survival of all kinds of organisms including bacteria. Therefore, many bacteria actively seek conditions of optimal metabolic activity, a behaviour which can be termed "energy taxis". Motility, combined with the sensory perception of the internal energetic conditions, is prerequisite for tactic responses to different energy levels and metabolic yields. Diverse mechanisms of energy sensing and tactic response have evolved among various bacteria. Many of the known energy taxis sensors group among the methyl-accepting chemotaxis protein (MCP)-like sensors. This review summarizes recent advances in the field of energy taxis and explores the current concept that energy taxis is an important part of the bacterial behavioural repertoire in order to navigate towards more favourable metabolic niches and to survive in a specific habitat.

Salinibacter sensory rhodopsin: sensory rhodopsin I-like protein from a eubacterium

Halobacterium salinarum sensory rhodopsin I (HsSRI), a dual receptor regulating both negative and positive phototaxis in haloarchaea, transmits light signals through changes in protein-protein interactions with its transducer, halobacterial transducer protein I (HtrI). Haloarchaea also have another sensor pigment, sensory rhodopsin II (SRII), which functions as a receptor regulating negative phototaxis. Compared with HsSRI, the signal relay mechanism of SRII is well characterized because SRII from Natronomonus pharaonis (NpSRII) is much more stable than HsSRI and HsSRII, especially in dilute salt solutions and is much more resistant to detergents. Two genes encoding SRI homologs were identified from the genome sequence of the eubacterium Salinibacter ruber. Those sequences are distantly related to HsSRI ( approximately 40% identity) and contain most of the amino acid residues identified as necessary for its function. To determine whether those genes encode functional protein(s), we cloned and expressed them in Escherichia coli. One of them (SrSRI) was expressed well as a recombinant protein having all-trans retinal as a chromophore. UV-Vis, low-temperature UV-Vis, pH-titration, and flash photolysis experiments revealed that the photochemical properties of SrSRI are similar to those of HsSRI. In addition to the expression system, the high stability of SrSRI makes it possible to prepare large amounts of protein and enables studies of mutant proteins that will allow new approaches to investigate the photosignaling process of SRI-HtrI.

Recombinant gas vesicles from Halobacterium sp. displaying SIV peptides demonstrate biotechnology potential as a pathogen peptide delivery vehicle

Background

Previous studies indicated that recombinant gas vesicles (r-GV) from a mutant strain of Halobacterium sp. NRC-1 could express a cassette containing test sequences of SIVmac gag derived DNA, and function as an antigen display/delivery system. Tests using mice indicated that the humoral immune response to the gag encoded sequences evoked immunologic memory in the absence of an exogenous adjuvant.

Results

The goal of this research was to extend this demonstration to diverse gene sequences by testing recombinant gas vesicles displaying peptides encoded by different SIV genes (SIV^{tat, rev or nef}). Verification that different peptides can be successfully incorporated into the GvpC surface protein of gas vesicle would support a more general biotechnology application of this potential display/delivery system. Selected SIVsm-GvpC fusion peptides were generated by creating and expressing fusion genes, then assessing the resulting recombinant gas vesicles for SIV peptide specific antigenic and immunogenic capabilities. Results from these analyses support three conclusions: (i) Different recombinant gvpC-SIV genes will support the biosynthesis of chimeric, GvpC fusion proteins which are incorporated into the gas vesicles and generate functional organelles. (ii) Monkey antibody elicited by in vivo infection with SHIV recognizes these expressed SIV sequences in the fusion proteins encoded by the gvpC-SIV fusion genes as SIV peptides. (iii) Test of antiserum elicited by immunizing mice with recombinant gas vesicles demonstrated notable and long term antibody titers. The observed level of humoral responses, and the maintenance of elevated responses to, Tat, Rev and Nef1 encoded peptides carried by the respective r-GV, are consistent with the suggestion that in vivo there may be a natural and slow release of epitope over time.

Conclusion

The findings therefore suggest that in addition to providing information about these specific inserts, r-GV displaying peptide inserts from other relevant pathogens could have significant biotechnological potential for display and delivery, or serve as a cost effective initial screen of pathogen derived peptides naturally expressed during infections in vivo.

Constitutive activity in chimeras and deletions localize sensory rhodopsin II/HtrII signal relay to the membrane-inserted domain

Halobacterium salinarum sensory rhodopsin II (HsSRII) is a phototaxis receptor for blue-light avoidance that relays signals to its tightly bound transducer HsHtrII (H. salinarum haloarchaeal transducer for SRII). We found that disruption of the salt bridge between the protonated Schiff base of the receptor's retinylidene chromophore and its counterion Asp73 by residue substitutions D73A, N or Q constitutively activates HsSRII, whereas the corresponding Asp75 counterion substitutions do not constitutively activate Natronomonas pharaonis SRII (NpSRII) when complexed with N. pharaonis haloarchaeal transducer for SRII (NpHtrII). However, NpSRII(D75Q) in complex with HsHtrII is fully constitutively active, showing that transducer sensitivity to the receptor signal contributes to the phenotype. The swimming behaviour of cells expressing chimeras exchanging portions of the two homologous transducers localizes their differing sensitivities to the HtrII transmembrane domains. Furthermore, deletion constructs show that the known contact region in the cytoplasmic domain of the NpSRII-NpHtrII complex is not required for phototaxis, excluding the domain as a site for signal transmission. These results distinguish between the prevailing models for SRII-HtrII signal relay, strongly supporting the 'steric trigger-transmembrane relay model', which proposes that retinal isomerization directly signals HtrII through the mid-membrane SRII-HtrII interface, and refuting alternative models that propose signal relay in the cytoplasmic membrane-proximal domain.

Microarray analysis in the archaeon Halobacterium salinarum strain R1

Background

Phototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy. The tool of choice to record transcriptional profiles is the DNA microarray technique. However, the technique is still rarely used for transcriptome analysis in archaea.

Methodology/Principal Findings

We developed a whole-genome DNA microarray based on our sequence data of the Hbt. salinarum strain R1 genome. The potential of our tool is exemplified by the comparison of cells growing under aerobic and phototrophic conditions, respectively. We processed the raw fluorescence data by several stringent filtering steps and a subsequent MAANOVA analysis. The study revealed a lot of transcriptional differences between the two cell states. We found that the transcriptional changes were relatively weak, though significant. Finally, the DNA microarray data were independently verified by a real-time PCR analysis.

Conclusion/Significance

This is the first DNA microarray analysis of Hbt. salinarum cells that were actually grown under phototrophic conditions. By comparing the transcriptomics data with current knowledge we could show that our DNA microarray tool is well applicable for transcriptome analysis in the extremely halophilic archaeon Hbt. salinarum. The reliability of our tool is based on both the high-quality array of DNA probes and the stringent data handling including MAANOVA analysis. Among the regulated genes more than 50% had unknown functions. This underlines the fact that haloarchaeal phototrophy is still far away from being completely understood. Hence, the data recorded in this study will be subject to future systems biology analysis.

Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors

Microbial rhodopsins have been intensively researched for the last three decades. Since the discovery of bacteriorhodopsin, the scope of microbial rhodopsins has been considerably extended, not only in view of the large number of family members, but also their functional properties as pumps, sensors, and channels. In this review, we give a short overview of old and newly discovered microbial rhodopsins, the mechanism of signal transfer and ion transfer, and we discuss structural and mechanistic aspects of phototaxis.

The distinct signaling mechanisms of microbial sensory rhodopsins in Archaea, Eubacteria and Eukarya

Most of the known archaeal-type microbial rhodopsins are retinal-binding ion transporters, such as bacteriorhodopsin (BR) and proteorhodopsin (PR). Their identification is the result of extensive studies of their photochemical and biophysical properties. The cells containing these pigments, however, use other microbial rhodopsins as photosensors to monitor environmental light signals. From the early studies of sensory rhodopsin I (HsSRI) in Halobacterium salinarum and sensory rhodopsin II (NpSRII) in Natronomonas pharaonis, we now know that several microbial sensory rhodopsins in the other major domain of life relay information on light intensity and quality to the cell. Three of the most studied photosensory transduction mechanisms of these microbial rhodopsins are dealt with in this review. We discuss recent progress in the understanding of genomic organization, photochemical properties and photosignaling mechanisms with respect to biological function.

Different dark conformations function in color-sensitive photosignaling by the sensory rhodopsin I-HtrI complex

The haloarchaeal phototaxis receptor sensory rhodopsin I (SRI) in complex with its transducer HtrI delivers an attractant signal from excitation with an orange photon and a repellent signal from a second near-UV photon excitation. Using a proteoliposome system with purified SRI in complex with its transducer HtrI, we identified by site-directed fluorescence labeling a site (Ser(155)) on SRI that is conformationally active in signal relay to HtrI. Using site-directed spin labeling of Ser(155)Cys with a nitroxide side chain, we detected a change in conformation following one-photon excitation such that the spin probe exhibits a splitting of the outer hyperfine extrema (2A'(zz)) significantly smaller than that of the electron paramagnetic resonance spectrum in the dark state. The dark conformations of five mutant complexes that do not discriminate between orange and near-UV excitation show shifts to lower or higher 2A'(zz) values correlated with the alterations in their motility behavior to one- and two-photon stimuli. These data are interpreted in terms of a model in which the dark complex is populated by two conformers in the wild type, one that inhibits the CheA kinase (A) and the other that activates it (R), shifted in the dark by mutations and shifted in the wild-type SRI-HtrI complex in opposite directions by one-photon and two-photon reactions.

A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control

By reverse-engineering we have detected eight kinetic phases of the symmetric switch cycle of the Halobacterium salinarum flagellar motor assembly and identified those steps in the switch cycle that are controlled by sensory rhodopsins during phototaxis. Upon switching the rotational sense, the flagellar motor assembly passes through a stop state from which all subunits synchronously resume rotation in the reverse direction. The assembly then synchronously proceeds through three subsequent functional states of the switch: Refractory, Competent, and Active, from which the rotational sense is switched again. Sensory control of the symmetric switch cycle occurs at two steps in each rotational sense by inversely regulating the probabilities for a change from the Refractory to the Competent and from Competent to the Active rotational mode. We provide a mathematical model for flagellar motor switching and its sensory control, which is able to explain all tested experimental results on spontaneous and light-controlled motor switching, and give a mechanistic explanation based on synchronous conformational transitions of the subunits of the switch complex after reversible dissociation and binding of a response regulator (CheYP). We conclude that the kinetic mechanism of flagellar motor switching and its sensory control is fundamentally different in the archaeon H. salinarum and the bacterium Escherichia coli.

Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis

Natronomonas pharaonis is an extremely haloalkaliphilic archaeon that was isolated from salt-saturated lakes of pH 11. We sequenced its 2.6-Mb GC-rich chromosome and two plasmids (131 and 23 kb). Genome analysis suggests that it is adapted to cope with severe ammonia and heavy metal deficiencies that arise at high pH values. A high degree of nutritional self-sufficiency was predicted and confirmed by growth in a minimal medium containing leucine but no other amino acids or vitamins. Genes for a complex III analog of the respiratory chain could not be identified in the N. pharaonis genome, but respiration and oxidative phosphorylation were experimentally proven. These studies identified protons as coupling ion between respiratory chain and ATP synthase, in contrast to other alkaliphiles using sodium instead. Secretome analysis predicts many extracellular proteins with alkaline-resistant lipid anchors, which are predominantly exported through the twin-arginine pathway. In addition, a variety of glycosylated cell surface proteins probably form a protective complex cell envelope. N. pharaonis is fully equipped with archaeal signal transduction and motility genes. Several receptors/transducers signaling to the flagellar motor display novel domain architectures. Clusters of signal transduction genes are rearranged in haloarchaeal genomes, whereas those involved in information processing or energy metabolism show a highly conserved gene order.

Posttranslational protein modification in Archaea

One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.

MpcT is the transducer for membrane potential changes in Halobacterium salinarum

In Halobacterium salinarum mutants containing either of the light-driven ion pumps bacteriorhodopsin (H(+)) or halorhodopsin (Cl(-)) as their only retinal protein, a decrease of irradiance in the absence of respiration causes a phototactic response. The conversion of the causal event, a decrease of proton motive force across the cell membrane, into a reversal of flagellar motor rotational direction was expected to involve a transducer. Via deletion analysis of all 18 known and putative halobacterial transducer (htr) genes, we found that Htr14, a methylatable membrane-bound transducer lacking an extracellular domain, mediates the biological response, which includes adaptive methylation. Based on a minimal stimulus length of 200 ms and the determined cytoplasmic buffering capacity, we conclude that the change in the membrane potential (DeltaPsi), and not that of the internal pH, is the signal-generating event. Htr14 was therefore renamed to Membrane potential change Transducer, or MpcT. It is the first transducer for which the causative stimulus could be narrowed to a change in DeltaPsi, as opposed to a change in pH or cellular redox state.

Time-resolved detection of sensory rhodopsin II-transducer interaction

The dynamics of protein conformational change of Natronobacterium pharaonis sensory rhodopsin II (NpSRII) and of NpSRII fused to cognate transducer (NpHtrII) truncated at 159 amino acid sequence from the N-terminus (NpSRII-DeltaNpHtrII) are investigated in solution phase at room temperature by the laser flash photolysis and the transient grating methods in real time. The diffusion coefficients of both species indicate that the NpSRII-DeltaNpHtrII exists in the dimeric form in 0.6% dodecyl-beta-maltopyranoside (DM) solution. Rate constants of the reaction processes in the photocycles determined by the transient absorption and grating methods agree quite well. Significant differences were found in the volume change and the molecular energy between NpSRII and NpSRII-DeltaNpHtrII samples. The enthalpy of the second intermediate (L) of NpSRII-DeltaNpHtrII is more stabilized compared with that of NpSRII. This stabilization indicates the influence of the transducer to the NpSRII structure in the early intermediate species by the complex formation. Relatively large molecular volume expansion and contraction were observed in the last two steps for NpSRII. Additional volume expansion and contraction were induced by the presence of DeltaNpHtrII. This volume change, which should reflect the conformational change induced by the transducer protein, suggested that this is the signal transduction process of the NpSRII-DeltaNpHtrII.

Role of Arg-72 of pharaonis Phoborhodopsin (sensory rhodopsin II) on its photochemistry

Pharaonis phoborhodopsin (ppR, or pharaonis sensory rhodopsin II, NpsRII) is a sensor for the negative phototaxis of Natronomonas (Natronobacterium) pharaonis. Arginine 72 of ppR corresponds to Arg-82 of bacteriorhodopsin, which is a highly conserved residue among microbial rhodopsins. Using various Arg-72 ppR mutants, we obtained the following results: 1). Arg-72(ppR) together possibly with Asp-193 influenced the pK(a) of the counterion of the protonated Schiff base. 2). The M-rise became approximately four times faster than the wild-type. 3). Illumination causes proton uptake and release, and the pH profiles of the sequence of these two proton movements were different between R72A mutant and the wild-type; it is inferred that Arg-72 connects the proton transfer events occurring at both the Schiff base and an extracellular proton-releasing residue (Asp-193). 4). The M-decays of Arg-72 mutants were faster ( approximately 8-27 folds at pH 8 depending on mutants) than the wild-type, implying that the guanidinium prevents the proton transfer from the extracellular space to the deprotonated Schiff base. 5), The proton-pumping activities were decreased for mutants having increased M-decay rates, but the extent of the decrease was smaller than expected. The role of Arg-72 of ppR on the photochemistry was discussed.

Interaction of Natronobacterium pharaonis Phoborhodopsin (Sensory Rhodopsin II) with its Cognate Transducer Probed by Increase in the Thermal Stability¶

Pharaonis phoborhodopsin (ppR, also called Natronobacterium pharaonis sensory rhodopsin II) and its transducer protein, pharaonis halobacterial transducer of ppR (pHtrII), form a signaling complex, and light signals are transmitted from the sensor to the transducer by the protein-protein interaction. A truncated pHtrII(1-159) consisting of intramembrane helices (expressing amino acid residues from the first to the 159th position) and ppR form the complex in a solution containing 0.1% n-dodecyl-beta-D-maltoside. At 75-85 degrees C, the time-dependent color loss of ppR was caused by denaturation. We found that pHtrII(1-159) retarded the denaturation rate of ppR. This increase in the thermal stability was used as a probe for the binding ability in the dark. Tyr199 of ppR and Asn74 of pHtrII(1-114) were proposed as amino acid residues interacting with each other through hydrogen bonding. Then,ppR and pHtrII(1-159) mutants at these positions were prepared to examine the effect on the binding in the dark. The wild-type and Y199F mutant can bind pHtrII(1-159), suggesting that the hydrogen bonding between these specific amino acid residues may not be the only cause of the binding, but the hydrophobic interaction via phenyl ring of ppR may contribute dominantly.

Light-induced behavioral responses (;phototaxis') in prokaryotes

Light-induced sensory responses are among the oldest scientific observations on bacterial behavior. Various types of response have been characterized physiologically in detail. However, the molecular basis of this type of response is only slowly emerging. In many of these systems photosynthetic pigments absorb the light. This then generates a signal via electron transport, feeding into a canonical chemotaxis signal transduction pathway. Nevertheless, several examples have been identified in which dedicated photoreceptor proteins do play a role. The intrinsic complexity of some of these signal transduction systems is overwhelming, in part because of the significant apparent redundancy. The genomics information that is now available for several model organisms (in particular Rhodobacter sphaeroides and Synechocystis sp. PCC6803) facilitates obtaining an increasingly detailed view of the molecular basis of the partial reactions that jointly form the basis of this type of elementary behavioral response.

An osmosensing histidine kinase mediates dicarboximide fungicide resistance in Botryotinia fuckeliana (Botrytis cinerea)

A two-component histidine protein kinase gene, homologous to os-1 from Neurospora crassa, was cloned and sequenced from a single ascospore isolate of Botryotinia fuckeliana. A series of nine spontaneous mutants resistant to dicarboximide fungicides was selected from this strain and characterized with respect to fungicide resistance and osmotic sensitivity. Genetic crosses of the mutants with an authentic Daf1 strain showed that the phenotypes mapped to this locus. Single point mutations (seven transitions, one transversion, and one short deletion) were detected in the alleles of the nine mutants sequenced. The mutational changes were shown to cosegregate with the dicarboximide resistance and osmotic sensitivity phenotypes in progeny obtained from crossing selected resistant strains with a sensitive strain. All mutations detected are predicted to result in amino acid changes in the coiled-coil region of the putative Daf1 histidine kinase, and it is proposed that dicarboximide fungicides target this domain.

A novel mode of sensory transduction in archaea: binding protein-mediated chemotaxis towards osmoprotectants and amino acids

Directly upstream of the Halobacterium salinarum transducer genes basT and htpIV we identified two open reading frames (orfs) with significant homologies to genes encoding binding proteins for amino acids and compatible solutes, respectively. Behavioral testing of deletion mutants indicates that halobacterial chemotaxis towards branched-chain amino acids as well as compatible osmolytes of the betaine family requires both a binding and a transducer protein. We therefore named the binding/transducer proteins BasB/BasT for branched-chain and sulfur-containing amino acids and CosB/CosT for compatible solutes. Our data support a signaling mechanism with the binding proteins functioning as lipid-anchored receptors interacting with the extracellular domain of their cognate transducers. Inspection of the halobacterial genome suggests that BasB and CosB exclusively mediate chemotaxis responses without any additional role in transport, which is in contrast to bacterial binding proteins, which are always part of ABC transport systems. The CosB/CosT system is the first instance of a chemotaxis signaling pathway for organic osmolytes in the living world and natural abundance 13C-NMR analysis of cytoplasmic extracts suggests that H.salinarum utilizes these solutes for osmotic adaptation.

Association of pharaonis phoborhodopsin with its cognate transducer decreases the photo-dependent reactivity by water-soluble reagents of azide and hydroxylamine

pharaonis phoborhodopsin (ppR; also pharaonis sensory rhodopsin II, psRII) is a receptor of the negative phototaxis of Natronobacterium pharaonis. In halobacterial membrane, ppR forms a complex with its transducer pHtrII, and this complex transmits the light signal to the sensory system in the cytoplasm. In the present work, the truncated transducer, t-Htr, was used which interacts with ppR [Sudo et al. (2001) Photochem. Photobiol. 74, 489-494]. Two water-soluble reagents, hydroxylamine and azide, reacted both with the transducer-free ppR and with the complex ppR/t-Htr (the complex between ppR and its truncated transducer). In the dark, the bleaching rates caused by hydroxylamine were not significantly changed between transducer-free ppR and ppR/t-Htr, or that of the free ppR was a little slower. Illumination accelerated the bleach rates, which is consistent with our previous conclusion that the reaction occurs selectively at the M-intermediate, but the rate of the complex was about 7.4-fold slower than that of the transducer-free ppR. Azide accelerated the M-decay, and its reaction rate of ppR/t-Htr was about 4.6-fold slower than free ppR. These findings suggest that the transducer binding decreases the water accessibility around the chromophore at the M-intermediate. Its implication is discussed.

Crystal structure of sensory rhodopsin II at 2.4 angstroms: insights into color tuning and transducer interaction

We report an atomic-resolution structure for a sensory member of the microbial rhodopsin family, the phototaxis receptor sensory rhodopsin II (NpSRII), which mediates blue-light avoidance by the haloarchaeon Natronobacterium pharaonis. The 2.4 angstrom structure reveals features responsible for the 70- to 80-nanometer blue shift of its absorption maximum relative to those of haloarchaeal transport rhodopsins, as well as structural differences due to its sensory, as opposed to transport, function. Multiple factors appear to account for the spectral tuning difference with respect to bacteriorhodopsin: (i) repositioning of the guanidinium group of arginine 72, a residue that interacts with the counterion to the retinylidene protonated Schiff base; (ii) rearrangement of the protein near the retinal ring; and (iii) changes in tilt and slant of the retinal polyene chain. Inspection of the surface topography reveals an exposed polar residue, tyrosine 199, not present in bacteriorhodopsin, in the middle of the membrane bilayer. We propose that this residue interacts with the adjacent helices of the cognate NpSRII transducer NpHtrII.

Retinylidene proteins: structures and functions from archaea to humans

Retinylidene proteins, containing seven membrane-embedded alpha-helices that form an internal pocket in which the chromophore retinal is bound, are ubiquitous in photoreceptor cells in eyes throughout the animal kingdom. They are also present in a diverse range of other organisms and locations, such as archaeal prokaryotes, unicellular eukaryotic microbes, the dermal tissue of frogs, the pineal glands of lizards and birds, the hypothalamus of toads, and the human brain. Their functions include light-driven ion transport and phototaxis signaling in microorganisms, and retinal isomerization and various types of photosignal transduction in higher animals. The aims of this review are to examine this group of photoactive proteins as a whole, to summarize our current understanding of structure/function relationships in the best-studied examples, and to report recent new developments.

Primary reactions of sensory rhodopsins

The first steps in the photocycles of the archaeal photoreceptor proteins sensory rhodopsin (SR) I and II from Halobacterium salinarum and SRII from Natronobacterium pharaonis have been studied by ultrafast pump/probe spectroscopy and steady-state fluorescence spectroscopy. The data for both species of the blue-light receptor SRII suggests that their primary reactions are nearly analogous with a fast decay of the excited electronic state in 300-400 fs and a transition between two red-shifted product states in 4-5 ps. Thus SRII behaves similarly to bacteriorhodopsin. In contrast for SRI at pH 6.0, which absorbs in the orange part of the spectrum, a strongly increased fluorescence quantum yield and a drastically slower and biexponential decay of the excited electronic state occurring on the picosecond time scale (5 ps and 33 ps) is observed. The results suggest that the primary reactions are controlled by the charge distribution in the vicinity of the Schiff base and demonstrate that there is no direct connection between absorption properties and reaction dynamics for the retinal protein family.

Primary reactions of sensory rhodopsins

The first steps in the photocycles of the archaeal photoreceptor proteins sensory rhodopsin (SR) I and II from Halobacterium salinarum and SRII from Natronobacterium pharaonis have been studied by ultrafast pump/probe spectroscopy and steady-state fluorescence spectroscopy. The data for both species of the blue-light receptor SRII suggests that their primary reactions are nearly analogous with a fast decay of the excited electronic state in 300-400 fs and a transition between two red-shifted product states in 4-5 ps. Thus SRII behaves similarly to bacteriorhodopsin. In contrast for SRI at pH 6.0, which absorbs in the orange part of the spectrum, a strongly increased fluorescence quantum yield and a drastically slower and biexponential decay of the excited electronic state occurring on the picosecond time scale (5 ps and 33 ps) is observed. The results suggest that the primary reactions are controlled by the charge distribution in the vicinity of the Schiff base and demonstrate that there is no direct connection between absorption properties and reaction dynamics for the retinal protein family.

Equal-quantum action spectra indicate fluence-rate-selective action of multiple photoreceptors for photomovement of the thermophilic cyanobacterium Synechococcus elongatus

Unicellular thermophilic cyanobacterium Synechococcus elongatus displayed phototaxis on agar plate at 55 degrees C. Equal-quantum action spectra for phototactic migration were determined at various fluence rates using the Okazaki Large Spectrograph as the light source. The shapes of the action spectra drastically changed depending on the fluence rate of the unilateral monochromatic irradiation: at a low fluence rate (3 mumol/m2/s), only lights in the red region had significant effect; at a medium fluence rate (10 mumol/m2/s), four major action peaks were observed at 530 nm (green), 570 nm (yellow), 640 nm (red) and 680 nm (red). At high fluence rates (30-90 mumol/m2/s), the former two peaks remained, while red peaks at 640 nm and 680 nm disappeared and, interestingly, an action peak around 700-740 nm (far-red) newly appeared. These results indicate that two or more distinct photoreceptors are involved in the phototaxis and that suitable photoreceptors are selectively active in response to the stimulus of light fluence rates. Far-red or red background lights irradiated vertically from above drastically inhibited phototaxis toward red light or far-red light, respectively. These results indicate involvement of some phytochrome(s).

Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon

Halobacterium species display a variety of responses to light, including phototrophic growth, phototactic behavior, and photoprotective mechanisms. The complete genome sequence of Halobacterium species NRC-1 (Proc Natl Acad Sci USA 97: 12176-12181, 2000), coupled with the availability of a battery of methods for its analysis makes this an ideal model system for studying photobiology among the archaea. Here, we review: (1) the structure of the 2.57 Mbp Halobacterium NRC-1 genome, including a large chromosome, two minichromosomes, and 91 transposable IS elements; (2) the purple membrane regulon, which programs the accumulation of large quantities of the light-driven proton pump, bacteriorhodopsin, and allows for a period of phototrophic growth; (3) components of the sophisticated pathways for color-sensitive phototaxis; (4) the gas vesicle gene cluster, which codes for cell buoyancy organelles; (5) pathways for the production of carotenoid pigments and retinal, (6) processes for the repair of DNA damage; and (7) putative homologs of circadian rhythm regulators. We conclude with a discussion of the power of systems biology for comprehensive understanding of Halobacterium NRC-1 photobiology.

Multicolored protein conformation states in the photocycle of transducer-free sensory rhodopsin-I

Sensory rhodopsin-I (SRI), a phototaxis receptor of archaebacteria, is a retinal-binding protein that exists in the cell membrane intimately associated with a signal-transducing protein (HtrI) homologous to eubacterial chemotaxis receptors. Transducer-free sensory rhodopsin-I (fSRI), from cells devoid of HtrI, undergoes a photochemical cycle kinetically different from that of native SRI. We report here on the measurement and analysis of the photochemical kinetics of fSRI reactions in the 350-750-nm spectral range and in a 10(-7) s to 1 s time window. The lack of specific intermolecular interactions between SRI and HtrI results in early return of the ground form via distinct branching reactions in fSRI, not evident in the photocycle of native SRI. The chromophore transitions are loosely coupled to protein structural transitions. The coexistence of multiple spectral forms within kinetic intermediates is interpreted within the concept of multicolored protein conformational states.

Evolutionary conservation of methyl-accepting chemotaxis protein location in Bacteria and Archaea

The methyl-accepting chemotaxis proteins (MCPs) are concentrated at the cell poles in an evolutionarily diverse panel of bacteria and an archeon. In elongated cells, the MCPs are located both at the poles and at regions along the length of the cells. Together, these results suggest that MCP location is evolutionarily conserved.

Genome sequence of Halobacterium species NRC-1

We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea.

Bacterial rhodopsin: evidence for a new type of phototrophy in the sea

Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.

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.

Proton transport by sensory rhodopsins and its modulation by transducer-binding

The study of light-induced proton transfers in the archaeal sensory rhodopsins (SR), phototaxis receptors in Halobacterium salinarum, has contributed important insights into their mechanism of signaling to their cognate transducer subunits in the signaling complex. Essential features of the bacteriorhodopsin (BR) pumping mechanism have been conserved in the evolution of the sensors, which carry out light-driven electrogenic proton transport when their transducers are removed. The interaction of SRI with its transducer blocks proton-conducting channels in the receptor thereby inhibiting its proton pumping, indicating that the pump machinery, rather than the transport activity itself, is functionally important for signaling. Analysis of SRII mutants has shown that the salt bridge between the protonated Schiff base and its counterion Asp73 constrains the receptor in its inactive conformation. Similarly, in BR, the corresponding salt bridge between the protonated Schiff base and Asp85 contributes to constraining the protein in a conformation in which its cytoplasmic channel is closed. Transducer chimera studies further indicate that the receptor conformational changes are transmitted from the sensors to their cognate transducers through transmembrane helix-helix interaction. These and other results reviewed here support a signaling mechanism in which tilting of helices on the cytoplasmic side (primarily outward tilting of helix F), similar to that which occurs in BR in its open cytoplasmic channel conformation, causes structural alterations in the transducer transmembrane helices.

BasT, a membrane-bound transducer protein for amino acid detection in Halobacterium salinarum

Halophilic archaea, such as eubacteria, use methyl-accepting chemotaxis proteins (MCPs) to sense their environment. We show here that BasT is a halobacterial transducer protein (Htp) responsible for chemotaxis towards five attractant amino acids. The C-terminus of the protein exhibits the highly conserved regions that are diagnostic for MCPs: the signalling domain for communication with the histidine kinase and the methylation sites that interact with the methylation/demethylation enzymes for adaptation. Hydropathy analysis predicts an enterobacterial-type transducer protein topology for BasT, with an extracellular putative ligand-binding domain flanked by two transmembrane helices and a cytoplasmic domain. BasT-inactivated mutant cells are missing a membrane protein radiolabelled with L-[methyl-3H]-methionine in wild-type cells, confirming that BasT is methylatable and membrane bound. Behavioural analysis of the basT mutant cells by capillary and chemical-in-plug assays demonstrates complete loss of chemotactic responses towards five (leucine, isoleucine, valine, methionine and cysteine) of the six attractant amino acids for Halobacterium salinarum, whereas they still respond to arginine. The volatile methyl group production assays also corroborate these findings and confirm that BasT signalling induces methyl group turnover. Our data identify BasT as the chemotaxis transducer protein for the branched chain amino acids leucine, isoleucine and valine as well as for methionine and cysteine. Thus, BasT and the arginine sensor Car cover the entire spectrum of chemotactic responses towards attractant amino acids in H. salinarum.

Proton circulation during the photocycle of sensory rhodopsin II

Sensory rhodopsin II (SRII) in Halobacterium salinarum membranes is a phototaxis receptor that signals through its bound transducer HtrII for avoidance of blue-green light. In the present study we investigated the proton movements during the photocycle of SRII in the HtrII-free and HtrII-complexed form. We monitored sustained light-induced pH changes with a pH electrode, and laser flash-induced pH changes with the pH indicator pyranine using sealed membrane vesicles and open sheets containing the free or the complexed receptor. The results demonstrated that SRII takes up a proton in M-to-O conversion and releases it during O-decay. The uptake and release are from and to the extracellular side, and therefore SRII does not transport the proton across the membrane. The pH dependence of the SRII photocycle indicated the presence of a protonatable group (pK(a) approximately 7.5) in the extracellular proton-conducting path, which plays a role in proton uptake by the Schiff base in the M-to-O conversion. The extracellular proton circulation produced by SRII was not blocked by HtrII complexation, unlike the cytoplasmic proton conduction in SRI that was found in the same series of measurements to be blocked by its transducer, HtrI. The implications of this finding for current models of SRI and SRII signaling are discussed.

Bacterial tactic responses

Many, if not most, bacterial species swim. The synthesis and operation of the flagellum, the most complex organelle of a bacterium, takes a significant percentage of cellular energy, particularly in the nutrient limited environments in which many motile species are found. It is obvious that motility accords cells a survival advantage over non-motile mutants under normal, poorly mixed conditions and is an important determinant in the development of many associations between bacteria and other organisms, whether as pathogens or symbionts and in colonization of niches and the development of biofilms. This survival advantage is the result of sensory control of swimming behaviour. Although too small to sense a gradient along the length of the cell, and unable to swim great distances because of buffetting by Brownian motion and the curvature resulting from a rotating flagellum, bacteria can bias their random swimming direction towards a more favourable environment. The favourable environment will vary from species to species and there is now evidence that in many species this can change depending on the current physiological growth state of the cell. In general, bacteria sense changes in a range of nutrients and toxins, compounds altering electron transport, acceptors or donors into the electron transport chain, pH, temperature and even the magnetic field of the Earth. The sensory signals are balanced, and may be balanced with other sensory pathways such as quorum sensing, to identify the optimum current environment. The central sensory pathway in this process is common to most bacteria and most effectors. The environmental change is sensed by a sensory protein. In most species examined this is a transmembrane protein, sensing the external environment, but there is increasing evidence for additional cytoplasmic receptors in many species. All receptors, whether sensing sugars, amino acids or oxygen, share a cytoplasmic signalling domain that controls the activity of a histidine protein kinase, CheA, via a linker protein, CheW. A reduction in an attractant generally leads to the increased autophosphorylation of CheA. CheA passes its phosphate to a small, single domain response regulator, CheY. CheY-P can interact with the flagellar motor to cause it to change rotational direction or stop. Signal termination either via a protein, CheZ, which increases the dephosphorylation rate of CheY-P or via a second CheY which acts as a phosphate sink, allows the cell to swim off again, usually in a new direction. In addition to signal termination the receptor must be reset, and this occurs via methylation of the receptor to return it to a non-signalling conformation. The way in which bacteria use these systems to move to optimum environments and the interaction of the different sensory pathways to produce species-specific behavioural response will be the subject of this review.

Bioenergetics of the Archaea

In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, Archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the molecular and mechanistic bases on which these organisms can cope with such adverse conditions. This review considers our cumulative knowledge on archaeal mechanisms of primary energy conservation, in relationship to those of bacteria and eucarya. Although the universal principle of chemiosmotic energy conservation also holds for Archaea, distinct features have been discovered with respect to novel ion-transducing, membrane-residing protein complexes and the use of novel cofactors in bioenergetics of methanogenesis. From aerobically respiring Archaea, unusual electron-transporting supercomplexes could be isolated and functionally resolved, and a proposal on the organization of archaeal electron transport chains has been presented. The unique functions of archaeal rhodopsins as sensory systems and as proton or chloride pumps have been elucidated on the basis of recent structural information on the atomic scale. Whereas components of methanogenesis and of phototrophic energy transduction in halobacteria appear to be unique to Archaea, respiratory complexes and the ATP synthase exhibit some chimeric features with respect to their evolutionary origin. Nevertheless, archaeal ATP synthases are to be considered distinct members of this family of secondary energy transducers. A major challenge to future investigations is the development of archaeal genetic transformation systems, in order to gain access to the regulation of bioenergetic systems and to overproducers of archaeal membrane proteins as a prerequisite for their crystallization.

Identification of methylation sites and effects of phototaxis stimuli on transducer methylation in Halobacterium salinarum

The two transducers in the phototaxis system of the archaeon Halobacterium salinarum, HtrI and HtrII, are methyl-accepting proteins homologous to the chemotaxis transducers in eubacteria. Consensus sequences predict three glutamate pairs containing potential methylation sites in HtrI and one in HtrII. Mutagenic substitution of an alanine pair for one of these, Glu265-Glu266, in HtrI and for the homologous Glu513-Glu514 in HtrII eliminated methylation of these two transducers, as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis autofluorography. Photostimulation of the repellent receptor sensory rhodopsin II (SRII) induced reversible demethylation of HtrII, while no detectable change in the extent of methylation of HtrI was observed in response to stimulation of its cognate sensory rhodopsin, the attractant receptor SRI. Cells containing HtrI or HtrII with all consensus sites replaced by alanine still exhibited phototaxis responses and behavioral adaptation, and methanol release assays showed that methyl group turnover was still induced in response to photostimulation of SRI or SRII. By pulse-chase experiments with in vivo L-[methyl-(3)H]methionine-labeled cells, we found that repetitive photostimulation of SRI complexed with wild-type (or nonmethylatable) HtrI induced methyl group turnover in transducers other than HtrI to the same extent as in wild-type HtrI. Both attractant and repellent stimuli cause a transient increase in the turnover rate of methyl groups in wild-type H. salinarum cells. This result is unlike that obtained with Escherichia coli, in which attractant stimuli decrease and repellent stimuli increase turnover rate, and is similar to that obtained with Bacillus subtilis, which also shows turnover rate increases regardless of the nature of the stimulus. We found that a CheY deletion mutant of H. salinarum exhibited the E. coli-like asymmetric pattern, as has recently also been observed in B. subtilis. Further, we demonstrate that the CheY-dependent feedback effect does not require the stimulated transducer to be methylatable and operates globally on other transducers present in the cell.