Calculated vibrational properties of pigments in protein binding sites 2: Semiquinones in photosynthetic proteins

[Q_A^- - Q_A] Fourier transform infrared difference spectra have previously been obtained using purple bacterial reaction centers from Rhodobacter sphaeroides with unlabeled, ¹⁸O and ¹³C isotope labeled phylloquinone (PhQ, also known as vitamin K₁) incorporated into the Q_A protein binding site (Breton, (1997), Proc. Natl. Acad. Sci. USA94 11318-11323). The nature of the bands in these spectra and the isotope induced band shifts are poorly understood, especially for the phyllosemiquinone anion (PhQ^-) state. To aid in the interpretation of the bands in these experimental spectra, ONIOM type QM/MM vibrational frequency calculations were undertaken. Calculations were also undertaken for PhQ^- in solution. Surprisingly, both sets of calculated spectra are similar and agree well with the experimental spectra. This similarity suggests pigment-protein interactions do not perturb the electronic structure of the semiquinone in the Q_A binding site. This is not found to be the case for the neutral PhQ species in the same protein binding site. PhQ also occupies the A₁ protein binding site in photosystem I, and the vibrational properties of PhQ^- in the Q_A and A₁ binding sites are compared and shown to exhibit considerable differences. These differences probably arise because of changes in the degree of asymmetry of hydrogen bonding of PhQ^- in the A₁ and Q_A binding sites.

Polyhydroxyalkanoates and 5-aminolevulinic acid production by a mixed phototrophic culture using medium-chain carboxylic acids from winery effluents

This work aimed to obtain polyhydroxyalkanoates (PHA) and 5-aminolevulinic acid (5-ALA) from medium-chain carboxylic acids (MCCA) using a mixed culture enriched in Rhodopseudomnas palustris. MCCA, obtained from residual wine lees, were tested in batch photofermentation experiments. First, the influence of individual MCCA (hexanoic, heptanoic, and octanoic acids) was evaluated; then, the MCCA coming directly from a fermentation reactor (LC-effluent) or after acids extraction (HC-effluent) were studied. Nutrient supplementation, bicarbonate, and acetic acid addition were also tested. Results showed that PHA production was higher in hexanoic (328 mg PHA/L) compared to heptanoic (152 mg PHA/L) and octanoic (164 mg PHA/L) acids. Bicarbonate addition and acetic acid as co-substrate improved the MCCA consumption, the PHA content and production rate. The HC-effluent, without nutrient supplementation, was allowed to increase 2.5 times the PHA content (reaching 40 % w/w and 584 mg/L) and to double 5-ALA production (7.6 µM) compared to the LC-effluent condition.

Characterisation of the photosynthetic complexes from the marine gammaproteobacterium Congregibacter litoralis KT71

Possibly the most abundant group of anoxygenic phototrophs are marine photoheterotrophic Gammaproteobacteria belonging to the NOR5/OM60 clade. As little is known about their photosynthetic apparatus, the photosynthetic complexes from the marine phototrophic bacterium Congregibacter litoralis KT71 were purified and spectroscopically characterised. The intra-cytoplasmic membranes contain a smaller amount of photosynthetic complexes when compared with anaerobic purple bacteria. Moreover, the intra-cytoplasmic membranes contain only a minimum amount of peripheral LH2 complexes. The complexes are populated by bacteriochlorophyll a, spirilloxanthin and two novel ketocarotenoids, with biophysical and biochemical properties similar to previously characterised complexes from purple bacteria. The organization of the RC-LH1 complex has been further characterised using cryo-electron microscopy. The overall organisation is similar to the complex from the gammaproteobacterium Thermochromatium tepidum, with the type-II reaction centre surrounded by a slightly elliptical LH1 antenna ring composed of 16 αβ-subunits with no discernible gap or pore. The RC-LH1 and LH2 apoproteins are phylogenetically related to other halophilic species but LH2 also to some alphaproteobacterial species. It seems that the reduction of light-harvesting apparatus and acquisition of novel ketocarotenoids in Congregibacter litoralis KT71 represent specific adaptations for operating the anoxygenic photosynthesis under aerobic conditions at sea.

Dissolution rate and growth performance reveal struvite as a sustainable nutrient source to produce a diverse set of microbial protein

To provide for the globally increasing demand for proteinaceous food, microbial protein (MP) has the potential to become an alternative food or feed source. Phosphorus (P), on the other hand, is a critical raw material whose global reserves are declining. Growing MP on recovered phosphorus, for instance, struvite obtained from wastewater treatment, is a promising MP production route that could supply protein-rich products while handling P scarcity. The aim of this study was to explore struvite dissolution kinetics in different MP media and characterize MP production with struvite as sole P-source. Different operational parameters, including pH, temperature, contact surface area, and ion concentrations were tested, and struvite dissolution rates were observed between 0.32 and 4.7 g P/L/d and a solubility between 0.23 and 2.22 g P-based struvite/L. Growth rates and protein production of the microalgae Chlorella vulgaris and Limnospira sp. (previously known as Arthrospira sp.), and the purple non‑sulfur bacterium Rhodopseudomonas palustris on struvite were equal to or higher than growth on conventional potassium phosphate. For aerobic heterotrophic bacteria, two slow-growing communities showed decreased growth on struvite, while the growth was increased for a third fast-growing one. Furthermore, MP protein content on struvite was always comparable to the one obtained when grown on standard media. Together with the low content in metals and micropollutants, these results demonstrate that struvite can be directly applied as an effective nutrient source to produce fast-growing MP, without any previous dissolution step. Combining a high purity recovered product with an efficient way of producing protein results in a strong environmental win-win.

Identification of amino acid residues in a proton release pathway near the bacteriochlorophyll dimer in reaction centers from Rhodobacter sphaeroides

Insight into control of proton transfer, a crucial attribute of cellular functions, can be gained from investigations of bacterial reaction centers. While the uptake of protons associated with the reduction of the quinone is well characterized, the release of protons associated with the oxidized bacteriochlorophyll dimer has been poorly understood. Optical spectroscopy and proton release/uptake measurements were used to examine the proton release characteristics of twelve mutant reaction centers, each containing a change in an amino acid residue near the bacteriochlorophyll dimer. The mutant reaction centers had optical spectra similar to wild-type and were capable of transferring electrons to the quinones after light excitation of the bacteriochlorophyll dimer. They exhibited a large range in the extent of proton release and in the slow recovery of the optical signal for the oxidized dimer upon continuous illumination. Key roles were indicated for six amino acid residues, Thr L130, Asp L155, Ser L244, Arg M164, Ser M190, and His M193. Analysis of the results points to a hydrogen-bond network that contains these residues, with several additional residues and bound water molecules, forming a proton transfer pathway. In addition to proton transfer, the properties of the pathway are proposed to be responsible for the very slow charge recombination kinetics observed after continuous illumination. The characteristics of this pathway are compared to proton transfer pathways near the secondary quinone as well as those found in photosystem II and cytochrome c oxidase.

Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics

Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.

In Silico Identification and Characterization of a Hypothetical Protein From Rhodobacter capsulatus Revealing S-Adenosylmethionine-Dependent Methyltransferase Activity

Rhodobacter capsulatus is a purple non-sulfur bacteria widely used as a model organism to study bacterial photosynthesis. It exhibits extensive metabolic activities and demonstrates other distinctive characteristics such as pleomorphism and nitrogen-fixing capability. It can act as a gene transfer agent (GTA). The commercial importance relies on producing polyester polyhydroxyalkanoate (PHA), extracellular nucleic acids, and commercially critical single-cell proteins. These diverse features make the organism an exciting and environmentally and industrially important one to study. This study was aimed to characterize, model, and annotate the function of a hypothetical protein (Accession no. CAA71016.1) of R capsulatus through computational analysis. The urf7 gene encodes the protein. The tertiary structure was predicted through MODELLER and energy minimization and refinement by YASARA Energy Minimization Server and GalaxyRefine tools. Analysis of sequence similarity, evolutionary relationship, and exploration of domain, family, and superfamily inferred that the protein has S-adenosylmethionine (SAM)-dependent methyltransferase activity. This was further verified by active site prediction by CASTp server and molecular docking analysis through Autodock Vina tool and PatchDock server of the predicted tertiary structure of the protein with its ligands (SAM and SAH). Normally, as a part of the gene product of photosynthetic gene cluster (PGC), the established roles of SAM-dependent methyltransferases are bacteriochlorophyll and carotenoid biosynthesis. But the STRING database unveiled its association with NADH-ubiquinone oxidoreductase (Complex I). The assembly and regulation of this Complex I is mediated by the gene products of the nuo operon. As a part of this operon, the urf7 gene encodes SAM-dependent methyltransferase. As a consequence of these findings, it is reasonable to propose that the hypothetical protein of interest in this study is a SAM-dependent methyltransferase associated with bacterial NADH-ubiquinone oxidoreductase assembly. Due to conservation of Complex I from prokaryotes to eukaryotes, R capsulatus can be a model organism of study to understand the common disorders which are linked to the dysfunctions of complex I.

FRET measurement of cytochrome bc1 and reaction centre complex proximity in live Rhodobacter sphaeroides cells

In the model purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides, solar energy is converted via coupled electron and proton transfer reactions within the intracytoplasmic membranes (ICMs), infoldings of the cytoplasmic membrane that form spherical 'chromatophore' vesicles. These bacterial 'organelles' are ideal model systems for studying how the organisation of the photosynthetic complexes therein shape membrane architecture. In Rba. sphaeroides, light-harvesting 2 (LH2) complexes transfer absorbed excitation energy to dimeric reaction centre (RC)-LH1-PufX complexes. The PufX polypeptide creates a channel that allows the lipid soluble electron carrier quinol, produced by RC photochemistry, to diffuse to the cytochrome bc₁ complex, where quinols are oxidised to quinones, with the liberated protons used to generate a transmembrane proton gradient and the electrons returned to the RC via cytochrome c₂. Proximity between cytochrome bc₁ and RC-LH1-PufX minimises quinone/quinol/cytochrome c₂ diffusion distances within this protein-crowded membrane, however this distance has not yet been measured. Here, we tag the RC and cytochrome bc₁ with yellow or cyan fluorescent proteins (YFP/CFP) and record the lifetimes of YFP/CFP Förster resonance energy transfer (FRET) pairs in whole cells. FRET analysis shows that that these complexes lie on average within 6 nm of each other. Complementary high-resolution atomic force microscopy (AFM) of intact, purified chromatophores verifies the close association of cytochrome bc₁ complexes with RC-LH1-PufX dimers. Our results provide a structural basis for the close kinetic coupling between RC-LH1-PufX and cytochrome bc₁ observed by spectroscopy, and explain how quinols/quinones and cytochrome c₂ shuttle on a millisecond timescale between these complexes, sustaining efficient photosynthetic electron flow.

The periodic table of photosynthetic purple non-sulfur bacteria: intact cell-metal ions interactions

Photosynthetic purple non-sulfur bacteria (PNB) have been widely utilized as model organisms to study bacterial photosynthesis. More recently, the remarkable resistance of these microorganisms to several metals ions called particular interest. As a result, several research efforts were directed toward clarifying the interactions of metal ions with PNB. The mechanisms of metal ions active uptake and bioabsorption have been studied in detail, unveiling that PNB enable harvesting and removing various toxic ions, thus fostering applications in environmental remediation. Herein, we present the most important achievements in the understanding of intact cell-metal ions interactions and the approaches utilized to study such processes. Following, the application of PNB-metal ions interactions toward metal removal from contaminated environments is presented. Finally, the possible coupling of PNB with abiotic electrodes to obtain biohybrid electrochemical systems is proposed as a sustainable pathway to tune and enhance metal removal and monitoring.

Temperature dependence of nanosecond charge recombination in mutant Rhodobacter sphaeroides reaction centers: modelling of the protein dynamics

We investigated the influence of a range of factors-temperature, redox midpoint potential of an electron carrier, and protein dynamics-on nanosecond electron transfer within a protein. The model reaction was back electron transfer from a bacteriopheophytin anion, H_A^-, to an oxidized primary electron donor, P⁺, in a wild type Rhodobacter sphaeroides reaction center (RC) with a permanently reduced secondary electron acceptor (quinone, Q_A^-). Also used were two modified RCs with single amino acid mutations near the monomeric bacteriochlorophyll, B_A, located between P and H_A. Both mutant RCs showed significant slowing down of this back electron transfer reaction with decreasing temperature, similar to that observed with the wild type RC, but contrasting with a number of single point mutant RCs studied previously. The observed similarities and differences are explained in the framework of a (P⁺B_A^- ↔ P⁺H_A^-) equilibrium model with an important role played by protein relaxation. The major cause of the observed temperature dependence, both in the wild type RC and in the mutant proteins, is a limitation in access to the thermally activated pathway of charge recombination via the state P⁺B_A^- at low temperatures. The data indicate that in all RCs both charge recombination pathways, the thermally activated one and a direct one without involvement of the P⁺B_A^- state, are controlled by the protein dynamics. It is concluded that the modifications of the protein environment affect the overall back electron transfer kinetics primarily by changing the redox potential of B_A and not by changing the protein relaxation dynamics.

Carotenoid-to-(bacterio)chlorophyll energy transfer in LH2 antenna complexes from Rba. sphaeroides reconstituted with non-native (bacterio)chlorophylls

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 S₁ 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 S₁ state, supporting a value in the vicinity of 13,400 cm^-1 (746 nm).

Unveiling salinity effects on photo-bioelectrocatalysis through combination of bioinformatics and electrochemistry

Little is known about the adaptation strategies utilized by photosynthetic microorganisms to cope with salinity changes happening in the environment, and the effects on microbial electrochemical technologies. Herein, bioinformatics analysis revealed a metabolism shift in Rhodobacter capsulatus resulting from salt stress, with changes in gene expression allowing accumulation of compatible solutes to balance osmotic pressure, together with the up-regulation of the nitrogen fixation cycle, an electron sink of the photosynthetic electron transfer chain. Using the transcriptome evidence of hindered electron transfer in the photosynthetic electron transport chain induced by adaption to salinity, increased understanding of photo-bioelectrocatalysis under salt stress is achieved. Accumulation of glycine-betaine allows immediate tuning of salinity tolerance but does not provide cell stabilization, with a 40 ± 20% loss of photo-bioelectrocatalysis in a 60 min time scale. Conversely, exposure to or inducing the expression of the Rhodobacter capsulatus gene transfer agent tunes salinity tolerance and increases cell stability. This work provides a proof of concept for the combination of bioinformatics and electrochemical tools to investigate microbial electrochemical systems, opening exciting future research opportunities.

Dual bloom of green algae and purple bacteria in an extremely shallow soda pan

In April 2014, dual bloom of green algae and purple bacteria occurred in a shallow, alkaline soda pan (Kiskunság National Park, Hungary). The water was only 5 cm deep, in which an upper green layer was clearly separated from a near-sediment purple one. Based on microscopy and DNA-based identification, the upper was inhabited by a dense population of the planktonic green alga, Oocystis submarina Lagerheim, while the deeper layer was formed by purple, bacteriochlorophyll-containing bacteria, predominated by Thiorhodospira and Rhodobaca. Additional bacterial taxa with a presumed capability of anoxygenic phototrophic growth belonged to the genera Loktanella and Porphyrobacter. Comparing the bacterial community of the purple layer with a former blooming event in a nearby soda pan, similar functional but different taxonomic composition was revealed. Members from many dominant bacterial groups were successfully cultivated including potentially new species, which could be the result of the application of newly designed media.

Differences in possible TCA cycle replenishing pathways in purple non-sulfur bacteria possessing glyoxylate pathway

Pathways replenishing tricarboxylic acid cycle were divided into four major groups based on metabolite serving as source for oxaloacetic acid or other tricarboxylic acid cycle component synthesis. Using this metabolic map, the analysis of genetic potential for functioning of tricarboxylic acid cycle replenishment pathways was carried out for seven strains of purple non-sulfur bacterium Rhodopseudomonas palustris. The results varied from strain to strain. Published microarray data for phototrophic acetate cultures of Rps. palustris CGA009 were analyzed to validate activity of the putative pathways. All the results were compared with the results for another purple non-sulfur bacterium, Rhodobacter capsulatus SB1003 and species-specific differences were clarified.

Modelling of the cathodic and anodic photocurrents from Rhodobacter sphaeroides reaction centres immobilized on titanium dioxide

As one of a number of new technologies for the harnessing of solar energy, there is interest in the development of photoelectrochemical cells based on reaction centres (RCs) from photosynthetic organisms such as the bacterium Rhodobacter (Rba.) sphaeroides. The cell architecture explored in this report is similar to that of a dye-sensitized solar cell but with delivery of electrons to a mesoporous layer of TiO₂ by natural pigment-protein complexes rather than an artificial dye. Rba. sphaeroides RCs were bound to the deposited TiO₂ via an engineered extramembrane peptide tag. Using TMPD (N,N,N',N'-tetramethyl-p-phenylenediamine) as an electrolyte, these biohybrid photoactive electrodes produced an output that was the net product of cathodic and anodic photocurrents. To explain the observed photocurrents, a kinetic model is proposed that includes (1) an anodic current attributed to injection of electrons from the triplet state of the RC primary electron donor (P^T) to the TiO₂ conduction band, (2) a cathodic current attributed to reduction of the photooxidized RC primary electron donor (P⁺) by surface states of the TiO₂ and (3) transient cathodic and anodic current spikes due to oxidation/reduction of TMPD/TMPD⁺ at the conductive glass (FTO) substrate. This model explains the origin of the photocurrent spikes that appear in this system after turning illumination on or off, the reason for the appearance of net positive or negative stable photocurrents depending on experimental conditions, and the overall efficiency of the constructed cell. The model may be a used as a guide for improvement of the photocurrent efficiency of the presented system as well as, after appropriate adjustments, other biohybrid photoelectrodes.

Energy transfer in purple bacterial photosynthetic units from cells grown in various light intensities

Three photosynthetic membranes, called intra-cytoplasmic membranes (ICMs), from wild-type and the ∆pucBA_abce mutant of the purple phototrophic bacterium Rps. palustris were investigated using optical spectroscopy. The ICMs contain identical light-harvesting complex 1-reaction centers (LH1-RC) but have various spectral forms of light-harvesting complex 2 (LH2). Spectroscopic studies involving steady-state absorption, fluorescence, and femtosecond time-resolved absorption at room temperature and at 77 K focused on inter-protein excitation energy transfer. The studies investigated how energy transfer is affected by altered spectral features of the LH2 complexes as those develop under growth at different light conditions. The study shows that LH1 → LH2 excitation energy transfer is strongly affected if the LH2 complex alters its spectroscopic signature. The LH1 → LH2 excitation energy transfer rate modeled with the Förster mechanism and kinetic simulations of transient absorption of the ICMs demonstrated that the transfer rate will be 2-3 times larger for ICMs accumulating LH2 complexes with the classical B800-850 spectral signature (grown in high light) compared to the ICMs from the same strain grown in low light. For the ICMs from the ∆pucBA_abce mutant, in which the B850 band of the LH2 complex is blue-shifted and almost degenerate with the B800 band, the LH1 → LH2 excitation energy transfer was not observed nor predicted by calculations.

Characterisation of a pucBA deletion mutant from Rhodopseudomonas palustris lacking all but the pucBAd genes

Rhodopseudomonas palustris is a species of purple photosynthetic bacteria that has a multigene family of puc genes that encode the alpha and beta apoproteins, which form the LH2 complexes. A genetic dissection strategy has been adopted in order to try and understand which spectroscopic form of LH2 these different genes produce. This paper presents a characterisation of one of the deletion mutants generated in this program, the pucBAd only mutant. This mutant produces an unusual spectroscopic form of LH2 that only has a single large NIR absorption band at 800 nm. Spectroscopic and pigment analyses on this complex suggest that it has basically a similar overall structure as that of the wild-type HL LH2 complex. The mutant has the unique phenotype where the mutant LH2 complex is only produced when cells are grown at LL. At HL the mutant only produces the LH1-RC core complex.

Carotenoid to bacteriochlorophyll energy transfer in the RC-LH1-PufX complex from Rhodobacter sphaeroides containing the extended conjugation keto-carotenoid diketospirilloxanthin

RC-LH1-PufX complexes from a genetically modified strain of Rhodobacter sphaeroides that accumulates carotenoids with very long conjugation were studied by ultrafast transient absorption spectroscopy. The complexes predominantly bind the carotenoid diketospirilloxanthin, constituting about 75% of the total carotenoids, which has 13 conjugated C=C bonds, and the conjugation is further extended to two terminal keto groups. Excitation of diketospirilloxanthin in the RC-LH1-PufX complex demonstrates fully functional energy transfer from diketospirilloxanthin to BChl a in the LH1 antenna. As for other purple bacterial LH complexes having carotenoids with long conjugation, the main energy transfer route is via the S₂-Q_x pathway. However, in contrast to LH2 complexes binding diketospirilloxanthin, in RC-LH1-PufX we observe an additional, minor energy transfer pathway associated with the S₁ state of diketospirilloxanthin. By comparing the spectral properties of the S₁ state of diketospirilloxanthin in solution, in LH2, and in RC-LH1-PufX, we propose that the carotenoid-binding site in RC-LH1-PufX activates the ICT state of diketospirilloxanthin, resulting in the opening of a minor S₁/ICT-mediated energy transfer channel.

Engineered biosynthesis of bacteriochlorophyll gF in Rhodobacter sphaeroides

Engineering photosynthetic bacteria to utilize a heterologous reaction center that contains a different (bacterio) chlorophyll could improve solar energy conversion efficiency by allowing cells to absorb a broader range of the solar spectrum. One promising candidate is the homodimeric type I reaction center from Heliobacterium modesticaldum. It is the simplest known reaction center and uses bacteriochlorophyll (BChl) g, which absorbs in the near-infrared region of the spectrum. Like the more common BChls a and b, BChl g is a true bacteriochlorin. It carries characteristic C3-vinyl and C8-ethylidene groups, the latter shared with BChl b. The purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides was chosen as the platform into which the engineered production of BChl g_F, where F is farnesyl, was attempted. Using a strain of Rba. sphaeroides that produces BChl b_P, where P is phytyl, rather than the native BChl a_P, we deleted bchF, a gene that encodes an enzyme responsible for the hydration of the C3-vinyl group of a precursor of BChls. This led to the production of BChl g_P. Next, the crtE gene was deleted, thereby producing BChl g carrying a THF (tetrahydrofarnesol) moiety. Additionally, the bchG^Rs gene from Rba. sphaeroides was replaced with bchG^Hm from Hba. modesticaldum. To prevent reduction of the tail, bchP was deleted, which yielded BChl g_F. The construction of a strain producing BChl g_F validates the biosynthetic pathway established for its synthesis and satisfies a precondition for assembling the simplest reaction center in a heterologous organism, namely the biosynthesis of its native pigment, BChl g_F.

Long-term H2 photoproduction from starch by co-culture of Clostridium butyricum and Rhodobacter sphaeroides in a repeated batch process

OBJECTIVES

To prove the possibility of efficient starch photofermentation in co-culture of heterotrophic and phototrophic bacteria over prolonged period.

RESULTS

Repeated batch photofermentation of starch was demonstrated in co-culture Clostridium butyricum and Rhodobacter sphaeroides under microaerobic conditions. It continued 15 months without addition of new inoculum or pH regulation when using 4-5 g starch l^-1 and 0.04 g yeast extract l^-1. The complete degradation of starch without volatile fatty acids accumulation was shown in this co-culture. The average H₂ yield of 5.2 mol/mol glucose was much higher than that in Clostridium monoculture. The species composition of co-culture was studied by q-PCR assay. The concentration of Clostridium cells in prolonged co-culture was lower than in monoculture and even in a single batch co-culture. This means that Clostridia growth was significantly limited whereas starch hydrolysis still took place.

CONCLUSION

The prolonged repeated batch photofermentation of starch by co-culture C. butyricum and R. sphaeroides provided efficient H₂ production without accumulation of organic acids under conditions of Clostridia limitation.

Apoprotein heterogeneity increases spectral disorder and a step-wise modification of the B850 fluorescence peak position

It has already been established that the quaternary structure of the main light-harvesting complex (LH2) from the photosynthetic bacterium Rhodopseudomonas palustris is a nonameric 'ring' of PucAB heterodimers and under low-light culturing conditions an increased diversity of PucB synthesis occurs. In this work, single molecule fluorescence emission studies show that different classes of LH2 'rings' are present in "low-light" adapted cells and that an unknown chaperon process creates multiple sub-types of 'rings' with more conformational sub-states and configurations. This increase in spectral disorder significantly augments the cross-section for photon absorption and subsequent energy flow to the reaction centre trap when photon availability is a limiting factor. This work highlights yet another variant used by phototrophs to gather energy for cellular development.

New insights into the photochemistry of carotenoid spheroidenone in light-harvesting complex 2 from the purple bacterium Rhodobacter sphaeroides

Light-harvesting complex 2 (LH2) from the semi-aerobically grown purple phototrophic bacterium Rhodobacter sphaeroides was studied using optical (static and time-resolved) and resonance Raman spectroscopies. This antenna complex comprises bacteriochlorophyll (BChl) a and the carotenoid spheroidenone, a ketolated derivative of spheroidene. The results indicate that the spheroidenone-LH2 complex contains two spectral forms of the carotenoid: (1) a minor, "blue" form with an S₂ (1¹B _u⁺ ) spectral origin band at 522 nm, shifted from the position in organic media simply by the high polarizability of the binding site, and (2) the major, "red" form with the origin band at 562 nm that is associated with a pool of pigments that more strongly interact with protein residues, most likely via hydrogen bonding. Application of targeted modeling of excited-state decay pathways after carotenoid excitation suggests that the high (92%) carotenoid-to-BChl energy transfer efficiency in this LH2 system, relative to LH2 complexes binding carotenoids with comparable double-bond conjugation lengths, derives mainly from resonance energy transfer from spheroidenone S₂ (1¹B _u⁺ ) state to BChl a via the Q_x state of the latter, accounting for 60% of the total transfer. The elevated S₂ (1¹B _u⁺ ) → Q_x transfer efficiency is apparently associated with substantially decreased energy gap (increased spectral overlap) between the virtual S₂ (1¹B _u⁺ ) → S₀ (1¹A _g^- ) carotenoid emission and Q_x absorption of BChl a. This reduced energetic gap is the ultimate consequence of strong carotenoid-protein interactions, including the inferred hydrogen bonding.

The kinetic model for slow photoinduced electron transport in the reaction centers of purple bacteria

The present work is related to the investigation of slow kinetics of electron transport in the reaction centers (RCs) of Rhodobacter sphaeroides. Experimental data on the absorption kinetics of aqueous solutions of reaction centers at different modes of photoexcitation are given. It is shown that the kinetics of oxidation and reduction of RCs are well described by the sum of three exponential functions. This allows to suggest a two-level kinetic model for electron transport in the RC as a system of four electron-conformational states which correspond to three balance differential equations combined with state equation. The solution of inverse problem made it possible to obtain the rate constant values in kinetic equations for different times and intensities of exciting light. Analysis of rate constant values in different modes of RC excitation allowed to suggest that two mechanisms of structural changes are involved in RC photo-oxidation. One mechanism leads to the increment of the rate of electron return, another one-to its drop. Structural changes were found out to occur in the RCs under incident light. After light was turned off, the reduction of RCs was determined by the second mechanism.

A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components

The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions [Formula: see text] is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

Inhibited growth of Clostridium butyricum in efficient H2-producing co-culture with Rhodobacter sphaeroides

Cell number of Clostridium butyricum and Rhodobacter sphaeroides in co-culture was measured using q-PCR approach. During efficient H₂ photoproduction from starch (6.2 mol H₂/mol glucose), Clostridia growth and starch-hydrolyzing activity was partly suppressed. Apparently, the effect of R. sphaeroides towards C. butyricum was not attributed to altered E_h or pH values in the presence of purple bacteria. Further, disk-diffusion test proved that R. sphaeroides was capable of producing inhibitors against another purple bacterium, Rhodospirillum rubrum, but not against C. butyricum. We suggested that at initial cell number ratio C. butyricum:R. sphaeroides 1:1 purple bacteria outcompeted C. butyricum for yeast extract at its low concentration (80 mg/L). Under these conditions, the H₂ yield was rather high (5.7 mol/mol). When the yeast extract concentration increased to 320 mg/L, this process was replaced by the low-yield H₂ production (1.8 mol/mol) characteristic of Clostridia. However, increased percentage of purple bacteria in inoculum under these conditions prevented this shift. The outcome of competition depended on both the yeast extract concentration and cell number ratio. Apparently, the competition for yeast extract helped to maintain balance between fast-growing C. butyricum and slower-growing R. sphaeroides for efficient H₂ photoproduction.

Purple non-sulfur photosynthetic bacteria monitor environmental stresses

Heavy metal ion pollution and oxygen deficiency are major environmental risks for microorganisms in aqueous habitat. The potential of purple non-sulfur photosynthetic bacteria for biomonitoring and bioremediation was assessed by investigating the photosynthetic capacity in heavy metal contaminated environments. Cultures of bacterial strains Rhodobacter sphaeroides, Rhodospirillum rubrum and Rubrivivax gelatinosus were treated with heavy metal ions in micromolar (Hg(2+)), submillimolar (Cr(6+)) and millimolar (Pb(2+)) concentration ranges. Functional assays (flash-induced absorption changes and bacteriochlorophyll fluorescence induction) and electron micrographs were taken to specify the harmful effects of pollution and to correlate to morphological changes of the membrane. The bacterial strains and functional tests showed differentiated responses to environmental stresses, revealing that diverse mechanisms of tolerance and/or resistance are involved. The microorganisms were vulnerable to the prompt effect of Pb(2+), showed weak tolerance to Hg(2+) and proved to be tolerant to Cr(6+). The reaction center controlled electron transfer in Rvx. gelatinosus demonstrated the highest degree of resistance against heavy metal exposure.

Diversity of purple nonsulfur bacteria in shrimp ponds with varying mercury levels

This research aimed to study the diversity of purple nonsulfur bacteria (PNSB) and to investigate the effect of Hg concentrations in shrimp ponds on PNSB diversity. Amplification of the pufM gene was detected in 13 and 10 samples of water and sediment collected from 16 shrimp ponds in Southern Thailand. In addition to PNSB, other anoxygenic phototrophic bacteria (APB) were also observed; purple sulfur bacteria (PSB) and aerobic anoxygenic phototrophic bacteria (AAPB) although most of them could not be identified. Among identified groups; AAPB, PSB and PNSB in the samples of water and sediment were 25.71, 11.43 and 8.57%; and 27.78, 11.11 and 22.22%, respectively. In both sample types, Roseobacter denitrificans (AAPB) was the most dominant species followed by Halorhodospira halophila (PSB). In addition two genera, observed most frequently in the sediment samples were a group of PNSB (Rhodovulum kholense, Rhodospirillum centenum and Rhodobium marinum). The UPGMA dendrograms showed 7 and 6 clustered groups in the water and sediment samples, respectively. There was no relationship between the clustered groups and the total Hg (Hg_T) concentrations in the water and sediment samples used (<0.002–0.03 μg/L and 35.40–391.60 μg/kg dry weight) for studying the biodiversity. It can be concluded that there was no effect of the various Hg levels on the diversity of detected APB species; particularly the PNSB in the shrimp ponds.