Spectroscopic and photochemical analysis of proteorhodopsin variants from the surface of the Arctic Ocean

Proteorhodopsin (PR), a retinal-containing seven transmembrane helix protein, functions as a light-driven proton pump. Using PCR, we isolated 18 PR variants originating from the surface of the Arctic Ocean. Their absorption maxima were between 517 and 546 nm at pH 7. One of the isolates turned out to be identical to GPR (green light-absorbing proteorhodopsin) from Monterey Bay. Interestingly, 10 isolates had replaced a tyrosine in the retinal-binding site (Tyr200 in GPR) with Asn. They showed a slower photocycle, more blue-shifted absorption maxima at pH 10, and relatively larger DeltaH and DeltaS of activation of the transition between the O intermediate and the ground state compared to GPR.     

The photochemical reaction cycle of proteorhodopsin at low pH

The proton acceptor group in the recently described retinal protein, proteorhodopsin has an unusually high pK(a) of 7.1. It was shown that at pH above this pK(a), illumination initiates a photocycle similar to that of bacteriorhodopsin, and the protein transports proton across the cell membrane. Recently it was reported that proteorhodopsin, unlike bacteriorhodopsin, transports protons at pH below the pK(a) of the proton acceptor, and this transport is in the reverse direction. We have investigated the photocycle of proteorhodopsin at such low pH. At pH 5, three spectrally distinct intermediates K, L, and N, and another spectrally silent one, PR', could be identified, but a deprotonated Schiff base containing M-like intermediate, characteristic for proton pumping activity, does not accumulate. All the reactions between the intermediates are close to equilibrium, except the last transition from PR' to PR, when the protein returns to its initial unexcited state in a quasiunidirectional reaction. The electric signal measurements indicate that although charge motions are detected inside the protein, their net dislocation is zero, indicating that contrary to the earlier reported, at low pH no charged particle is transported across the membrane.     

Proton transfers in the photochemical reaction cycle of proteorhodopsin

The spectral and photochemical properties of proteorhodopsin (PR) were determined to compare its proton transport steps to those of bacteriorhodopsin (BR). Static and time-resolved measurements on wild-type PR and several mutants were done in the visible and infrared (FTIR and FT-Raman). Assignment of the observed C=O stretch bands indicated that Asp-97 and Glu-108 serve as the proton acceptor and donor, respectively, to the retinal Schiff base, as do the residues at corresponding positions in BR, but there are numerous spectral and kinetic differences between the two proteins. There is no detectable dark-adaptation in PR, and the chromophore contains nearly entirely all-trans retinal. Because the pK(a) of Asp-97 is relatively high (7.1), the proton-transporting photocycle is produced only at alkaline pH. It contains at least seven transient states with decay times in the range from 10 micros to 200 ms, but the analysis reveals only three distinct spectral forms. The first is a red-shifted K-like state. Proton release does not occur during the very slow (several milliseconds) rise of the second, M-like, intermediate, consistent with lack of the residues facilitating extracellular proton release in BR. Proton uptake from the bulk, presumably on the cytoplasmic side, takes place prior to release (tau approximately 2 ms), and coincident with reprotonation of the retinal Schiff base. The intermediate produced by this process contains 13-cis retinal as does the N state of BR, but its absorption maximum is red-shifted relative to PR (like the O state of BR). The decay of this N-like state is coupled to reisomerization of the retinal to all-trans, and produces a state that is O-like in its C-C stretch bands, but has an absorption maximum apparently close to that of unphotolyzed PR.     

Isolation and characterization of proteorhodopsin homologue from Yellow Sea of Korea

Many organisms use proton pump to earn energy for living. Some proton pumps start to work by light and one of the famous proteins are called proteorhodopsin (PR). From recent study it used not only protons but also mono-valent cations, divalent cations, or mono-valent anions during pumping activity. The goal of this study is to find new types of proton pumping proteins in the surface of the ocean. Metagenome samples were collected from the beach in Taean-gun and Incheon (Kkotji beach (36°30′0′′N, 126°19′56′′E), Kkotji mud (36°30′8′′N, 126°19′60′′E), Duegi beach (36°31′6′′N, 126°19′39′′E), Sorae salt pond (37°24′25′′N, 126°44′41′′E), swamp (37°24′59′′N, 126°44′54′′E) and reservoir (37°24′39′′N, 126°45′5′′E) in West Sea of Korea. Genomic DNA of each sample was isolated and used for PCR with specific primers for PR and sodium pumping rhodopsin. As a result, we obtained an unidentified PR in Duegi beach sample. The unidentified PR was expressed with chimeric expression system. It has 528 nm absorption maximum at pH 7. By the light differential spectrum measurement, putative M and O photo-intermediates were detected at around 400 and 600 nm, respectively. Similar to GPR, it has light driven outward proton transfer activity.     

Folding and assembly of proteorhodopsin

Proteorhodopsins (PRs), the recently discovered light-driven proton pumps, play a major role in supplying energy for microbial organisms of oceans. In contrast to PR, rhodopsins found in Archaea and Eukarya are structurally well characterized. Using single-molecule microscopy and spectroscopy, we observed the oligomeric assembly of native PR molecules and detected their folding in the membrane. PR showed unfolding patterns identical with those of bacteriorhodopsin and halorhodopsin, indicating that PR folds similarly to archaeal rhodopsins. Surprisingly, PR predominantly assembles into hexameric oligomers, with a smaller fraction assembling into pentamers. Within these oligomers, PR arranged into radial assemblies. We suggest that this structural assembly of PR may have functional implications.     

Screening and characterization of proteorhodopsin color-tuning mutations in Escherichia coli with endogenous retinal synthesis

Proteorhodopsin is photoactive 7-transmembrane protein, which uses all-trans retinal as a chromophore. Proteorhodopsin subfamilies are spectrally tuned in accordance with the depth of habitat of the host organisms, numerous species of marine picoplankton. We try to find residues critical for the spectral tuning through the use of random PCR mutagenesis and endogenous retinal biosynthesis. We obtained 16 isolates with changed color by screening in Escherichia coli with internal retinal biosynthesis system containing genes for beta-carotene biosynthesis and retinal synthase. Some isolates contained multiple substitutions, which could be separated to give 20 single mutations influencing the spectral properties. The color-changing residues are distributed through the protein except for the helix A, and about a half of the mutations is localized on the helices C and D, implying their importance for color tuning. In the pumping form of the pigment, absorption maxima in 8 mutants are red-shifted and in 12 mutants are blue-shifted compared to the wild-type. The results of flash-photolysis showed that most of the low pumping activity mutants possess slower rates of M decay and O decay. These results suggest that the color-tuning residues are not restricted to the retinal binding pocket, in accord with a recent evolutionary analysis.     

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%–86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.     

Spectroscopic and functional characterization of human beta-synuclein

To elucidate potential biological roles of human beta-synuclein, we studied its conformational changes under various conditions. The structural and functional properties of beta-synuclein were characterized using biochemical and bio-physical methods including: a functional assay, mass spectrometry, size exclusion chromatography, circular dichroism (CD), and fluorescence spectroscopy. The results showed beta-synuclein has a high proportion of random coil in solution.     

Spectroscopic studies of the low-lying singlet excited electronic states and photochemical properties of carotenoids

Investigations of the singlet excited state properties of carotenoids using steady-state fluorescence, transient absorption pump-probe, two-photon excitation, and resonance Raman excitation spectroscopies are described. The application of these experimental techniques to the specific problem of determining the S1 excited energies of carotenoids is discussed in detail, and the recent literature pertaining to the assignment of charge transfer states in carotenoids and states described as having particular pseudoparity elements is reviewed. Hypothetical schemes for how these states may account for some of the dynamic and photochemical behavior of carotenoids are presented.     

Screening and characterization of proteorhodopsin color-tuning mutations in Escherichia coli with endogenous retinal synthesis

Proteorhodopsin is photoactive 7-transmembrane protein, which uses all-trans retinal as a chromophore. Proteorhodopsin subfamilies are spectrally tuned in accordance with the depth of habitat of the host organisms, numerous species of marine picoplankton. We try to find residues critical for the spectral tuning through the use of random PCR mutagenesis and endogenous retinal biosynthesis. We obtained 16 isolates with changed color by screening in Escherichia coli with internal retinal biosynthesis system containing genes for beta-carotene biosynthesis and retinal synthase. Some isolates contained multiple substitutions, which could be separated to give 20 single mutations influencing the spectral properties. The color-changing residues are distributed through the protein except for the helix A, and about a half of the mutations is localized on the helices C and D, implying their importance for color tuning. In the pumping form of the pigment, absorption maxima in 8 mutants are red-shifted and in 12 mutants are blue-shifted compared to the wild-type. The results of flash-photolysis showed that most of the low pumping activity mutants possess slower rates of M decay and O decay. These results suggest that the color-tuning residues are not restricted to the retinal binding pocket, in accord with a recent evolutionary analysis.     

Spectroscopic characterization of plastocyanin from hornwort

Plastocyanin isolated from an aquatic higher plant, Ceratophyllum demersum L. (hornwort), has been characterized by electronic absorption, circular dichroism (CD), and electron paramagnetic resonance (EPR) spectroscopies. The visible absorption, CD, and EPR spectra of hornwort plastocyanin indicated a complete similarity of blue copper center to those of terrestrial higher plants and algae. However, the ultraviolet absorption spectrum of hornwort plastocyanin exhibited a lower tyrosine (Tyr) and a higher phenylalanine (Phe) content of the protein comparing with other plastocyanins. The ratio of Phe/Tyr residues was estimated to be 9 by amino acid analysis. The hornwort plastocyanin resembles in amino acid composition terrestrial higher plant plastocyanins rather than alga plastocyanins but is peculiar in the content of Phe and Tyr residues.     

Spectroscopic characterization of Phaseolus vulgaris leucoagglutinin

Phaseolus vulgaris leucoagglutinin is a homotetrameric legume lectin possessing the canonical dimeric structure common to other legume lectins. In order to gain insight into the stability of the protein in an acidic environment, it was characterized by CD and fluorescence studies at pH 2.5. This was then compared with the native protein at physiological pH (7.2). The extinction coefficient of the native protein was calculated to be 3.58x10(4) from its UV absorption spectra. The far- and near-UV CD spectra of the protein at pH 2.5 showed very little difference even though the protein was found to exist as a dimer at pH 2.5. The fluorescence emission maxima of the protein upon excitation at 280 nm were found to shift only from 331 nm at pH 7.2 to 333 nm at pH 2.5. Based on the above observation it was concluded that the protein exhibits extreme pH stability especially in the acidic range. The secondary and tertiary structure of the protein is lost only when it is incubated for two days in 6 M GdnHCl at pH 2.5. At pH 7.2 it could be denatured in 6 M GdnHCl after one week of incubation.     

Spectroscopic characterization and conformation of oligo kappa carrageenans

Identification of oligo-carrageenans by ¹³C n.m.r., infrared spectroscopy and optical rotation is presented. ¹³C n.m.r. signals have been assigned for d-galactose 4-sulphate and oligomers of kappa carrageenan on the basis of model spectra of parent polymer and deuterium isotopic effect. Optical rotation measurements give evidence of the conformational transition of such oligomers, depending on their degree of polymerizations.     

L105K mutant of proteorhodopsin

Proteorhodopsin (PR) is a light-driven proton pump found in marine bacteria. Thousands of PRs are classified into blue-absorbing (λ(max) ~ 490 nm) and green-absorbing (λ(max) ~ 525 nm) PR, and the color determinant is known to be at position 105, where blue-absorbing and green-absorbing PR possess Gln and Leu, respectively. Position 105 is in contact with the retinal chromophore in the hydrophobic region of the cytoplasmic side. In this paper, we have introduced a positively charged lysine group at position 105, which is the first report of the introduction of a positively charged group into the hydrophobic cytoplasmic domain in microbial rhodopsins. The L105K mutant PR shows an ~21 nm red shift (λ(max) ~ 549 nm) at pH 7.0, and the pK(a) of the counterion (7.2) does not change significantly compared to that of wild-type PR (6.8). The analysis of thermal stability shows that the mutation causes some destabilization of structure, but the mutant is more stable toward hydroxylamine reaction than the wild type. The flash photolysis measurement at pH 9.0 shows that the decay of the M intermediate of L105K is ~3 times slower than that of the wild type. The slow M decay possibly originates from the perturbation of the proton donor (Glu108) and the retinal Schiff base due to positioning of a positively charged lysine group in the proton transfer pathway. The perturbation of proton transport is also observed when we measure light-induced proton pumping. The rate of proton transport in L105K mutant is 6 times slower than that of the wild type, which corroborates our flash photolysis result.     

Arylazoimidazoliumchloride and chlorometallates: Spectroscopic and structural characterization

Protonation or dialkylation of 2-(arylazo)imidazoles (RaaiH) has generated azoimidazolium motif (RaaiH₂⁺, RaaiR^′H⁺, RaaiR^′₂⁺ where R = H, CH₃ and R^′ = Me, Et, -CH₂Ph). Electrostatic attraction between imdazolium cation and counter ions like Cl⁻, , has generated hydrogen bonded azoimidazolium-chloride/chlorometallated networks. The single crystal X-ray structure of 1-benzyl-2-(phenylazo)imidazolium chloride shows tape like 1-D network of [Cl(H₂O)₄]⁻. Aquated Cl⁻ forms 10 membered supracycle through hydrogen bonding with imidazolium ion. The X-ray structures of [HaaiMe₂ (1,3)]⁺[Me₂NH₂]⁺ [ZnCl₄]²⁻ and [MeaaiH₂⁺·H₂O]₂[PtCl₆]²⁻ show hydrogen bonded chlorometallate chain penetrated into the channel developed by organic motif. Azoimidazolium units are associated through π···π and C-H···π interactions to strengthen the supramolecular geometry.     

pH-dependent photoisomerization of retinal in proteorhodopsin

The early steps in the photocycle of the bacterial proton pump proteorhodopsin (PR) were analyzed by ultrafast pump/probe spectroscopy to compare the rate of retinal isomerization at alkaline and acidic pH values. At pH 9, the functionally important primary proton acceptor (Asp97, pK(a) = 7.7) is negatively charged; consequently, a reaction cycle analogous to the archaeal bacteriorhodopsin (BR) is observed. The excited electronic state of PR displays a pronounced biphasic decay with time constants of 400 fs and 8 ps. At pH 6 where Asp97 is protonated a similar biphasic decay is observed, although it is significantly slower (700 fs and 15 ps). The results indicate, in agreement to similar findings in other retinal proteins, that also in PR the charge distribution within the chromophore binding pocket is a major determinant for the rate and the efficiency of the primary reaction.