Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin

Translocation of negatively charged ions across cell membranes by ion pumps raises the question as to how protein interactions control the location and dynamics of the ion. Here we address this question by performing extensive molecular dynamics simulations of wild type and mutant halorhodopsin, a seven-helical transmembrane protein that translocates chloride ions upon light absorption. We find that inter-helical hydrogen bonds mediated by a key arginine group largely govern the dynamics of the protein and water groups coordinating the chloride ion.     

Fourier transform infrared study of the halorhodopsin chloride pump

Halorhodopsin (hR) is a light-driven chloride pump located in the cell membrane of Halobacterium halobium. Fourier transform infrared difference spectroscopy has been used to study structural alterations occurring during the hR photocycle. The frequencies of peaks attributed to the retinylidene chromophore are similar to those observed in the spectra of the related protein bacteriorhodopsin (bR), indicating that in hR as in bR an all-trans----13-cis isomerization occurs during formation of the early bathoproduct. Spectral features due to protein structural alterations are also similar for the bR and hR photocycles. For example, formation of the red-shifted primary photoproducts of both hR and bR results in similar carboxyl peaks in the 1730-1745-cm-1 region. However, in contrast to bR, no further changes are observed in the carboxyl region during subsequent steps in the hR photocycle, indicating that additional carboxyl groups are not directly involved in chloride translocation. Overall, the close similarity of vibrations in hR and bR photoproduct difference spectra supports the existence of some common elements in the molecular mechanisms of energy transduction and active transport by these two proteins.     

Effects of chloride on the absorption spectrum and photoreactions of halorhodopsin

The absorption maximum of halorhodopsin in a membrane fraction prepared from the cells of Halobacterium halobium under low-salt conditions shifted to longer wavelenghts upon addition of NaCl (Ogurusu, T., Maeda, A., Sasaki, N. and Yoshizawa, T. (1981) J. Biochem. (Tokyo) 90, 1267–1273). This bathochromic shift was due to chloride, not sodium. Bromide and iodide were also effective. The bathochromic shift of the absorption maximum was not accompanied by any change in the isomer composition of retinal in halorhodopsin. The same ionic species were essential for the formation of the hypsochromic photoproduct at −75°C. These effects of NaCl on halorhodopsin are discussed in terms of the presence of the two forms of halorhodopsin, a form binding chloride and a chloride-free form.     

Mechanism of a molecular valve in the halorhodopsin chloride pump

Halorhodopsin is a light-driven chloride anion pump in which the trans-->cis photoisomerization of a retinal chromophore triggers a photocycle resulting in the translocation of chloride across the plasma membrane. The mechanism of chloride transfer past the cis retinal is determined here by computing multiple pathways for this process. The calculations reveal two conditions of the valve mechanism. First, a lumen absent in the ground state structure is transiently opened by chloride passage. Second, this activated opening, which is achieved by flexible deformation of the surrounding protein, is shown to significantly raise the chloride translocation barrier between photocycles, thus preventing chloride backflow. Unlike macroscopic valve designs, the protein allows differential ion flows in the pumping and resting states that are tuned to match the physiological timescales of the cell, thus creating a "kinetic" valve.     

Effect of anions on the photocycle of halorhodopsin. Substitution of chloride with formate anion

Halorhodopsin from Natronomonas pharaonis is a light-driven chloride pump which transports a chloride anion across the plasma membrane following light absorption by a retinal chromophore which initiates a photocycle. It was shown that the chloride anion bound in the vicinity of retinal PSB can be replaced by several inorganic anions, including azide which converts the chloride pump into a proton pump and induces formation of an M-like intermediate detected in the bR photocycle but not in native halorhodopsin. Here we have studied the possibility of replacing the chloride anion with organic anions and have followed the photocycle under several conditions. It is revealed that the chloride can be replaced with a formate anion but not with larger organic anions such as acetate. Flash photolysis experiments detected in the formate pigment an M-like intermediate characterized by a lifetime much longer than that of the O intermediate. The lifetime of the M-like intermediate depends on the pH, and its decay is significantly accelerated at low pH. The decay rate exhibited a titration-like curve, suggesting that the protonation of a protein residue controls the rate of M decay. Similar behavior was detected in N. pharaonis pigments in which the chloride anion was replaced with NO(2)(-) and OCN(-) anions. It is suggested that the formation of the M-like intermediate indicates branching pathways from the L intermediate or basic heterogeneity in the original pigment.     

Specific arginine and threonine residues control anion binding and transport in the light-driven chloride pump halorhodopsin.

The light-driven chloride pump halorhodopsin (HR), a halobacterial retinal protein, was studied by comparing wild type with specific mutants. Changes of conserved arginine and threonine residues in the transmembrane regions could be classified in two categories: in the extracellular half of the molecule, mutations influence anion uptake and binding. R108 mutations abolish all anion effects previously attributed to two distinct binding sites and change the characteristic photochemistry. Neutral residues at position 108 completely inactivate the pump. T111 increases the affinity of this anion binding site without being essentially important. In the photochemical cycles of the mutants T111V and Q105E, a red-shifted absorbing intermediate is enriched indicating retarded anion uptake. On the cytoplasmic side, mutations do not change anion binding properties of the unphotolyzed protein, but slow down anion release thereby reducing the chloride transport activity and the photocycling rate. The lowest activity is found for T203V, while R200 mutations have weaker effects. Thus, in the symmetrically arranged pairs R108/T111 and T203/R200, threonine and arginine play different roles, reflecting high affinity anion uptake by the former and effective anion release catalyzed by the latter residues. A model for the anion transport mechanism in HR is suggested comprising the specific functions of channel-lining residues.     

Ser-130 of Natronobacterium pharaonis halorhodopsin is important for the chloride binding

Pharaonis halorhodopsin (phR) is an inward light-driven chloride ion pump from Natronobacterium pharaonis. In order to clarify the role of Ser-130(phR) residue which corresponds to Ser-115(shR) for salinarum hR on the anion-binding affinity, the wild-type and Ser-130 mutants substituted with Thr, Cys and Ala were expressed in E. coli cells and solubilized with 0.1% n-dodecyl beta-D-maltopyranoside The absorption maximum (lambda(max)) of the S130T mutant indicated a blue shift from that of the wild type in the absence and presence of chloride. For S130A, a large red shift (12 nm) in the absence of chloride was observed. The wild-type and all mutants showed the blue-shift of lambda(max) upon Cl(-) addition, from which the dissociation constants of Cl(-) were determined. The dissociation constants were 5, 89, 153 and 159 mM for the wild-type, S130A, S130T and S130C, respectively, at pH 7.0 and 25 degrees C. Circular dichroic spectra of the wild-type and the Ser-130 mutants exhibited an oligomerization. The present study revealed that the Ser-130 of N. pharaonis halorhodopsin is important for the chloride binding.     

Roles of Ser130 and Thr126 in chloride binding and photocycle of pharaonis halorhodopsin

Pharaonis halorhodopsin (phR) is an inward light-driven chloride ion pump in Natronobacterium pharaonis. In order to clarify the roles of the Ser130(phR) and Thr126(phR) residues, which correspond to Ser115(shR) and Thr111(shR) of salinarum hR (shR), with regard to their Cl(-)binding affinity and the photocycle, the wild-type phR, and S130 and T126 mutants were expressed in Escherichia coli cells. The photocycles of the wild-type phR, and S130 and T126 mutants were investigated in the presence of 1 M NaCl. Based on results of kinetic analysis involving singular value decomposition and global fitting, typical photointermediates K, L and O were identified, and the kinetic constants of decay or formation varied depending on the mutant. The photocycle scheme was linear for the wild-type phR, and S130C, S130T and T126V mutants. On the other hand, the S130A mutant showed a branched pathway between the L-hR and L-O steps. The present study revealed the following two facts with respect to the Ser130(phR) residue: 1) The OH group of this residue is important for Cl(-) ion binding next to the Schiff base nitrogen, and 2) replacement of an Ala residue, which is unable to form a hydrogen bond, results in a branched photocycle. The implication of this branching was discussed.     

Anion binding to the chloride pump, halorhodopsin, and its implications for the transport mechanism.

The light-driven chloride pump, halorhodopsin, binds and transports chloride across the membrane, and to a lesser extent nitrate. Binding and transport kinetics, and resonance Raman spectra of the retinal Schiff base, with these anions suggest the existence of two mutually exclusive binding sites. One of these may be the uptake site, and the other the release site during the transport. Plausible locations can be suggested for these sites, because halorhodopsin is a small protein with few buried positively charged residues, and the primary structure of a second pigment with similar function has recently become available for comparison.     

Bacterial pigments and their applications

Natural pigments sourced from ores, insects, plants and animals were the colorants used since prehistoric period. Synthetic dyes which took the place of natural pigments in the middle of 19th century still rule the field to the maximum extent in spite of its hazardous effect to humans, animals and environment. As an alternative to synthetic pigments, bacterial pigments due to their better biodegradability and higher compatibility with the environment, offer promising avenues for various applications. The industry is now able to produce some bacterial pigments for applications in food, pharmaceuticals, cosmetics and textiles. Extraction of bacterial pigments in relatively pure and concentrated forms is the main technological challenge. Optimization of fermentation process and the medium components are reported as key strategies for economic recovery of pigments. Research work needs to be carried out to formulate the fermentation media for each bacterial pigment on large scale by using economical and easily available sources for commercial process. Recent advances in synthetic biology, metabolic engineering efforts of bacteria will greatly expand the pigments that could be produced economically in sufficient amounts for industrial application. This review summarizes the current technology status and challenges, economics, novel strategies for production of bacterial pigments and metabolic engineering of bacteria with a focus on applications of bacterial pigments in food industry, pharmaceutical industry, dyeing as well as on other applications.     

Photocycle of halorhodopsin from Halobacterium salinarium.

The light-driven chloride pump, halorhodopsin, is a mixture containing all-trans and 13-cis retinal chromophores under both light and dark-adapted conditions and can exist in chloride-free and chloride-binding forms. To describe the photochemical cycle of the all-trans, chloride-binding state that is associated with the transport, and thereby initiate study of the chloride translocation mechanism, one must first dissect the contributions of these species to the measured spectral changes. We resolved the multiple photochemical reactions by determining flash-induced difference spectra and photocycle kinetics in halorhodopsin-containing membranes prepared from Halobacterium salinarium, with light- and dark-adapted samples at various chloride concentrations. The high expression of cloned halorhodopsin made it possible to do these measurements with unfractionated cell envelope membranes in which the chromophore is photostable not only in the presence of NaCl but also in the Na2SO4 solution used for reference. Careful examination of the flash-induced changes at selected wavelengths allowed separating the spectral changes into components and assigning them to the individual photocycles. According to the results, a substantial revision of the photocycle model for H. salinarium halorhodopsin, and its dependence on chloride, is required. The cycle of the all-trans chloride-binding form is described by the scheme, HR-hv-->K<==>L1<==>L2<==>N-->HR, where HR, K, L, and N designate halorhodopsin and its photointermediates. Unlike the earlier models, this is very similar to the photoreaction of bacteriorhodopsin when deprotonation of the Schiff base is prevented (e.g., at low pH or in the D85N mutant). Also unlike in the earlier models, no step in this photocycle was noticeably affected when the chloride concentration was varied between 20 mM and 2 M in an attempt to identify a chloride-binding reaction.     

Crystallization of halorhodopsin from Halobacterium sp. shark

The chloride-ion-pumping channel, halorhodopsin from Halobacterium sp. shark was detergent-solubilized and 3-D crystallized. Proteins were solubilized using the nonionic detergent n-octyl-beta-D-glucoside and were crystallized as thin-plate crystals with polyethylene glycol 4000 as a precipitant. The crystals belong to the space group P4(1)2(1)2 with unit-cell dimensions a=b=74.5 A and c=138.6 A. The diffraction pattern was slightly anisotropic. The best ordered crystal diffracted up to 3.3 A resolution along c axis with synchrotron radiation.     

ATP-driven chloride pumping and ATPase activity in theLimonium salt gland

Summary Using the short-circuit current as a measure of the electrogenic chloride transport in the salt glands ofLimonium, the effects of various inhibitors, of light-dark changes and of oxygen removal have been studied during steady-state pumping. The results are consistent with the hypothesis that ATP is the energy source for the chloride pump in this system.When microsomes from salt-loaded tissue are tested for ATPase activity, a substantial fraction of this is found to be chloride-stimulated. In uninduced tissue the Cl-ATPase activity is very much lower, and the induction by salt-loading can be blocked by puromycin. The parallels with Cl-pumping in this tissue are close enough to assume that the Cl-ATPase activity is that of the pump itself; the way is therefore open to study the pumpin vitro.     

Leukaemomycin-blocked mutants of Streptomyces griseus and their pigments

In a continued search for leukaemomycin-blocked mutants of three leukaemomycin-producing strains IMET JA 3933, IMET JA 5142 and IMET JA 5570 of Streptomyces griseus, 32 mutants producing aerial mycelium and spores were detected. Furthermore, in all mutants cosynthetic capability has been observed. This report describes characterization of leukaemomycin-blocked mutants obtained by mutagenic treatment experiments using NTG and combined UV-/X-rays. According to the biosynthetic capability for anthracyclinones or other pigments the mutants could be divided into six classes. The first class contains 14 leukaemomycin-blocked mutants unable to synthesize anthracyclinones. Besides two classes of mutants (12)synthesizing well-known anthracyclinones as epsilon-rhodomycinone, 7-deoxy-epsilon-rhodomycinone, 11-deoxy-derivatives of daunomycinone, three new classes of mutants (6) synthesizing reddish-brown, brown and blue-violet pigments on solid media with structures not elucidated as yet, will be described.     

Functional reconstitution of halorhodopsin. Properties of halorhodopsin-containing proteoliposomes

A one-step purification method for halorhodopsin was developed. Functional proteoliposomes were prepared from this preparation using cholate, which is removed by dialysis in the presence of asolectin or the polar halobacterial lipids. Light-induced outward directed transport of chloride by halorhodopsin was followed by measuring passive proton efflux in the presence of uncoupler; initial rates and extents amounted to significant fractions of values obtained for halorhodopsin-containing cell envelope vesicles. The transport activity was much higher when cholate rather than octyl glucoside was used in the reconstitution. Since CD spectra in cholate but not in octyl glucoside showed band-splitting in the visible region, suggestive of exciton interaction between halorhodopsin monomers, the reconstitution may depend on an aggregate state of the halorhodopsin. The rate constants for three thermal steps in the halorhodopsin photocycle were greatly reduced in the detergent-solubilized samples, but they increased in the proteoliposomes to values similar to those for halorhodopsin in cell envelope vesicles. Thus, the reconstitution yields halorhodopsin with both photochemical and transport activities restored. Freeze-fracture electron micrographs of the proteoliposomes showed unilammellar liposomes with numerous particles of 100-150 A diameter at the fracture faces. These should correspond to halorhodopsin aggregates, formed in the bilayer in an apparently concentration-dependent manner.     

Light and dark adaptation of halorhodopsin

Dark incubation of envelope vesicles derived from a strain of Halobacterium halobium that lacks bacteriorhodopsin but contains halorhodopsin and a third rhodopsin-like pigment caused a decrease in the flash yield [the amplitude of a transient absorbance change of flash reactive component(s) by flash] of halorhodopsin but not the rhodopsin-like pigment. The flash yield decreased to reach a low steady level after incubation for about 4 days in the dark. The flash yield of halorhodopsin at any stage of dark incubation was increased by actinic illumination of the vesicles. The flash yield at 490 nm (absorbance increase) was found to be approximately proportional to that at 590 nm (absorbance decrease). These results indicate that halorhodopsin in the envelope vesicles has two forms, dark and light adapted, and that the halorhodopsin phototransient absorbing at 490 nm is originated from the light-adapted form. A difference spectrum between these two forms of halorhodopsin shows that the light-adapted halorhodopsin was red-shifted from the dark-adapted form. The light-induced membrane potential was measured by tetraphenylphosphonium uptake. The uptake by the dark-adapted vesicles was slower than that by the light-adapted vesicles, suggesting that only the light-adapted halorhodopsin has ion-transporting activity.     

Antimicrobial activities of amino acid derivatives of monascus pigments

Amino acid derivatives of monascus pigments were produced by fermentation, and their antimicrobial activities were determined. Thirty-nine l- and d-forms of amino acids were added as a precursor to the fermentation medium for derivation of pigments. Derivatives with L-Phe, D-Phe, L-Tyr, and D-Tyr exhibited high activities against Gram(+) and Gram(-) bacteria with MIC values of c. 4-8 microg mL(-1). The control red pigment exhibited minimal inhibitory concentration (MIC) values higher than 32 microg mL(-1). Derivatives with L-Asp, D-Asp, L-Tyr, and D-Tyr were effective against the filamentous fungi Aspergillus niger, Penicillium citrinum, and Candida albicans. Monascus derivatives of amino acids having a phenyl ring like Phe and Tyr derivatives showed high antimicrobial activities. Incubation of the l-Phe derivative with Bacillus subtilis caused cells to aggregate with formation of pellets. Easy adsorption of the L-Phe pigment derivative to the surface of Escherichia coli cells was observed via SEM and TEM. Addition of monascus pigment derivatives decreased the oxygen uptake rate of E. coli in culture. The antimicrobial activities of pigment derivatives are considered to be related to the reduced availability of oxygen for the cells adsorbed with pigment.     

Existence of two L photointermediates of halorhodopsin from Halobacterium salinarium, differing in their protein and water FTIR bands.

FTIR difference spectra were recorded for the photoreactions of halorhodopsin from Halobacterium salinarium at 170 and 250 K. Obvious differences at the two temperatures were noted in neither the visible spectra nor the FTIR bands of the chromophore. However, perturbation of Asp141 is observed in the L intermediate at 250 K but not at 170 K. We named these photoproducts La (at 170 K) and Lb (at 250 K). The spectrum of Lb is distinct from that of La also in the different shifts of water O-H stretching bands, and larger changes in the bands from the protein backbone with different sensitivities to varying the halide. These results suggest that the photocycle of halorhodopsin contains two L states, La and Lb, in which the structure of protein and internal water molecules is different but chloride stays at the same site close to the Schiff base.     

Relationship between mycobacterial species and their carotenoid pigments

A study of the relationship between mycobacterial species and their carotenoid pigments was carried out. According to the carotenoid pigments contained, the mycobacterial species tested were divided into four groups: the first group of Mycobacterium kansasii and M. marinum, which formed principally only beta-carotene; the second group of M. gordonae, M. scrofulaceum, M. szulgai, M. xenopi, M. flavescens, M. phlei, M. rhodesiae, M. neoaurum, and M. aichiense, which formed beta-carotene and a zeaxanthin-like substance; the third group of M. aurum and M. obuense, which formed beta-carotene and an eschscholtzxanthin-like substance; and the fourth group of M. chubuense and M. tokaiense, which formed beta-carotene and zeaxanthin- and eschscholtzxanthin-like substances. The common carotenoid pigment throughout the genus Mycobacterium was beta-carotene and the hypophasic carotenoids differed according to the species.