Roseococcus pinisoli sp. nov., lacking pufL and pufM bacteriochlorophyll a: synthesizing genes.

A Gram-stain-negative, cocci-to-oval-shaped bacterial strain, designated XZZS9T, was isolated from the rhizosphere soil of Pinus sylvestris var. mongolica and characterized taxonomically using a polyphasic approach. Growth occurred at 20-35 °C (optimum, 28 °C), pH 6.0-11.0 (optimum, pH 7.0), and in 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain XZZS9T was related to members of the genus Roseococcus, with the highest sequence identity to Roseococcus microcysteis NIBR12T (96.9%). The major cellular fatty acids (> 5% of the total) were C18:1 ω7c and C19:0 cyclo ω8c. The major isoprenoid quinone was Q-9 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified glycophospholipid, and an unidentified phospholipid. Genome sequencing revealed that had a genome size of 4.79 Mbp with a G + C content of 69.5%. Comparative genomic analyses clearly separated strain XZZS9T from the known species of the genus Roseococcus based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. Genome annotations did not find pufL and pufM genes in strain XZZS9T, suggesting a possible lack of photosynthetic reaction. Based on genotypic and phenotypic characteristics, strain XZZS9T represents a novel species of the genus Roseococcus, for which we propose the name Roseococcus pinisoli sp. nov. The type strain is XZZS9T (= KCTC 82435T = JCM 34402T = GDMCC 1.2158T).

Coherent wavepackets in the Fenna-Matthews-Olson complex are robust to excitonic-structure perturbations caused by mutagenesis.

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.

Origin of Bacteriochlorophyll a and the Early Diversification of Photosynthesis.

Photosynthesis originated in the domain Bacteria billions of years ago; however, the identity of the last common ancestor to all phototrophic bacteria remains undetermined and speculative. Here I present the evolution of BchF or 3-vinyl-bacteriochlorophyll hydratase, an enzyme exclusively found in bacteria capable of synthetizing bacteriochlorophyll a. I show that BchF exists in two forms originating from an early divergence, one found in the phylum Chlorobi, including its paralogue BchV, and a second form that was ancestral to the enzyme found in the remaining anoxygenic phototrophic bacteria. The phylogeny of BchF is consistent with bacteriochlorophyll a evolving in an ancestral phototrophic bacterium that lived before the radiation event that gave rise to the phylum Chloroflexi, Chlorobi, Acidobacteria, Proteobacteria, and Gemmatimonadetes, but only after the divergence of Type I and Type II reaction centers. Consequently, it is suggested that the lack of phototrophy in many groups of extant bacteria is a derived trait.

Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea.

Four heterotrophic bacterial strains belonging to the globally distributed marine RCA (Roseobacter clade-affiliated) cluster (family Rhodobacteraceae, class Alphaproteobacteria) were obtained from coastal seawater samples. Strain RCA23(T) was isolated from a 10(-7) dilution culture inoculated with seawater from the German Wadden Sea (southern North Sea), reflecting the high abundance of RCA bacteria in this habitat. Strains IMCC1909, IMCC1923 and IMCC1933 were isolated from diluted seawater (10(-3)) of the Yellow Sea, South Korea. Based on 16S rRNA gene sequence comparison, Octadecabacter antarcticus 307(T) is the closest described relative of the RCA strains, with 95.4-95.5 % sequence similarity. Cells of RCA23(T), IMCC1909, IMCC1923 and IMCC1933 are small motile rods requiring sodium ions. Optimal growth of RCA23(T) occurs at 25 °C and within a very narrow pH range (pH 7-8, optimum pH 7.5). The DNA G+C base content of RCA23(T) is 53.67 mol%. The major respiratory lipoquinone is ubiquinone-10 (Q-10) and the dominant fatty acids (>1 %) are 12 : 1 3-OH, 16 : 1ω7c, 16 : 0, 18 : 1ω7c, 18 : 0 and 11-methyl 18 : 1ω7c. The polar lipid pattern indicated the presence of phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. On marine agar, RCA23(T) forms non-pigmented, transparent to light beige, small (<1 mm), circular, convex colonies. Strain RCA23(T) harbours all genes for the production of bacteriochlorophyll a (BChl a). Genes encoding the light-harvesting reaction centre of BChl a (pufM) were identified in all RCA strains. No visible pigmentation was observed for any of the strains under laboratory conditions, but spectrophotometric analysis revealed weak production of BChl a by RCA23(T). Morphological, physiological and genotypic features of strain RCA23(T) suggest that it represents a novel species of a new genus within the Rhodobacteraceae, for which we propose the name Planktomarina temperata gen. nov., sp. nov., described previously by Giebel et al. [ISME J 5 (2011), 8-19] as 'Candidatus Planktomarina temperata'. The type strain of Planktomarina temperata is RCA23(T) ( = DSM 22400(T) = JCM 18269(T)).

Marivita roseacus sp. nov., of the family Rhodobacteraceae, isolated from a temperate estuary and an emended description of the genus Marivita.

A gram-negative, non-motile, pigmented, rod-shaped and strictly aerobic bacterium (CB1052(T)) was isolated from a temperate estuary. On the basis of 16S rRNA gene sequence similarity, strain CB1052(T) belongs to the α-3 subclass of the Proteobacteria, within the family Rhodobacteraceae, having the highest similarity to members of the genus Marivita (97.8%) of the Roseobacter lineage. Pylogenetic analysis showed CB1052(T) to be a distinct sister clade to M. litorea and M. cryptomonadis and DNA-DNA relatedness was quite low amongst the strains (< 35%). Strain CB1052(T) cells are non-motile and display a needle-like filamentous form, where individual cells can become quite elongated (up to 15 µm). Similar to M. litorea and M. cryptomonadis, CB1052(T) harbors aerobic anoxygenic photosynthesis genes. However, in contrast to other described Marivita species, strain CB1052(T) actively produces bacteriochlorophyll a. Further physiological features, including antibiotic sensitivities, differentiate strain CB1052(T) from the other members of the genus. Therefore, strain CB1052(T) is considered to represent a novel species of the genus Marivita, for which the name Marivita roseacus sp. nov. is proposed, with the type strain CB1052(T) (=DSM 23118(T) =ATCC BAA 1914(T)).

Robustness of electronic coherence in the Fenna-Matthews-Olson complex to vibronic and structural modifications.

We present the first two-dimensional electronic spectra of photosynthetic antenna complexes bearing modifications to the protein and the chromophores. The vibronic structure of the Fenna-Matthews-Olson complex was altered by near-complete substitution of 13C for naturally abundant carbon and separately by randomly distributed partial deuteration. The structure and arrangement of the bacteriochlorophyll a chromophores were modified by deletion of the gene encoding the enzyme responsible for reducing the isoprenoid tail of the bacteriochlorophylls. Analysis of the time-dependent amplitude of the crosspeak corresponding to excitons 1 and 2 indicates that these modifications do not affect the frequency or dephasing of the beating observed in this particular peak. This result leads us to conclude that this beating indeed arises from electronic coherence and not vibrational wavepacket motion. We further conclude that the protection of zero-quantum coherences afforded by the protein matrix of this photosynthetic complex is not the result of a finely-tuned series of system-bath interactions perfected by billions of years of evolution but rather a simple downstream property of a close arrangement of chromophores within a phonon bath. We conclude with a brief discussion of the outstanding questions and possible applications of this phenomenon.

Structural and spectroscopic consequences of hexacoordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides reaction center .

The structural and functional consequences of changing the coordination state of one of the bacteriochlorophyll (BChl) cofactors in the purple bacterial reaction center have been explored. A combination of steady state spectroscopy and X-ray crystallography was used to demonstrate that mutagenesis of residue 181 of the L-polypeptide from Phe to Arg (FL181R) causes the BChl at the accessory (B(B)) position on the so-called inactive cofactor branch to become hexacoordinated, with no significant changes to the structure of the surrounding protein. This change was accompanied by the appearance of a distinctive absorbance band at 631 nm in the room-temperature absorbance spectrum. The ligand donor was not the Arg side chain but rather an intervening water molecule, and contrary to expectations, the Mg of B(B) did not adopt a more in-plane geometry in response to hexacoordination. The mutation caused a disturbance to the detailed conformation of the BChl macrocycle that manifested in a number of subtle changes to the resonance Raman spectrum. Hexacoordination of B(B) produced a small increase in the lifetime of the excited electronic state of the primary donor bacteriochlorophylls (P*), indicating some disturbance to light-driven energy and/or electron transfer events on the time scale of a few picoseconds after light excitation. The B(B) bacteriochlorophyll returned to a pentacoordinated state in a double mutant where the FL181R mutation was combined with removal of the native axial ligand through mutation of His M182 to Leu. Experimental evidence of hexacoordinated bacteriochlorophylls in the literature on antenna proteins is considered, and possible reasons why hexacoordinated bacteriochlorophylls and chlorophylls appear to be avoided in photosynthetic proteins are discussed.

On the photosynthetic properties of marine bacterium COL2P belonging to Roseobacter clade.

Aerobic anoxygenic phototrophs (AAPs) are prokaryotic microorganisms capable of harvesting light using bacteriochlorophyll-based reaction centres. Marine AAP communities are generally dominated by species belonging to the Roseobacter clade. For this reason, we used marine Roseobacter-related strain COL2P as a model organism to characterize its photosynthetic apparatus, level of pigmentation and expression of photosynthetic complexes. This strain contained functional photosynthetic reaction centres with bacteriochlorophyll a and spheroidenone as the main light-harvesting pigments, but the expression of the photosynthetic apparatus was significantly reduced when compared to truly photoautotrophic species. Moreover, the absence of peripheral light-harvesting complexes largely reduced its light-harvesting capacity. The size of the photosynthetic unit was limited to 35.4 +/- 1.0 BChl a molecules supplemented by the same number of spheroidenone molecules. The contribution of oxidative phosphorylation and photophosphorylation was analysed by respiration and fluorometric measurements. Our results indicate that even with a such reduced photosynthetic apparatus, photophosphorylation provides up to three times higher electron fluxes than aerobic respiration. These results suggest that light-derived energy can provide a substantial fraction of COL2P metabolic needs.

Reconstitution and replacement of bacteriochlorophyll a molecules in photosynthetic reaction centers.

Reaction centers (RCs) of the photosynthetic bacterium Rhodobacter sphaeroides R-26 were reconstituted in liposomes after release of pigments (bacteriochlorophyll a (BChla) and bacteriopheophytin a (BPhea)) by treatment with acetone. As shown by absorption and circular dichroism spectroscopies, the reconstituted RCs had the same arrangement of pigments as the native RC and exhibited photoactivity of the special pair. The recovery yield of RCs of up to 30% was achieved by addition of 7.8-fold excess of BChla in the acetone treatment. Furthermore BChla was partially replaced with Zn-BChla by addition of the pigments during the acetone treatment. About 30% and 50% of the special pair and accessory pigments can be replaced with Zn-BChla, respectively. From this rate, an oxidation-reduction potential of 520 mV (vs. the normal hydrogen electrode NHE) was derived by the simulation of the experimental data, which is 35 mV higher than that of the native RC (484 mV vs. NHE).

Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria.

Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria. However, members of the two taxa that comprise this group, the green sulfur bacteria (Chlorobi) and the filamentous anoxygenic phototrophic bacteria ("Chloroflexales"), are otherwise quite different, both physiologically and phylogenetically. This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus and the oxidation of inorganic sulfur compounds in two model organisms that represent these taxa, Chlorobium tepidum and Chloroflexus aurantiacus. The genes involved in bacteriochlorophyll (BChl) c and carotenoid biosynthesis in these two organisms were identified by sequence homology with known BChl a and carotenoid biosynthesis enzymes, gene cluster analysis in Cfx. aurantiacus, and gene inactivation studies in Chl. tepidum. Based on these results, BChl a and BChl c biosynthesis is similar in the two organisms, whereas carotenoid biosynthesis differs significantly. In agreement with its facultative anaerobic nature, Cfx. aurantiacus in some cases apparently produces structurally different enzymes for heme and BChl biosynthesis, in which one enzyme functions under anoxic conditions and the other performs the same reaction under oxic conditions. The Chl. tepidum mutants produced with modified BChl c and carotenoid species also allow the functions of these pigments to be studied in vivo.