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Chlorophylls and bacteriochlorophylls are the primary pigments used by photosynthetic organisms for light harvesting, energy transfer, and electron transfer. Many molecular structures of (bacterio)chlorophyll-containing protein complexes are available, some of which contain mixtures of different (bacterio)chlorophyll types. Differentiating these, which sometimes are structurally similar, is challenging but is required for leveraging structural data to gain functional insight. The reaction center complex from Chloroacidobacterium thermophilum has a hybrid (bacterio)chlorophyll antenna system containing both chlorophyll a and bacteriochlorophyll a molecules. The recent availability of its cryogenic electron microscopy (cryo-EM) structure provides an opportunity for a quantitative analysis of their identities and chemical environments. Here, we describe a theoretical basis for differentiating chlorophyll a and bacteriochlorophyll a in a cryo-EM map, and apply the approach to the experimental cryo-EM maps of the (bacterio)chlorophyll sites of the chloroacidobacterial reaction center. The comparison reveals that at ~ 2.2-Å resolution, chlorophyll a and bacteriochlorophyll a are easily distinguishable, but the orientation of the bacteriochlorophyll a acetyl moiety is not; however, the latter can confidently be assigned by identifying a hydrogen bond donor from the protein environment. This study reveals the opportunities and challenges in assigning (bacterio)chlorophyll types in structural biology, the accuracy of which is vital for downstream investigations., Competing Interests: Declarations. Conflict of interest: The authors declare that they have no conflict of interest., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Spectral variations of light-harvesting (LH) proteins of purple photosynthetic bacteria provide insight into the molecular mechanisms underlying spectral tuning of circular bacteriochlorophyll (BChl) arrays, which play crucial roles in photoenergy conversion in these organisms. Here we investigate spectral changes of the Q y band of B850 BChl a in LH2 protein from purple sulfur bacterium Thermochromatium tepidum (tepidum-LH2) by detergents and Ca 2+ . The tepidum-LH2 solubilized with lauryl dimethylamine N-oxide and n-octyl-β-D-glucoside (LH2 LDAO and LH2 OG , respectively) exhibited blue-shift of the B850 Q y band with hypochromism compared with the tepidum-LH2 solubilized with n-dodecyl-β-D-maltoside (LH2 DDM ), resulting in the LH3-like spectral features. Resonance Raman spectroscopy indicated that this blue-shift was ascribable to the loss of hydrogen-bonding between the C3-acetyl group in B850 BChl a and the LH2 polypeptides. Ca 2+ produced red-shift of the B850 Q y band in LH2 LDAO by forming hydrogen-bond for the C3-acetyl group in B850 BChl a, probably due to a change in the microenvironmental structure around B850. Ca 2+ -induced red-shift was also observed in LH2 OG although the B850 acetyl group is still free from hydrogen-bonding. Therefore, the Ca 2+ -induced B850 red-shift in LH2 OG would originate from an electrostatic effect of Ca 2+ . The current results suggest that the B850 Q y band in tepidum-LH2 is primarily tuned by two mechanisms, namely the hydrogen-bonding of the B850 acetyl group and the electrostatic effect., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Using femtosecond differential spectroscopy, excitation energy transfer in reaction centers (RCs) of the carotenoidless strain of purple bacteria Rhodospirillum rubrum G9 was studied at room temperature. Excitation and probing of the Q y , Q x and Soret absorption bands of the RCs were carried out by pulses with duration of 25-30 fs. Modeling of ΔA (light - dark) kinetics made it possible to estimate the characteristic time of various stages of excitation energy transformation. It is shown that the dynamics of the downhill energy flow in the RCs is determined both by the internal energy conversion Soret→ Q x  → Q y in each cofactor and by the energy transfer H* → B* → P* (H - bacteriopheophytin, B - bacteriochlorophyll a, P - bacteriochlorophyll a dimer) between cofactors. The transfer of energy between the upper excited levels (Soret and Q x ) of the cofactors accelerates its arrival to the lower exciton level of the P, from where charge separation begins. It turned out that all conversion and energy transfer processes occur within 40-160 fs: the conversion Soret → Q x occurs in 40-50 fs, the conversion Q x  → Q y occurs in 100-140 fs, the transfer H* → B* has a time constant of 80-120 fs, and the transfer B* → P* has a time constant of 130-160 fs. The rate of energy transfer between the upper excited levels is close to the rate of transfer between Q y levels., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The resilience of biological systems to fluctuating environmental conditions is a crucial evolutionary advantage. In this study, we examine the thermo- and piezo-stability of the LH1-RC pigment-protein complex, the simplest photosynthetic unit, in three species of phototropic purple bacteria, each containing only this core complex. Among these species, Blastochloris viridis and Blastochloris tepida utilize bacteriochlorophyll b as the main light-harvesting pigment, while Rhodospirillum rubrum relies on bacteriochlorophyll a. Through spectroscopic analyses, we observed limited reversibility in the effects of temperature and pressure, likely due to the malleability of pigment binding sites within the light-harvesting LH1 complex. In terms of thermal robustness, LH1 complexes in a detergent environment progressively dissociate into dimeric (B820) and monomeric (B777) subunits. However, in the native membrane, degradation primarily occurs directly into B777 without the intermediate formation of B820. Interestingly, while high-pressure compression of core complexes from Blastochloris viridis and Blastochloris tepida caused significant changes in compressibility around 1.3 kbar and the formation of B777 and B820 subunits upon decompression, no such compressibility changes or pressure-induced dissociation were observed in Rhodospirillum rubrum complexes, even at pressures as high as 11 kbar. This study reveals significant differences in the piezo- and thermal properties of phototrophs containing either BChl a or BChl b, underscoring the critical role of structural factors in understanding the temperature- and pressure-induced denaturation phenomena in photosynthetic complexes. Rhodospirillum rubrum, in particular, stands out as one of the most thermodynamically stable systems among phototrophic microorganisms, capable of withstanding temperatures up to 70 °C and pressures exceeding 11 kbar., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Exchange of B800 bacteriochlorophyll (BChl) a in light-harvesting complex 2 (LH2) is promising for a better understanding of the mechanism on intracomplex excitation energy transfer of this protein. Structural and spectroscopic properties of LH2 lacking B800 BChl a (B800-depleted LH2), which is an important intermediate protein in the B800 exchange, will be useful to tackle the energy transfer mechanism in LH2 by the B800 exchange strategy. In this study, we report a unique spectral change of B800-depleted LH2, in which the Q y absorption band of B800 BChl a is automatically recovered under neutral pH conditions. This spectral change was facilitated by factors for destabilization of LH2, namely, a detergent, lauryl dimethylamine N-oxide, and an increase in temperature. Spectral analyses in the preparation of an LH2 variant denoted as B800-recovered LH2 indicated that most BChl a that was released by decomposition of part of B800-depleted LH2 was a source of the production of B800-recovered LH2. Characterization of purified B800-recovered LH2 demonstrated that its spectroscopic and structural features was quite similar to those of native LH2. The current results indicate that the recovery of the B800 Q y band of B800-depleted LH2 originates from the combination of decomposition of part of B800-depleted LH2 and in situ reconstitution of BChl a into the B800 binding pockets of residual B800-depleted LH2, resulting in the formation of stable B800-recovered LH2., (© 2024. The Author(s), under exclusive licence to European Photochemistry Association, European Society for Photobiology.)

Chlorosomes of green photosynthetic bacteria are large light-harvesting complexes enabling these organisms to survive at extremely low-light conditions. Bacteriochlorophylls found in chlorosomes self-organize and are ideal candidates for use in biomimetic light-harvesting in artificial photosynthesis and other applications for solar energy utilization. Here we report on the construction and characterization of an artificial antenna consisting of bacteriochlorophyll c co-aggregated with β-carotene, which is used to extend the light-harvesting spectral range, and bacteriochlorophyll a, which acts as a final acceptor for excitation energy. Efficient energy transfer between all three components was observed by means of fluorescence spectroscopy. The efficiency varies with the β-carotene content, which increases the average distance between the donor and acceptor in both energy transfer steps. The efficiency ranges from 89 to 37% for the transfer from β-carotene to bacteriochlorophyll c, and from 93 to 69% for the bacteriochlorophyll c to bacteriochlorophyll a step. A significant part of this study was dedicated to a development of methods for determination of energy transfer efficiency. These methods may be applied also for study of chlorosomes and other pigment complexes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

We observed the mid-infrared (MIR) response of a single pigment of bacteriochlorophyll a at the B800 binding site of a light-harvesting 2 complex. At a temperature of 1.5 K, a single complex in a spatially isolated spot in a near-infrared (NIR) fluorescence image was selected and was simultaneously irradiated with MIR and NIR light. We found that the temporal behavior of the NIR fluorescence excitation spectrum of individual pigments in a single complex was modulated by the MIR irradiation at 1650 cm -1 . The MIR modulation of a single pigment was linearly proportional to the MIR intensity. The MIR linear response was detected in the range from 1580 to 1670 cm -1 .

The spectral features of energy donors and acceptors and the relationship between them in photosynthetic light-harvesting proteins are crucial for photofunctions of these proteins. Engineering energy donors and acceptors in light-harvesting proteins affords the means to increase our understanding of their photofunctional mechanisms. Herein, we demonstrate the conversion of energy-donating B800 bacteriochlorophyll (BChl) a to 3-acetyl chlorophyll (AcChl) a in light-harvesting complex 3 (LH3) from Rhodoblastus acidophilus by in situ oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone. AcChl a in the B800 site exhibited a Q y band that was 111 nm blue-shifted with respect to BChl a in oxidized LH3. The structure of LH3 was barely influenced by the oxidation process, based on circular dichroism spectroscopy and size-exclusion chromatography evidence. In oxidized LH3, AcChl a transferred excitation energy to B820 BChl a , but the rate of excitation energy transfer (EET) was lower than in native LH3. The intracomplex EET in oxidized LH3 was slightly faster than in oxidized light-harvesting complex 2 (LH2). This difference is rationalized by an increase in overlap of the luminescence band of AcChl a with the long tail of the B820 absorption band in oxidized LH3 compared with that of the B850 band in oxidized LH2.

Much of the thermodynamic parameter values that support life are set by the properties of proteins. While the denaturing effects of pressure and temperature on proteins are well documented, their precise structural nature is rarely revealed. This work investigates the destabilization of multiple Ca 2+ binding sites in the cyclic LH1 light-harvesting membrane chromoprotein complexes from two Ca-containing sulfur purple bacteria by hydrostatic high-pressure perturbation spectroscopy. The native (Ca-saturated) and denatured (Ca-depleted) phases of these complexes are well distinguishable by much-shifted bacteriochlorophyll a exciton absorption bands serving as innate optical probes in this study. The pressure-induced denaturation of the complexes related to the failure of the protein Ca-binding pockets and the concomitant breakage of hydrogen bonds between the pigment chromophores and protein environment were found cooperative, involving all or most of the Ca 2+ binding sites, but irreversible. The strong hysteresis observed in the spectral and kinetic characteristics of phase transitions along the compression and decompression pathways implies asymmetry in the relevant free energy landscapes and activation free energy distributions. A phase transition pressure equal to about 1.9 kbar was evaluated for the complexes from Thiorhodovibri o strain 970 from the pressure dependence of biphasic kinetics observed in the minutes to 100 h time range.

In almost all photosynthetic organisms the photosynthetic pigments chlorophyll and bacteriochlorophyll (BChl) are Mg 2+ containing complexes, but Mg 2+ may be exchanged against other metal ions when these are present in toxic concentrations, leading to inactivation of photosynthesis. In this report we studied mechanisms of copper toxicity to the photosynthetic apparatus of Acidiphilium rubrum, an acidophilic purple bacterium that uses Zn 2+ instead of Mg 2+ as the central metal in the BChl molecules ([Zn]-BChl) of its reaction centres (RCs) and light harvesting proteins (LH1). We used a combination of in vivo measurements of photosynthetic activity (fast fluorescence and absorption kinetics) together with analysis of metal binding to pigments and pigment-protein complexes by HPLC-ICP-sfMS to monitor the effect of Cu 2+ on photosynthesis of A. rubrum. Further, we found that its cytoplasmic pH is neutral. We compared these results with those obtained from Rhodospirillum rubrum, a purple bacterium for which we previously reported that the central Mg 2+ of BChl can be replaced in vivo in the RCs by Cu 2+ under environmentally realistic Cu 2+ concentrations, leading to a strong inhibition of photosynthesis. Thus, we observed that A. rubrum is much more resistant to copper toxicity than R. rubrum. Only slight changes of photosynthetic parameters were observed in A. rubrum at copper concentrations that were severely inhibitory in R. rubrum and in A. rubrum no copper complexes of BChl were found. Altogether, the data suggest that [Zn]-BChl protects the photosynthetic apparatus of A. rubrum from detrimental insertion of Cu 2+ (trans-metallation) into BChl molecules of its RCs., (Copyright © 2021. Published by Elsevier B.V.)

All possible natural amino acids have been substituted for the native LeuL185 positioned near the B-side bacteriopheophytin (H B ) in the bacterial reaction center (RC) from Rhodobacter sphaeroides . Additional mutations that enhance electron transfer to the normally inactive B-side cofactors are present. Approximately half of the isolated RCs with Glu at L185 contain a magnesium chlorin (C B ) in place of H B . The chlorin is not the common BChl a oxidation product 3-desvinyl-3-acetyl chlorophyll a with a C-C bond in ring D and a C═C bond in ring B but has properties consistent with reversal of these bond orders, giving 17,18-didehydro BChl a . In such RCs, charge-separated state P + C B - forms in ∼5% yield. The other half of the GluL185-containing RCs have a bacteriochlorophyll a (BChl a ) denoted β B in place of H B . Residues His, Asp, Asn, and Gln at L185 yield RCs with ≥85% β B in the H B site, while most other amino acids result in RCs that retain H B (≥95%). To the best of our knowledge, neither bacterial RCs that harbor five BChl a molecules and one chlorophyll analogue nor those with six BChl a molecules have been reported previously. The finding that altering the local environment within a cofactor binding site of a transmembrane complex leads to in situ generation of a photoactive chlorin with an unusual ring oxidation pattern suggests new strategies for amino acid control over pigment type at specific sites in photosynthetic proteins.

Bacteriochlorophyll a (BChl) is an essential pigment for anoxygenic photosynthesis. In late steps of the BChl biosynthesis of Rhodobacter capsulatus, the C8 vinyl group and C7=C8 double bond of 8-vinyl chlorophyllide a (8 V-Chlide) are reduced by a C8 vinyl reductase (8VR), BciA, and a nitrogenase-like enzyme, chlorophyllide a oxidoreductase (COR), respectively, to produce 3-vinyl-bacteriochlorphyllide a. Recently, we discovered 8VR activity in COR. However, the kinetic parameters of the COR 8VR activity remain unknown, while those of the COR C7=C8 reductase activity and BciA have been reported. Here, we determined the kinetic parameters of COR 8VR activity by using 8 V-Chlide. The K m value for 8 V-Chlide was 1.4 μM, which is much lower than the 6.2 μM determined for the C7=C8 reduction of Chlide. The kinetic parameters of the dual activities of COR suggest that COR catalyzes the reduction of the C8 vinyl group of 8 V-Chlide preferentially over C7=C8 reduction when both substrates are supplied during BChl biosynthesis., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree-Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna-Matthews-Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future.

Challenges to the de novo synthesis of bacteriochlorophyll a ( BChl a ), the chief pigment for anoxygenic bacterial photosynthesis, include creating the macrocycle along with the trans -dialkyl substituents in both pyrroline rings (B and D). A known route to a model bacteriochlorophyll with a gem-dimethyl group in each pyrroline ring has been probed for utility in the synthesis of BChl a by preparation of a hybrid macrocycle ( BC-1 ), which contains a trans -dialkyl group in ring D and a gem-dimethyl group in ring B. Stereochemical definition began with the synthesis of (2 S ,3 S )-2-ethyl-3-methylpent-4-ynoic acid, a precursor to the trans -dialkyl-substituted AD dihydrodipyrrin. Knoevenagel condensation of the latter and a gem-dimethyl, β-ketoester-substituted BC dihydrodipyrrin afforded the enone (E, 70%; Z, 3%); subsequent double-ring cyclization of the E -enone (via Nazarov, electrophilic aromatic substitution, and elimination reactions) gave BC-1 (53% yield) along with a trace of chlorin byproduct (1.4% relative to BC-1 upon fluorescence assay). BC-1 exhibited the desired trans -dialkyl stereochemistry in ring D and was obtained as a 7:1 mixture of (expected) epimers owing to the configuration of the 13 2 -carbomethoxy substituent. The strategy wherein trans -dialkyl substituents are installed very early and carried through to completion, as validated herein, potentially opens a synthetic path to native photosynthetic pigments.

Six variants of the LH2 antenna complex from Rba. sphaeroides, comprising the native B800-B850, B800-free LH2 (B850) and four LH2s with various (bacterio)chlorophylls reconstituted into the B800 site, have been investigated with static and time-resolved optical spectroscopies at room temperature and at 77 K. The study particularly focused on how reconstitution of a non-native (bacterio)chlorophylls affects excitation energy transfer between the naturally bound carotenoid spheroidene and artificially substituted pigments in the B800 site. Results demonstrate there is no apparent trend in the overall energy transfer rate from spheroidene to B850 bacteriochlorophyll a; however, a trend in energy transfer rate from the spheroidene S 1 state to Q y of the B800 (bacterio)chlorophylls is noticeable. These outcomes were applied to test the validity of previously proposed energy values of the spheroidene S 1 state, supporting a value in the vicinity of 13,400 cm -1 (746 nm).

Chloracidobacterium (C.) thermophilum is a microaerophilic, chlorophototrophic species in the phylum Acidobacteria that uses homodimeric type-1 reaction centers (RC) to convert light energy into chemical energy using (bacterio)chlorophyll ((B)Chl) cofactors. Pigment analyses show that these RCs contain BChl a P , Chl a PD , and Zn 2+ -BChl a P ' in the approximate ratio 7.1 : 5.4 : 1. However, the functional roles of these three different Chl species are not yet fully understood. It was recently demonstrated that Chl a PD is the primary electron acceptor. Because Zn 2+ -(B)Chl a P ' is present at low abundance, it was suggested that the primary electron donor might be a dimer of Zn 2+ -BChl a P ' molecules. In this study, we utilize isotopic enrichment and high-resolution two-dimensional (2D) 14 N and 67 Zn hyperfine sublevel correlation (HYSCORE) spectroscopy to demonstrate that the primary donor cation, P 840 + , in the C. thermophilum RC is indeed a Zn 2+ -BChl a P ' dimer. Density functional theory (DFT) calculations and the measured electron-nuclear hyperfine parameters of P 840 + indicate that the electron spin density on P 840 + is distributed nearly symmetrically over two Zn 2+ -(B)Chl a P ' molecules as expected in a homodimeric RC. To our knowledge this is the only example of a photochemical RC in which the Chl molecules of the primary donor are metallated differently than those of the antenna.

High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a ) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding quantum mechanics/molecular mechanics with the effective fragment potentials, we computed the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild-type and mutated photosynthetic pigment-protein complexes.

The predominance of the maximum at 800 nm for the light-harvesting complex LH4 (B800) and at 850 nm for LH2 (B800-850) from Rps. palustris is determined by the composition of αβ-polypeptides and pigments. In low light (LL) for Rps. palustris, strain KM 286 (1e5), along with LH4, the LL LH2 complex was synthesized with the same absorption at 800 and 850 nm. It differed from the LH4 and LH2 complex, which is synthesized under high illumination, in the composition and content of carotenoids (Car) and bacteriochlorophyll a (BChl a). LH4 differed from LL LH2 and LH2 by an additional emission maximum at 766 nm in the BChl a fluorescence spectra. All three complexes had approximately the same level (about 45%) of the energy transfer efficiency from Car to BChl a. Isolation of LL LH2 complex from Rps. palustris confirms the hypothesis of the synthesis in these bacteria under low light conditions of other types of complexes, except LH4, which is due to the multiple biosynthesis genes of αβ-polypeptides and the possibility of their various combinations.

In order to study Förster resonance energy transfer (FRET), the fragment molecular orbital (FMO) method is extended to compute electronic couplings between local excitations via the excited state transition density model, enabling efficient calculations of nonlocal excitations in a large molecular system and overcoming the previous limitation of being able to compute only local excitations. The results of these simple but accurate models are validated against full quantum calculations without fragmentation. The developed method is applied to a very important photosynthetic pigment-protein complex, the Fenna-Matthews-Olson complex (FMOc), that is responsible for the energy transfer from a chlorosome to the reaction center in the green sulfur bacteria. Absorption and circular dichroism spectra of FMOc are simulated, and the role of the molecular environment on the excitations is revealed.

A strictly aerobic, bacteriochlorophyll a -containing betaproteobacterium , designated strain W35 T , was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds, and showed an in vivo absorption maximum at 871 nm in the near-infrared region, typical for the presence of bacteriochlorophyll a . The new bacterial strain is Gram-negative, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain W35 T was closely related to species in the genus Aquabacterium . The closest phylogenetic relatives of strain W35 T were Aquabacterium commune B8 T (97.9 % sequence similarity), Aquabacterium citratiphilum B4 T (97.2 %) and Aquabacterium limnoticum ABP-4 T (97.0 %). The major cellular fatty acids were C 16  :  1 ω7 c (50.4 %), C 16  :  0 (22.7 %), summed feature 8 (C 18  :  1 ω7 c /C 18  :  1 ω6 c ; 9.7 %), C 18  :  3 ω6 c (5.5 %), C 12  :  0 (5.3 %) and C 10  :  0 3OH (2.7 %). The respiratory quinone was ubiquinone-8. Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA was 70.4 mol% (genome data) and 71.4 mol% (HPLC). The genome size of strain W35 T is 6.1 Mbp and average nucleotide identity analysis indicated genome similarities of strain W35 T and related Aquabacterium type strains to be 78-79 %. The results of polyphasic comparisons showed that strain W35 T was clearly distinguishable from other members of the genus Aquabacterium . Therefore, we propose a new species in the genus Aquabacterium , namely, Aquabacterium pictum sp. nov. The type strain is W35 T (=DSM 106757 T =NBRC 111963 T ). The description of the genus Aquabacterium is also emended.

An oval- to rod-shaped, motile, Gram-stain-negative, oxidase-positive, catalase-negative, pink-coloured phototrophic bacterium (designated as strain JA968 T ) was isolated from an estuary near Pata, Gujarat, India. Cells had an intracytoplasmic membrane architecture as lamellae and divided by budding. Strain JA968 T had bacteriochlorophyll- a and spirilloxanthin series carotenoids as photosynthetic pigments. The strain exhibited photolithoautotrophic, photoorganoheterotrophic and chemoorganoheterotrophic growth modes and required thiamine as a growth factor. Strain JA968 T had C 18 : 1 ω7 c /C 18  : 1 ω6 c as the predominant fatty acid with ubiquinone-10 (Q-10) and menaquinone-10 (MK-10) forming the quinone composition. The genomic DNA G+C content of the strain was 63.5 mol%. Pairwise comparison of 16S rRNA gene sequences showed that strain JA968 T was highly similar to Afifella marina DSM 2698 T (99.9 %) and Afifella pfennigii DSM 17143 T (98.4 %). The average nucleotide identity values were 92 % between strain JA968 T and A. marina DSM 2698 T , and 78 % between strain JA968 T and A. pfennigii DSM 17143 T . The digital DNA-DNA hybridization values between strain JA968 T and A. marina and A. pfennigii were 49 and 19 %, respectively. The genomic distinction was also supported by differences in phenotypic and chemotaxonomic characteristics. We propose that strain JA968 T represents a new species of the genus Afifella with the name Afifella aestuarii sp. nov. The type strain is JA968 T (=KCTC 15634 T =NBRC 113338 T ).

A Gram-stain-negative, motile, alkali-tolerant, swollen-rod shaped, reddish brown coloured, phototrophic bacterium designated as strain JA980 T , was isolated from freshwater sampled at Umiam lake, Shillong, India. Strain JA980 T grew well up to pH 9.0. Respiratory quinones were ubiquinone 10 and rhodoquinone 10. The major fatty acid was C 18: 1 ω7 c /C 18:1 ω6c with minor amounts of C 18:0 , C 16:0 , C 18:0 3-OH and C 16:0 3-OH. Strain JA980 T contained bacteriochlorophyll- a and carotenoids of the spirilloxanthin series. The polar lipids of strain JA980 T comprised phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified phospholipid, unidentified amino lipids (AL1,3,4,5) and an unidentified lipid (L1). Strain JA980 T had the highest (99.57 %) 16S rRNA gene sequence similarity to the type strains of Rhodomicrobium vannielii ATCC17100 T and Rhodomicrobium udaipurense JA643 T . The genome of strain JA980 T was 3.88 Mbp with a DNA G+C content of 62.4 mol%. Based on the results of phylogenetic analyses, low in silico DNA-DNA hybridization values (33 %), low (87 %) average nucleotide identity results, chemotaxonomic characteristics and differential physiological properties, strain JA980 T could not be classified into either of the two recognized species of the genus Rhodomicrobium , suggesting that it represents a novel species, for which the name Rhodomicrobium lacus sp. nov. is proposed. The type strain is JA980 T (=KCTC 15697 T = MCC 3714 T = NBRC 113803 T ).

The cyanobacterial culture HT-58-2, composed of a filamentous cyanobacterium and accompanying community bacteria, produces chlorophyll a as well as the tetrapyrrole macrocycles known as tolyporphins. Almost all known tolyporphins (A-M except K) contain a dioxobacteriochlorin chromophore and exhibit an absorption spectrum somewhat similar to that of chlorophyll a. Here, hyperspectral confocal fluorescence microscopy was employed to noninvasively probe the locale of tolyporphins within live cells under various growth conditions (media, illumination, culture age). Cultures grown in nitrate-depleted media (BG-11 0 vs. nitrate-rich, BG-11) are known to increase the production of tolyporphins by orders of magnitude (rivaling that of chlorophyll a) over a period of 30-45 days. Multivariate curve resolution (MCR) was applied to an image set containing images from each condition to obtain pure component spectra of the endogenous pigments. The relative abundances of these components were then calculated for individual pixels in each image in the entire set, and 3D-volume renderings were obtained. At 30 days in media with or without nitrate, the chlorophyll a and phycobilisomes (combined phycocyanin and phycobilin components) co-localize in the filament outer cytoplasmic region. Tolyporphins localize in a distinct peripheral pattern in cells grown in BG-11 0 versus a diffuse pattern (mimicking the chlorophyll a localization) upon growth in BG-11. In BG-11 0 , distinct puncta of tolyporphins were commonly found at the septa between cells and at the end of filaments. This work quantifies the relative abundance and envelope localization of tolyporphins in single cells, and illustrates the ability to identify novel tetrapyrroles in the presence of chlorophyll a in a photosynthetic microorganism within a non-axenic culture.

Optical absorption and fluorescence spectra of molecules in condensed phases often show extensive sidebands. Originating from electron-vibrational and electron-phonon couplings, these spectral tails bear important information on the dynamics of electronic states and processes the molecules are involved in. The vibronic sidebands observed in conjugate Q y absorption and fluorescence spectra of chlorophyll a and bacteriochlorophyll a are relatively weak, characterized by the total Huang-Rhys factor which is less than one. Therefore, it is widely considered that only fundamental intramolecular modes are responsible for their formation. Here, we provide evidence for extra-long and structured fluorescence tails of chlorophyll a and bacteriochlorophyll a as far as 4000 cm -1 from respective spectral origins, far beyond the frequency range of fundamental modes. According to quantum chemical simulations, these sidebands extending to ∼960 nm in chlorophyll a and ∼1140 nm in bacteriochlorophyll a into the infrared part of the optical spectrum are mainly contributed to by vibrational overtones of the fundamental modes. Because energy transfer and relaxation processes generally depend on vibronic overlap integrals, these findings potentially contribute to better understanding of many vital photo-induced phenomena, including photosynthetic light harvesting.

Although the cofactors in the bacterial reaction centre of Rhodobacter sphaeroides wild type (WT) are arranged almost symmetrically in two branches, the light-induced electron transfer occurs selectively in one branch. As origin of this functional symmetry break, a hydrogen bond between the acetyl group of P L in the primary donor and His-L168 has been discussed. In this study, we investigate the existence and rigidity of this hydrogen bond with solid-state photo-CIDNP MAS NMR methods offering information on the local electronic structure due to highly sensitive and selective NMR experiments. On the time scale of the experiment, the hydrogen bond between P L and His-L168 appears to be stable and not to be affected by illumination confirming a structural asymmetry within the Special Pair.

Light-harvesting systems 2 and 3 (LH2 and LH3) act as antennas for the initial light capture by photosynthetic purple bacteria, thus initiating the conversion of solar energy into chemical energy. The main absorbers are carotenoids and bacteriochlorophylls (BChls), which harvest different parts of the solar spectrum. The first two optical transitions in BChl produce the Q y and Q x absorption bands. The large size of BChl molecules has prevented accurate computational determination of the electronic structures for the relevant states, until we recently succeeded in obtaining the excitation energies and transition dipole moments of the first (Q y ) transition for all BChls in LH2 and LH3 using multi-state multiconfigurational second-order perturbation theory calculations. In this work, we go one step further, compute the corresponding values for the Q x transition, in line with previous work [ J. Am. Chem. Soc . 2017 , 139 , 7558 - 7567 ], and compare and assess our data against excitation energies obtained through time-dependent density functional theory methods. Interestingly, we find that the two transitions respond differently to BChls' geometrical factors, such as the macrocycle ring curvature and the dihedral torsion of the acetyl moiety. These findings will aid the unraveling of structure-function relationships for absorption and energy transfer processes in purple bacteria, and once again this demonstrates the viability of multireference quantum chemical methods as computational tools for the photophysics of biomolecules.

The light-harvesting 1 reaction center (LH1-RC) complex in the purple sulfur bacterium Thiorhodovibrio ( Trv.) strain 970 cells exhibits its LH1 Q y transition at 973 nm, the lowest-energy Q y absorption among purple bacteria containing bacteriochlorophyll a (BChl a). Here we characterize the origin of this extremely red-shifted Q y transition. Growth of Trv. strain 970 did not occur in cultures free of Ca 2+ , and elemental analysis of Ca 2+ -grown cells confirmed that purified Trv. strain 970 LH1-RC complexes contained Ca 2+ . The LH1 Q y band of Trv. strain 970 was blue-shifted from 959 to 875 nm upon Ca 2+ depletion, but the original spectral properties were restored upon Ca 2+ reconstitution, which also occurs with the thermophilic purple bacterium Thermochromatium ( Tch.) tepidum. The amino acid sequences of the LH1 α- and β-polypeptides from Trv. strain 970 closely resemble those of Tch. tepidum; however, Ca 2+ binding in the Trv. strain 970 LH1-RC occurred more selectively than in Tch. tepidum LH1-RC and with a reduced affinity. Ultraviolet resonance Raman analysis indicated that the number of hydrogen-bonding interactions between BChl a and LH1 proteins of Trv. strain 970 was significantly greater than for Tch. tepidum and that Ca 2+ was indispensable for maintaining these bonds. Furthermore, perfusion-induced Fourier transform infrared analyses detected Ca 2+ -induced conformational changes in the binding site closely related to the unique spectral properties of Trv. strain 970. Collectively, our results reveal an ecological strategy employed by Trv. strain 970 of integrating Ca 2+ into its LH1-RC complex to extend its light-harvesting capacity to regions of the near-infrared spectrum unused by other purple bacteria.

Halorhodospira halochloris is an anaerobic, halophilic, purple photosynthetic bacterium belonging to γ-Proteobacteria. H. halochloris is also characteristic as a thermophilic phototrophic isolate producing bacteriochlorophyll (BChl) b. Here, we report the complete genome sequence of H. halochloris DSM 1059. The genetic arrangement for this bacterium's photosynthetic apparatus is of particular interest; its genome contains two sets of puf operons encoding the reaction center and core light-harvesting 1 (LH1) complexes having almost identical nucleotide sequences (e.g., 98.8-99.9% of nucleotide identities between two sets of pufLM genes, but 100% of deduced amino acid sequence identities). This duplication of photosynthetic genes may provide a glimpse at natural selection in action. The β-polypeptides of the LH1 complex in purple bacteria usually contain two histidine residues to bind BChl a; however, those of H. halochloris were revealed to have four histidine residues, indicating unusual pigment organization in the LH1 complex of this species. Like in other BChl b-producing phototrophs, the genome of H. halochloris lacks the divinyl reductase genes bciA and bciB. The phylogeny of chlorophyllide a oxidoreductase, which catalyzes committed steps in the synthesis of BChl a and BChl b, indicates that evolution toward BChl b production is convergent. Geranylgeranyl reductase (BchP) of H. halochloris has an insertion region in its primary structure, which could be important for its unusual sequential reduction reactions.

We report the in vitro activity of recombinant BchC oxidoreductase involved in bacteriochlorophyll a biosynthesis. BchC of Rhodobacter capsulatus preferentially oxidizes 3 1 R-3-(1-hydroxyethyl)-chlorophyllide a and 3 1 R-3-(1-hydroxyethyl)-bacteriochlorophyllide a in the presence of NAD + to 3-acetyl-chlorophyllide a and bacteriochlorophyllide a, respectively, leaving the unreacted 3 1 S-epimers. In the reverse reaction, BchC with NADH predominately produces 3 1 R-epimeric alcohols from the 3-acetyl-(bacterio)chlorins. BchC of Chlorobaculum tepidum demonstrates the same 3 1 R-selectivity, suggesting that utilization of 3 1 R-epimers in BchC-catalyzed reductions may be conserved across different phyla of photosynthetic bacteria. Additionally, the presence of BchC accelerates the 3-vinyl hydration by BchF hydratase of Chlorobaculum tepidum during conversion of chlorophyllide a to 3-acetyl-chlorophyllide a through 3-(1-hydroxyethyl)-chlorophyllide a, indicating that these enzymes work cooperatively to promote efficient bacteriochlorophyll a biosynthesis., (© 2019 Federation of European Biochemical Societies.)

Τhe morphology, physiology and immunology, of solid tumors exhibit spatial heterogeneity which complicates our understanding of cancer progression and therapy response. Understanding spatial heterogeneity necessitates high resolution in vivo imaging of anatomical and pathophysiological tumor information. We introduce Rhodobacter as bacterial reporter for multispectral optoacoustic (photoacoustic) tomography (MSOT). We show that endogenous bacteriochlorophyll a in Rhodobacter gives rise to strong optoacoustic signals >800 nm away from interfering endogenous absorbers. Importantly, our results suggest that changes in the spectral signature of Rhodobacter which depend on macrophage activity inside the tumor can be used to reveal heterogeneity of the tumor microenvironment. Employing non-invasive high resolution MSOT in longitudinal studies we show spatiotemporal changes of Rhodobacter spectral profiles in mice bearing 4T1 and CT26.WT tumor models. Accessibility of Rhodobacter to genetic modification and thus to sensory and therapeutic functions suggests potential for a theranostic platform organism.

Engineering chlorophyll (Chl) pigments that are bound to photosynthetic light-harvesting proteins is one promising strategy to regulate spectral coverage for photon capture and to improve the photosynthetic efficiency of these proteins. Conversion from the bacteriochlorophyll (BChl) skeleton (7,8,17,18-tetrahydroporphyrin) to the Chl skeleton (17,18-dihydroporphyrin) produces the most drastic change of the spectral range of absorption by light-harvesting proteins. We demonstrated in situ selective oxidation of B800 BChl a in light-harvesting protein LH2 from a purple bacterium Rhodoblastus acidophilus by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone. The newly formed pigment, 3-acetyl Chl a, interacted with the LH2 polypeptides in the same manner as native B800. B850 BChl a was not oxidized in this reaction. CD spectroscopy indicated that the B850 orientation and the content of the α-helices were unchanged by the B800 oxidation. The nonameric circular arrangement of the oxidized LH2 protein was visualized by AFM; its diameter was almost the same as that of native LH2. The in situ oxidation of B800 BChl a in LH2 protein with no structural change will be useful not only for manipulation of the photofunctional properties of photosynthetic pigment-protein complexes but also for understanding the substitution of BChl to Chl pigments in the evolution from bacterial to oxygenic photosynthesis.

The role of the environment in excitation energy transport in the pigment-protein complexes (PPCs) of photosynthetic organisms is a widely investigated topic. The spectral density is a key component in understanding this protein-pigment interaction; however, the typical approach for calculating spectral density, combining molecular dynamics with quantum chemistry (QC) calculations, suffers from the geometry mismatch problem, arising from the structural inconsistency between the force field (FF) and the QC calculation. Existing parameterization methods demand much time-consuming manual inputs, limiting the number of systems that can be studied. We present a method, utilizing force matching for the autoparameterization of new pigment FFs for the use in spectral density calculations of PPCs, and apply the method to three pigments. The use of these optimized FFs in spectral density computation results in a notable difference in comparison to the original FF.

Bacteriochlorophyll a (BChla) is the most abundant pigment found in the Bacterial Reaction Center (BRC) and light-harvesting proteins of photosynthetic purple and green bacteria. Recent two-dimensional electronic spectroscopy (2DES) studies of photosynthetic pigment-protein complexes including the BRC and the Fenna-Matthews-Olson (FMO) complex have shown oscillatory signals, or coherences, whose physical origin has been hotly debated. To better understand the observations of coherence in larger photosynthetic systems, it is important to carefully characterize the spectroscopic signatures of the monomeric pigments. Prior spectroscopic studies of BChla have differed significantly in their observations, with some studies reporting little to no coherence. Here we present evidence of strong coherences in monomeric BChla in isopropanol using 2DES at 77 K. We resolve many modes with frequencies that correspond well with known vibrational modes. We confirm their vibrational origin by comparing the 2D spectroscopic signatures with expectations based on a purely vibrational model.

Mapping the multidimensional energy landscape of photosynthetic systems is crucial for understanding their high efficiencies. Multidimensional coherent spectroscopy is well suited to this task but has difficulty distinguishing between vibrational and electronic degrees of freedom. In pigment-protein complexes, energy differences between vibrations within a single electronic manifold are similar to differences between electronic states, leading to ambiguous assignments of spectral features and diverging physical interpretations. An important control experiment is that of the pigment monomer, but previous attempts using multidimensional coherent spectroscopy lacked the sensitivity to capture the relevant spectroscopic signatures. Here we apply a variety of methods to rapidly acquire 3D electronic-vibrational spectra in seconds, leading to a mapping of the vibrational states of Bacteriochlorophyll a (BChl a) in solution. Using this information, we can distinguish features of proteins containing BChl a from the monomer subunit and show that many of the previously reported contentious spectral signatures are vibrations of individual pigments.

A novel Gram-stain-negative, aerobic, non-flagellated, pink-pigmented and rod-shaped strain with gliding motility, designated strain CCMM001 T , was isolated from a mixed culture of Synechococcus species PCC7002 and a natural bacterial community from a sample of offshore seawater from Qingdao, China, during September 2014. The strain contained bacteriochlorophyll a with a small peak at 802 nm and a large in vivo absorption band at 870 nm. Strain CCMM001 T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CCMM001 T is most closely related to the genus Roseicyclus and its type and only species Roseicyclus mahoneyensis ML6 T with 96.9 % sequence similarity. The polar lipids of strain CCMM001 T consisted of phosphatidylethanolamine, phosphatidylcholine, one unidentified aminolipid, and five unidentified lipids. The predominant isoprenoid quinone was Q-10. The major fatty acids included C18 : 1ω7c and C19 : 0cyclo ω8c. The DNA G+C content of strain CCMM001 T was 63.5 mol%. These phylogenetic, physiological and chemotaxonomic data indicated that strain CCMM001 T represents a novel species of the genus Roseicyclus, for which the name Roseicyclus marinus sp. nov. is proposed. The type strain is CCMM001 T (=MCCC 1K03242 T =KCTC 52641 T ).

We demonstrate that electronic excitations and their transition densities can be obtained from real-time density functional theory calculations with great accuracy by relating the data from numerical propagation to the analytical form of the electronic response after a boost excitation. The latter is derived in this article. This approach facilitates quantitatively obtaining oscillator strengths, identifying excitations that carry very small oscillator strengths, and assessing electronic couplings from transition densities based on comparatively short propagation times. These features are of interest in particular for studying light-harvesting systems. For demonstration purposes, we study the Q band excitations of bacteriochlorophyll a (BChl a) and calculate coupling strengths between two BChl a's to check the validity of the dipole-dipole and pure Coulomb coupling mechanisms. For further illustration, we investigate the paradigm test system Na 4 and the coupling between two Na 2 dimers.

We discuss the excitonic energy landscape of the typically studied wild-type (WT) Fenna-Matthews-Olson (FMO) antenna protein from the green sulfur bacterium Chlorobaculum tepidum (referred to as WT M ), which is described as a mixture of intact (WT I ) and destabilized (WT D ) complexes. Optical spectra of WT M and the L122Q mutant (where leucine 122 near BChl 8 is replaced with glutamine) are compared to WT I FMO. We show that WT M and L122Q samples are mixtures of two subpopulations of proteins, most likely induced by protein conformational changes during the isolation/purification procedures. Absorption, emission, and HB spectra of WT M and L122Q mutant are very similar, in which the low-energy trap (revealed by the nonresonant HB spectra) shifts to higher energies as a function of fluence, supporting a mixture model. No fluence-dependent shift is observed in the WT I FMO trimers. New Hamiltonians are provided for WT I and WT D proteins. Resonant HB spectra show that the internal energy relaxation times in the WT M and L122Q mutant are similar, and depend on excitation frequency. Fast average relaxation times (excited state lifetimes) are observed for burning into the main broad absorption band near 805nm. Burning at longer wavelengths reveals slower total dephasing times. No resonant bleach is observed at λ B ≤803nm, implying much faster (femtosecond) energy relaxation in this spectral range in agreement with 2D electronic spectroscopy frequency maps., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Femtosecond pulsed excitation of light-harvesting complexes creates oscillatory features in their response. This phenomenon has inspired a large body of work aimed at uncovering the origin of the coherent beatings and possible implications for function. Here we exploit site-directed mutagenesis to change the excitonic level structure in Fenna-Matthews-Olson (FMO) complexes and compare the coherences using broadband pump-probe spectroscopy. Our experiments detect two oscillation frequencies with dephasing on a picosecond timescale-both at 77 K and at room temperature. By studying these coherences with selective excitation pump-probe experiments, where pump excitation is in resonance only with the lowest excitonic state, we show that the key contributions to these oscillations stem from ground-state vibrational wavepackets. These experiments explicitly show that the coherences-although in the ground electronic state-can be probed at the absorption resonances of other bacteriochlorophyll molecules because of delocalization of the electronic excitation over several chromophores.

Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0.2 and 0.3GPa and at about 0.55GPa, respectively. The free energy change associated with the rupture of the single hydrogen bond present in wild-type reaction centers was estimated to be equal to 13-14kJ/mol. In the mutant with two symmetrical hydrogen bonds (FM197H) a single cooperative rupture of the two bonds was observed corresponding to an about twice stronger bond, rather than a sequential rupture of two individual bonds., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Two strains of thermotolerant phototrophic alphaproteobacteria, designated strains TUT3542 T and TUT3581 T , were isolated from sediment mud and cyanobacterial mats in a geothermal spring in Japan, respectively, and taxonomically characterized. Both the strains were budding motile rods and were able to grow at 45 °C. Phototrophically grown cells of strains TUT3542 T and TUT3581 T produced pink and brownish red cultures, respectively, and showed in vivo absorption maxima at 800, 858-859 and 892-895 nm in the near infrared region, indicating the presence of a core reaction centre and peripheral pigment complexes with bacteriochlorophyll a. The intracytoplasmic membrane system was of the lamellar type parallel to the cytoplasmic membrane. 16S rRNA gene sequence comparisons showed that strains TUT3542 T and TUT3581 T had the highest similarity level to Rhodoplanes oryazae NBRC 109406 T (99.6 %) and Rhodoplaneselegans AS130 T (99.3 %), respectively. Genomic DNA-DNA reassociation studies revealed that strains TUT3542 T and TUT3581 T had hybridization levels of less than 62 and 56 % to the type strains of all established species of the genus Rhodoplanes, respectively. The G+C contents of genomic DNA were 67.7 mol% for strain TUT3542 T and 70.4 mol% for strain TUT3581 T . Results of phenotypic studies showed that the two novel strains could be differentiated from any of the previously described Rhodoplanes species. Thus, the author proposes the names Rhodoplanes tepidicaeni sp. nov. for strain TUT3542 T and Rhodoplanes azumiensis sp. nov. for strain TUT3581 T . The type strain of Rhodoplanes tepidicaeni is TUT3542 T (=KCTC 15602 T =NBRC 112815 T ) and the type strain of Rhodoplanes azumiensis is TUT3581 T (=KCTC 15603 T =NBRC 112816 T ).

A strain of anoxygenic phototrophic bacteria isolated from paddy soil (designated strain TUT3615T) was studied taxonomically in comparison with Rhodopseudomonasstrain ATCC 17005 as its nearest phylogenetic relative. Strains TUT3615T and ATCC 17005 had budding rod-shaped cells and showed in vivo absorption maxima at 804 and 860 nm in the near infrared region, indicating the presence of bacteriochlorophyll a. The intracytoplasmic membrane system was of the lamellar type parallel to the cytoplasmic membrane. 16S rRNA gene sequence comparisons showed that strains TUT3615T and ATCC 17005 had a 99.7 % level of similarity to one another and were closest to Rhodopseudomonas palustris ATCC 17001T (98.6 % similarity) among the established species of the genus Rhodopseudomonas. Genomic DNA-DNA hybridization studies revealed that strains TUT3615T and ATCC 17005 had an average similarity level of 65 % to one another and of less than 40 % to the available type strains of Rhodopseudomonas species. Results of phenotypic studies showed that strains TUT3615T and ATCC 17005 could be differentiated from one another and from any previously described species of Rhodopseudomonas. The G+C contents of the genomic DNA of strain TUT3615T and ATCC 17005 were 66.3 and 66.5 mol%, respectively. Based on these data, we propose the name Rhodopseudomonas telluris sp. nov. for strain TUT3615T. The type strain is TUT3615T (=KCTC 23279T=NBRC 107609T). We suspend a proposal to reclassify strain ATCC 17005 as a novel species or subspecies until a genome-wide analysis provides more definite information on its taxonomic position.

A Gram-stain-negative, facultatively anaerobic, dark-yellow-pigmented bacterium, named SSR2A-4-2T, was isolated from coastal water in the East China Sea. Cells were ovoid or short rods with peritrichous flagella and contained carotenoid in addition to bacteriochlorophyll a pigment. A phylogenetic dendrogram based on 16S rRNA gene sequences showed that strain SSR2A-4-2T formed a distinct clade with members of the genus Blastomonas, with Blastomonasnatatoria EY 4220T (=DSM 3183T) (similarity 95.6 %), Blastomonasursincola KR-99T (=DSM 9006T) (95.5 %) and Blastomonasaquatica PE4-5T (=JCM 30179T) (94.8 %) as its closest phylogenetic relatives. Q-10 was the predominant respiratory quinone. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C17 : 1ω6c and C18 : 1ω7c 11-methyl. The polar lipids contained diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, sphingoglycolipid, four unknown glycolipids and one unknown lipid. The DNA G+C content was 65.1 mol%. On the basis of the evidence presented in this study, strain SSR2A-4-2T represents a novel species of the genus Blastomonas, for which the name Blastomonas marina sp. nov. is proposed, with strain SSR2A-4-2T (=CGMCC 1.15297T=DSM 103453T) as the type strain.

Light-harvesting complex 2 (LH2) is an integral membrane protein in purple photosynthetic bacteria. This protein possesses two types of bacteriochlorophyll (BChl) a, termed B800 and B850, which exhibit lowest-energy absorption bands (Q y bands) around 800 and 850 nm. These BChl a pigments in the LH2 protein play crucial roles not only in photosynthetic functions but also in folding and maintaining its protein structure. We report herein the reversible structural changes in the LH2 protein derived from a purple photosynthetic bacterium, Rhodoblastus acidophilus, induced by the removal of B800 BChl a (denoted as B800-free LH2) and the reconstitution of exogenous BChl a. Atomic force microscopy observation clearly visualized the nonameric ring structure of the B800-free LH2 with almost the same diameter as the native LH2. Size exclusion chromatography measurements indicated a considerable decrease in the size of the protein induced by the removal of B800 BChl a. The protein size was almost recovered by the insertion of BChl a pigments into the B800 binding sites. The decrease in the LH2 size would mainly originate from the shrinkage of the B800 binding sites perpendicular to the macrocycle of B800 BChl a without deformation of the circular arrangement. The reversible changes in the LH2 structure induced by the removal and reconstitution of B800 BChl a will be helpful for understanding the structural principle and the folding mechanism of photosynthetic pigment-protein complexes.

Strain JA878T was purified from a photoheterotrophic enrichment obtained from a sediment sample of a brown pond near Nari Salt Pan, Bhavnagar, Gujarat, India. Cells of the isolate were coccoid, motile by means of single polar flagellum and Gram-stain-negative. The internal photosynthetic membrane architecture was vesicular. Strain JA878T contained bacteriochlorophyll a and spirilloxanthin series of carotenoids with rhodopin (>85 %) as the major component. Strain JA878T grew optimally at pH 10-11, and had no requirement for NaCl (tolerated up to 6 %, w/v) or vitamins for growth. C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c/C18 : 1ω6c and C16 : 0 were identified as the major fatty acids (>10 %). Phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown polar lipid were identified. Q8 was the predominant quinone system in strain JA878T. The DNA G+C content was 62.4 mol%. Highest 16S rRNA gene sequence similarity through EzTaxon-based blast analysis of strain JA878T was found with the type strains of Thiorhodococcus fuscus (99 %), Thiorhodococcus kakinadensis (98.6 %), Thiohalobacter thiocyanaticus (98.4 %), Thiophaeococcus fuscus (97.3 %) and other members of the class Gammaproteobacteria (<97.3 %), revealing a close affiliation to the genera Thiorhodococcus, Thiohalobacter and Thiophaeococcus. However, the phylogenetic treeing firmly placed the strain in the genus Thiorhodococcus. Phenotypic and chemotaxonomic evidence supported the affiliation of strain JA878T to the genus Thiorhodococcus and not to Thiohalobacter, Thiophaeococcus or other known genera of Chromatiaceae. Distinct physiological, genotypic and chemotaxonomic differences indicate that strain JA878T represents a novel species of the genus Thiorhodococcus, for which the name Thiorhodococcus alkaliphilus sp. nov. is proposed. The type strain is JA878T (=KCTC 15531T=JCM 31245T).

A coccoid-shaped phototrophic purple sulfur bacterium, strain AK35T, was isolated from a coastal surface water sample collected from Visakhapatnam, India. Cells were Gram-stain-negative, motile and purple, containing bacteriochlorophyll a and the carotenoid rhodopinal as major photosynthetic pigments. Strain AK35T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically. Strain AK35T was able to utilize sulfide and thiosulfate as electron donors. The main fatty acids present were identified as C16 : 0, C18 : 1ω7c, and C16 : 1ω7c and/or iso-C15 : 0 2OH (summed feature 3). Strain AK35T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and six unidentified lipids as polar lipids. The G+C content of the DNA of strain AK35T was 63.1 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae. 16S rRNA gene sequence analysis indicated that strain AK35T is phylogenetically distinctly positioned outside the groups of most members of the genus Thiorhodococcus, clustered with members of the genera Marichromatium and Phaeochromatium, but was most closely related to Thiorhodococcus bheemlicus with a pairwise sequence similarity of 98.75 %. Based on DNA-DNA hybridization between strain AK35T and Thiorhodococcus bheemlicus MTCC 8120T a relatedness of 39.46 % was established. Distinct morphological, physiological and genotypic differences from these previously described taxa supported the classification of the new isolate as a representative of a novel species in a new genus, for which the name Imhoffiella purpurea gen. nov., sp. nov. is proposed. The type strain of Imhoffiella purpurea is AK35T (=JCM 18851T=KCTC 15575T=MTCC 12304T). In addition, Thiorhodococcus bheemlicus is recognized as another species of this genus and transferred to Imhoffiella bheemlica comb. nov.

We investigate the extent to which the dynamics of excitons in the light-harvesting complex LH2 of purple bacteria can be described using a Markovian approximation. To analyse the degree of non-Markovianity in these systems, we introduce a measure based on fitting Lindblad dynamics, as well as employing a recently introduced trace-distance measure. We apply these measures to a chromophore-dimer model of exciton dynamics and use the hierarchical equation-of-motion method to take into account the broad, low-frequency phonon bath. With a smooth phonon bath, small amounts of non-Markovianity are present according to the trace-distance measure, but the dynamics is poorly described by a Lindblad master equation unless the excitonic dimer coupling strength is modified. Inclusion of underdamped, high-frequency modes leads to significant deviations from Markovian evolution in both measures. In particular, we find that modes that are nearly resonant with gaps in the excitonic spectrum produce dynamics that deviate most strongly from the Lindblad approximation, despite the trace distance measuring larger amounts of non-Markovianity for higher frequency modes. Overall we find that the detailed structure in the high-frequency region of the spectral density has a significant impact on the nature of the dynamics of excitons.

Bacteriochlorophylls contain a bacteriochlorin macrocycle bearing an annulated fifth ring. The fifth ring, termed the isocyclic ring or ring E, is equipped with 13 1 -oxo and 13 2 -carbomethoxy substituents. Herein, a general route to stable, synthetic bacteriochlorophyll analogues is described. Knoevenagel condensation (∼40 mM, rt, CH 2 Cl 2 , piperidine/AcOH/molecular sieves) of a dihydrodipyrrin-carboxaldehyde (AD half) and a dihydrodipyrrin substituted with a β-ketoester (BC half) forms a propenone bearing the two halves (a hydrobilin analogue). Subsequent treatment (0.2 mM) with acid (Yb(OTf) 3 , CH 3 CN, 80 °C) promotes a double ring-closure process: (i) condensation between the α-position of pyrrole ring A and the α-acetal unit attached to pyrroline ring B forms the bacteriochlorin macrocycle, and (ii) Nazarov cyclization of the β-(propenoyl)-substituted ring C forms the isocyclic ring (E). Five new bacteriochlorins bearing various substituents (alkyl/alkyl, aryl, and alkyl/ester) at positions 2 and 3 (β-pyrrole sites, ring A) and 13 2 carboalkoxy groups (R = Me or Et) were constructed in 37-61% yield from the hydrobilin analogues. The BC half and AD half are available in five and eight steps, respectively, from the corresponding pyrrole-2-carboxaldehyde and unsaturated ketone. The bacteriochlorins exhibit absorption spectra typical of bacteriopheophytins (free base bacteriochlorophylls), with a strong near-infrared absorption band (707-751 nm).

Bacteriochlorophyll a (BChl a), a photosynthetic pigment performing the same functions of chlorophylls in plants, features a bacteriochlorin macrocycle ring (18 π electrons) with two reduced pyrrole rings along with a hydrophobic terpenoid side chain (i.e., the phytol residue). Chlorophylls analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is not so straightforward since pheophytinization (i.e., release of the central metal ion) and cleavage of the phytol-ester linkage are invariably observed by employing protonating matrices such as 2,5-dihydroxybenzoic acid, sinapinic acid, and α-cyano-4-hydroxycinnamic acid. Using BChl a from Rhodobacter sphaeroides R26 strain as a model system, different electron-transfer (ET) secondary reaction matrices, leading to the formation of almost stable radical ions in both positive ([M] +• ) and negative ([M] -• ) ionization modes at m/z 910.55, were evaluated. Compared with ET matrices such as trans-2-[3-(4-t-butyl-phenyl)-2-methyl-2-propenylidene]malononitrile (DCTB), 2,2':5',2''-terthiophene (TER), anthracene (ANT), and 9,10-diphenylanthracene (DP-ANT), 1,5-diaminonaphthalene (DAN) was found to provide the highest ionization yield with a negligible fragmentation. DAN also displayed excellent ionization properties for two metal ion-substituted bacteriochlorophylls, (i.e., Zn- and Cu-BChl a at m/z 950.49 and 949.49), respectively. MALDI MS/MS of both radical charged molecular species provide complementary information, thus making analyte identification more straightforward. Graphical Abstract ᅟ.

Constructing a reliable potential energy surface (PES) is a key step toward computationally studying the chemical dynamics of any molecular system. The interpolation scheme is a useful tool that can closely follow the accuracy of quantum chemical means at a dramatically reduced computational cost. However, applying interpolation to building a PES of a large molecule is not a straightforward black-box approach, as it frequently encounters practical difficulties associated with its large dimensionality. Here, we present detailed courses of applying interpolation toward building a PES of a large chromophore molecule. We take the example of S 0 and S 1 electronic states of bacteriochlorophyll a (BChla) molecules in the Fenna-Matthews-Olson light harvesting complex. With a reduced model molecule that bears BChla's main π-conjugated ring, various practical approaches are designed for improving the PES quality in a stable manner and for fine-tuning the final surface such that the surface can be adopted for long time molecular dynamics simulations. Combined with parallel implementation, we show that interpolated mechanics/molecular mechanics (IM/MM) simulations of the entire complex in the nanosecond time scale can be conducted readily without any practical issues. With 1500 interpolation data points for each chromophore unit, the PES error relative to the reference quantum chemical calculation is found to be ∼0.15 eV in the thermally accessible region of the conformational space, together with ∼0.01 eV error in S 0 - S 1 transition energies. The performance issue related to the use of a large interpolation database within the framework of our parallel routines is also discussed.

Strain Ery9T, isolated from surface seawater of the Atlantic Ocean, and strain Ery22T, isolated from deep-sea sediment of the Indian Ocean, were subjected to a taxonomic study using a polyphasic approach. Cells of the two strains were Gram-stain-negative, aerobic and rod-shaped. They produced yellow pigments and lacked bacteriochlorophyll a. On the basis of 16S rRNA gene sequence analysis, strain Ery9T was closely related to Croceicoccus naphthovorans PQ-2T (with 16S rRNA gene sequence similarity of 97.7 %), and strain Ery22T was closely related to Croceicoccusmarinus E4A9T (98.3 %). The 16S rRNA gene sequence similarity between strain Ery9T and strain Ery22T was 96.6 %. Phylogenetic analyses revealed that strains Ery9T and Ery22T fell within the cluster of the genus Croceicoccus and represented two independent lineages. The average nucleotide identity (ANI) values and the genome-to-genome distances between strains Ery9T and Ery22T and the type strains of species of the genus Croceicoccus with validly published names were 73.7-78.4 % and 20.1-22.3 %, respectively. The major respiratory quinone of the two isolates was ubiquinone-10 (Q-10). The DNA G+C contents of strains Ery9T and Ery22T were 62.8 and 62.5 mol%, respectively. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with phenotypic properties, revealed that strains Ery9T and Ery22T could be differentiated from their closely related species. Therefore, it is concluded that strains Ery9T and Ery22T represent two novel species of the genus Croceicoccus, for which the names Croceicoccus pelagius sp. nov. (type strain Ery9T=CGMCC 1.15358T=DSM 101479T) and Croceicoccus mobilis sp. nov. (type strain Ery22T=CGMCC 1.15360T=DSM 101481T), are proposed.