Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 478
Filtrar
1.
Int J Mol Sci ; 22(12)2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-34203823

RESUMO

There are two main types of bacterial photosynthesis: oxygenic (cyanobacteria) and anoxygenic (sulfur and non-sulfur phototrophs). Molecular mechanisms of photosynthesis in the phototrophic microorganisms can differ and depend on their location and pigments in the cells. This paper describes bacteria capable of molecular oxidizing hydrogen sulfide, specifically the families Chromatiaceae and Chlorobiaceae, also known as purple and green sulfur bacteria in the process of anoxygenic photosynthesis. Further, it analyzes certain important physiological processes, especially those which are characteristic for these bacterial families. Primarily, the molecular metabolism of sulfur, which oxidizes hydrogen sulfide to elementary molecular sulfur, as well as photosynthetic processes taking place inside of cells are presented. Particular attention is paid to the description of the molecular structure of the photosynthetic apparatus in these two families of phototrophs. Moreover, some of their molecular biotechnological perspectives are discussed.


Assuntos
Chlorobi/genética , Chlorobi/fisiologia , Chromatiaceae/genética , Chromatiaceae/fisiologia , Processos Fototróficos/genética , Anaerobiose , Chlorobi/classificação , Chromatiaceae/classificação , Filogenia , Enxofre/metabolismo
2.
J Phys Chem B ; 125(30): 8313-8324, 2021 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-34314175

RESUMO

The structural basis for the spectral differences between the Fenna-Matthews-Olson (FMO) proteins from Chlorobaculum tepidum (C. tepidum) and Prosthecochloris aestuarii 2K (P. aestuarii) is yet to be fully understood. Mutation-induced perturbation to the exciton structure and the optical spectra of the complex provide a suitable means to investigate the critical role played by the protein scaffold. In this work, we have performed quantum-mechanics/molecular-mechanics calculations over the molecular dynamics simulation trajectories with the polarized protein-specific charge scheme for both wild-type FMOs and two mutants. Our result reveals that a single-point mutation in the vicinity of BChl 6, namely, W183F of C. tepidum, significantly affects the absorption spectrum, resulting in a switch of the absorption spectrum from type 2, for which the 806 nm band is more pronounced than the 815 nm band, to type 1, for which the 815 nm band is pronounced. Our observations agree with the single-point mutation experiments reported by Saer et al. (Biochim. Biophys. Acta, Bioenerg. 2017, 1858, 288-296) and Khmelnitskiy et al. (J. Phys. Chem. Lett. 2018, 9, 3378-3386). In contrast, the absorption spectrum of the P. aestuarii experiences the opposite transition (from type 1 to type 2) upon the same mutation. Furthermore, by comparing the contributions of individual pigments to the spectra in the wild type and its mutant, we find that a single-point mutation near BChl 6 not only induces changes in excitation energy of BChl 6 per se but also affects the excitonic structures of the neighboring BChls 5 and 7 through strong interpigment electronic couplings, resulting in a significant change in the absorption spectra.


Assuntos
Chlorobi , Proteínas de Bactérias/genética , Chlorobi/metabolismo , Complexos de Proteínas Captadores de Luz/genética , Complexos de Proteínas Captadores de Luz/metabolismo , Simulação de Dinâmica Molecular
3.
Bioorg Med Chem Lett ; 40: 127931, 2021 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-33705911

RESUMO

Green photosynthetic bacteria with an efficient light-harvesting system contain special chlorophyll molecules, called bacteriochlorophylls c, d, e, in their main antennae. In the biosynthetic pathway, a BciC enzyme is proposed to catalyze the hydrolysis of the C132-methoxycarbonyl group of chlorophyllide a, but the resulting C132-carboxy group has not been detected yet because it is spontaneously removed due to the instability of the ß-keto-carboxylic acid. In this study, the in vitro BciC enzymatic reactions of zinc methyl (131R/S)-hydroxy-mesochlorophyllides a were examined and a carboxylic acid possessing the C132S-OH was first observed as the hydrolyzed product of the C132-COOCH3.


Assuntos
Hidrolases de Éster Carboxílico/metabolismo , Clorofilídeos/metabolismo , Metaloporfirinas/metabolismo , Proteínas de Bactérias/metabolismo , Chlorobi/enzimologia , Clorofilídeos/química , Hidrólise , Metaloporfirinas/química , Estrutura Molecular , Zinco/química
4.
Molecules ; 26(4)2021 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-33572047

RESUMO

Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.


Assuntos
Proteínas de Bactérias/química , Bacterioclorofilas/metabolismo , Chlorobi/metabolismo , Complexos de Proteínas Captadores de Luz/química , Organelas/metabolismo , Fotossíntese , Proteínas de Bactérias/metabolismo , Bacterioclorofilas/química , Complexos de Proteínas Captadores de Luz/efeitos da radiação , Fenômenos Ópticos , Espectrometria de Fluorescência
5.
Nat Commun ; 12(1): 830, 2021 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-33547297

RESUMO

In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, the influence of the ACM on nitrogen and carbon cycling remains poorly understood. Using a suite of stable isotope tracer experiments, we examined the transformation of nitrogen and carbon under an ACM (comprising of Chlorobiaceae and Synechococcales) and a non-ACM scenario in the anoxic zone of Lake Tanganyika. We find that the ACM hosts a tight coupling of photo/litho-autotrophic and heterotrophic processes. In particular, the ACM was a hotspot of organic matter remineralization that controlled an important supply of ammonium driving a nitrification-anammox coupling, and thereby played a key role in regulating nitrogen loss in the oxygen-deficient zone.


Assuntos
Ciclo do Carbono/fisiologia , Carbono/química , Chlorobi/metabolismo , Ciclo do Nitrogênio/fisiologia , Nitrogênio/química , Synechococcus/metabolismo , Compostos de Amônio/química , Compostos de Amônio/metabolismo , Anaerobiose/fisiologia , Processos Autotróficos , Carbono/metabolismo , Chlorobi/química , Clorofila/química , Clorofila/metabolismo , República Democrática do Congo , Ecossistema , Marcação por Isótopo , Lagos/química , Lagos/microbiologia , Nitrificação/fisiologia , Nitrogênio/metabolismo , Oxirredução , Synechococcus/química , Tanzânia
6.
ISME J ; 15(6): 1569-1584, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33452481

RESUMO

Temperate phages are viruses of bacteria that can establish two types of infection: a lysogenic infection in which the virus replicates with the host cell without producing virions, and a lytic infection where the host cell is eventually destroyed, and new virions are released. While both lytic and lysogenic infections are routinely observed in the environment, the ecological and evolutionary processes regulating these viral dynamics are still not well understood, especially for uncultivated virus-host pairs. Here, we characterized the long-term dynamics of uncultivated viruses infecting green sulfur bacteria (GSB) in a model freshwater lake (Trout Bog Lake, TBL). As no GSB virus has been formally described yet, we first used two complementary approaches to identify new GSB viruses from TBL; one in vitro based on flow cytometry cell sorting, the other in silico based on CRISPR spacer sequences. We then took advantage of existing TBL metagenomes covering the 2005-2018 period to examine the interactions between GSB and their viruses across years and seasons. From our data, GSB populations in TBL were constantly associated with at least 2-8 viruses each, including both lytic and temperate phages. The dominant GSB population in particular was consistently associated with two prophages with a nearly 100% infection rate for >10 years. We illustrate with a theoretical model that such an interaction can be stable given a low, but persistent, level of prophage induction in low-diversity host populations. Overall, our data suggest that lytic and lysogenic viruses can readily co-infect the same host population, and that host strain-level diversity might be an important factor controlling virus-host dynamics including lytic/lysogeny switch.


Assuntos
Bacteriófagos , Chlorobi , Viroses , Bacteriófagos/genética , Humanos , Lisogenia , Prófagos
7.
Can J Microbiol ; 67(4): 332-341, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33136441

RESUMO

Hot Lake is a small heliothermal and hypersaline lake in far north-central Washington State (USA) and is limnologically unusual because MgSO4 rather than NaCl is the dominant salt. In late summer, the Hot Lake metalimnion becomes distinctly green from blooms of planktonic phototrophs. In a study undertaken over 60 years ago, these blooms were predicted to include green sulfur bacteria, but no cultures were obtained. We sampled Hot Lake and established enrichment cultures for phototrophic sulfur bacteria in MgSO4-rich sulfidic media. Most enrichments turned green or red within 2 weeks, and from green-colored enrichments, pure cultures of a lobed green sulfur bacterium (phylum Chlorobi) were isolated. Phylogenetic analyses showed the organism to be a species of the prosthecate green sulfur bacterium Prosthecochloris. Cultures of this Hot Lake phototroph were halophilic and tolerated high levels of sulfide and MgSO4. In addition, unlike all recognized species of Prosthecochloris, the Hot Lake isolates grew at temperatures up to 45 °C, indicating an adaptation to the warm summer temperatures of the lake. Photoautotrophy by Hot Lake green sulfur bacteria may contribute dissolved organic matter to anoxic zones of the lake, and their diazotrophic capacity may provide a key source of bioavailable nitrogen, as well.


Assuntos
Chlorobi/isolamento & purificação , Chlorobi/fisiologia , Lagos/microbiologia , Chlorobi/classificação , Temperatura Alta , Lagos/química , Sulfato de Magnésio/análise , Sulfato de Magnésio/metabolismo , Fixação de Nitrogênio , Processos Fototróficos , Filogenia , Estações do Ano , Sulfetos/análise , Sulfetos/metabolismo , Washington
8.
Arch Microbiol ; 203(2): 799-808, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33051772

RESUMO

The green sulfur bacterium, Chlorobaculum tepidum, is an anaerobic photoautotroph that performs anoxygenic photosynthesis. Although genes encoding rubredoxin (Rd) and a putative flavodiiron protein (FDP) were reported in the genome, a gene encoding putative NADH-Rd oxidoreductase is not identified. In this work, we expressed and purified the recombinant Rd and FDP and confirmed dioxygen reductase activity in the presence of ferredoxin-NAD(P)+ oxidoreductase (FNR). FNR from C. tepidum and Bacillus subtilis catalyzed the reduction of Rd at rates comparable to those reported for NADH-Rd oxidoreductases. Also, we observed substrate inhibition at high concentrations of NADPH similar to that observed with ferredoxins. In the presence of NADPH, B. subtilis FNR and Rd, FDP promoted dioxygen reduction at rates comparable to those reported for other bacterial FDPs. Taken together, our results suggest that Rd and FDP participate in the reduction of dioxygen in C. tepidum and that FNR can promote the reduction of Rd in this bacterium.


Assuntos
Chlorobi/química , Chlorobi/enzimologia , Ferredoxina-NADP Redutase/metabolismo , Rubredoxinas/metabolismo , Bacillus subtilis/enzimologia , Proteínas de Bactérias/metabolismo , NAD/metabolismo , NADP/metabolismo , Oxirredução , Enxofre/metabolismo
9.
Biochemistry ; 59(49): 4622-4626, 2020 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-33258578

RESUMO

Chlorosomes in green photosynthetic bacteria are the largest and most efficient light-harvesting antenna systems of all phototrophs. The core part of chlorosomes consists of bacteriochlorophyll c, d, or e molecules. In their biosynthetic pathway, a BciC enzyme catalyzes the removal of the C132-methoxycarbonyl group of chlorophyllide a. In this study, the in vitro enzymatic reactions of chlorophyllide a analogues, C132-methylene- and ethylene-inserted zinc complexes, were examined using a BciC protein from Chlorobaculum tepidum. As the products, their hydrolyzed free carboxylic acids were observed without the corresponding demethoxycarbonylated compounds. The results showed that the in vivo demethoxycarbonylation of chlorophyllide a by an action of the BciC enzyme would occur via two steps: (1) an enzymatic hydrolysis of a methyl ester at the C132-position, followed by (2) a spontaneous (nonenzymatic) decarboxylation in the resulting carboxylic acid.


Assuntos
Clorofilídeos/química , Clorofilídeos/metabolismo , Proteínas de Bactérias/metabolismo , Bacterioclorofilas/biossíntese , Bacterioclorofilas/química , Biocatálise , Vias Biossintéticas , Chlorobi/enzimologia , Hidrolases/metabolismo , Hidrólise , Técnicas In Vitro , Estrutura Molecular , Zinco/química
10.
Science ; 370(6519)2020 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-33214250

RESUMO

The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from Chlorobaculum tepidum The GsbRC binds considerably fewer (bacterio)chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.


Assuntos
Proteínas de Bactérias/química , Chlorobi/enzimologia , Fotossíntese , Complexo de Proteína do Fotossistema I/química , Complexo de Proteína do Fotossistema II/química , Microscopia Crioeletrônica , Citoplasma/enzimologia , Transferência de Energia , Periplasma/enzimologia , Conformação Proteica
11.
ISME J ; 14(11): 2732-2747, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32747714

RESUMO

Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron-sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel "Candidatus Chlorobium canadense", encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in "Ca. Chlorobium canadense". Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth's early microbial communities.


Assuntos
Chlorobi , Lagos , Chlorobi/genética , Ferro , Oxirredução , Fotossíntese , Enxofre
12.
Science ; 368(6498): 1490-1495, 2020 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-32587021

RESUMO

Photosynthesis achieves near unity light-harvesting quantum efficiency yet it remains unknown whether there exists a fundamental organizing principle giving rise to robust light harvesting in the presence of dynamic light conditions and noisy physiological environments. Here, we present a noise-canceling network model that relates noisy physiological conditions, power conversion efficiency, and the resulting absorption spectra of photosynthetic organisms. Using light conditions in full solar exposure, light filtered by oxygenic phototrophs, and light filtered under seawater, we derived optimal absorption characteristics for efficient solar power conversion. We show how light-harvesting antennae can be tuned to maximize power conversion efficiency by minimizing excitation noise, thus providing a unified theoretical basis for the observed wavelength dependence of absorption in green plants, purple bacteria, and green sulfur bacteria.


Assuntos
Complexos de Proteínas Captadores de Luz/fisiologia , Fotossíntese , Plantas/metabolismo , Proteobactérias/metabolismo , Adsorção , Chlorobi , Transferência de Energia , Luz , Oxigênio , Energia Solar
13.
Chemosphere ; 256: 127101, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32450355

RESUMO

Previous studies of the dynamics of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have focused on deep stratified lakes. The objective of this study is to present an in-depth investigation of the structure and dynamics of sulfur bacteria (including SRB and SOB) in the water column of shallow freshwater lakes. A cyanobacterial bloom biomass (CBB)-amended mesocosm experiment was conducted in this study, in which water was taken from a shallow eutrophic lake with sulfate levels near 40 mg L-1. Illumina sequencing was used to investigate SRB and SOB species involved in CBB decomposition and the effects of the increases in sulfate input on the water column microbial community structure. The accumulation of dissolved sulfide (∑H2S) produced by SRB during CBB decomposition stimulated the growth of SOB, and ∑H2S was then oxidized back to sulfate by SOB in the water column. Chlorobaculum sequences (the main SOB species in the study) were significantly influenced by increases in sulfate input, with relative abundance increasing approximately four-fold in treatments amended with 40 mg L-1 sulfate (referred to as 40S) when compared to the treatment without additional sulfate addition (referred to as CU). Additionally, an increase in SOB number was observed from day 26-37, concurrent with the decrease in SRB number, indicating the succession of sulfur bacteria. These findings suggest that biological sulfur oxidation and succession of sulfur bacteria occur in the water column during CBB decomposition in shallow freshwater ecosystems, and the increases in sulfate input stimulate microbial sulfur oxidation.


Assuntos
Cianobactérias/crescimento & desenvolvimento , Lagos/microbiologia , Biomassa , Chlorobi , Ecossistema , Oxirredução , Sulfatos , Sulfetos , Enxofre/química
14.
Biochem J ; 477(7): 1203-1218, 2020 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-32167135

RESUMO

Mutations in the Parkinson's disease (PD)-associated protein leucine-rich repeat kinase 2 (LRRK2) commonly lead to a reduction of GTPase activity and increase in kinase activity. Therefore, strategies for drug development have mainly been focusing on the design of LRRK2 kinase inhibitors. We recently showed that the central RocCOR domains (Roc: Ras of complex proteins; COR: C-terminal of Roc) of a bacterial LRRK2 homolog cycle between a dimeric and monomeric form concomitant with GTP binding and hydrolysis. PD-associated mutations can slow down GTP hydrolysis by stabilizing the protein in its dimeric form. Here, we report the identification of two Nanobodies (NbRoco1 and NbRoco2) that bind the bacterial Roco protein (CtRoco) in a conformation-specific way, with a preference for the GTP-bound state. NbRoco1 considerably increases the GTP turnover rate of CtRoco and reverts the decrease in GTPase activity caused by a PD-analogous mutation. We show that NbRoco1 exerts its effect by allosterically interfering with the CtRoco dimer-monomer cycle through the destabilization of the dimeric form. Hence, we provide the first proof of principle that allosteric modulation of the RocCOR dimer-monomer cycle can alter its GTPase activity, which might present a potential novel strategy to overcome the effect of LRRK2 PD mutations.


Assuntos
Proteínas de Bactérias/metabolismo , Chlorobi/metabolismo , GTP Fosfo-Hidrolases/metabolismo , Serina-Treonina Proteína Quinase-2 com Repetições Ricas em Leucina/metabolismo , Domínios Proteicos , Anticorpos de Domínio Único/metabolismo , Proteínas ras/química , Regulação Alostérica , Animais , Camelídeos Americanos , Desenho de Fármacos , Escherichia coli/metabolismo , Hidrólise , Mutação , Doença de Parkinson/tratamento farmacológico , Doença de Parkinson/genética , Multimerização Proteica
15.
J Phys Chem Lett ; 11(5): 1636-1643, 2020 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-32013435

RESUMO

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.


Assuntos
Proteínas de Bactérias/metabolismo , Complexos de Proteínas Captadores de Luz/metabolismo , Simulação de Dinâmica Molecular , Teoria Quântica , Proteínas de Bactérias/química , Bacterioclorofila A/química , Bacterioclorofila A/metabolismo , Chlorobi/metabolismo , Dicroísmo Circular , Transferência de Energia , Gases/química , Complexos de Proteínas Captadores de Luz/química , Fotossíntese
16.
Chembiochem ; 21(10): 1473-1480, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-31900999

RESUMO

Bacteriochlorophyll c molecules self-aggregate to form large oligomers in the core part of chlorosomes, which are the main light-harvesting antenna systems of green photosynthetic bacteria. In the biosynthetic pathway of bacteriochlorophyll c, a BciC enzyme catalyzes the removal of the C132 -methoxycarbonyl group of chlorophyllide a, which possesses a free propionate residue at the C17-position and a magnesium ion as the central metal. The in vitro C132 -demethoxycarbonylations of chlorophyll a derivatives with various alkyl propionate residues and central metals were examined by using the BciC enzyme derived from one green sulfur bacteria species, Chlorobaculum tepidum. The BciC enzymatic reactions of zinc pheophorbide a alkyl esters were gradually suppressed with an increase of the alkyl chain length in the C17-propionate residue (from methyl to pentyl esters) and finally the hexyl ester became inactive for the BciC reaction. Although not only the zinc but also nickel and copper complexes were demethoxycarbonylated by the BciC enzyme, the reactions were largely dependent on the coordination ability of the central metals: Zn>Ni>Cu. The above substrate specificity indicates that the BciC enzyme would not bind directly to the carboxy group of chlorophyllide a, but would bind to its central magnesium to form the stereospecific complex of BciC with chlorophyllide a, giving pyrochlorophyllide a, which lacks the (132 R)-methoxycarbonyl group.


Assuntos
Proteínas de Bactérias/metabolismo , Bacterioclorofilas/metabolismo , Radioisótopos de Carbono/química , Chlorobi/metabolismo , Clorofila/análogos & derivados , Ésteres/química , Metais/química , Proteínas de Bactérias/química , Bacterioclorofilas/química , Vias Biossintéticas , Catálise , Clorofila/química , Especificidade por Substrato
17.
Phys Chem Chem Phys ; 22(19): 10500-10518, 2020 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-31950960

RESUMO

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.


Assuntos
Bacteriorodopsinas/química , Complexos de Proteínas Captadores de Luz/química , Bacterioclorofila A/química , Beijerinckiaceae/química , Chlorobi/química , Teoria da Densidade Funcional , Modelos Químicos , Retinaldeído/química , Rhodospirillaceae/química
18.
Int J Syst Evol Microbiol ; 70(1): 358-363, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31622236

RESUMO

Two Gram-stain-negative, moderately halophilic bacteria, designated strains ECH52T and KHM46, were isolated from the sediment of a grey saltern located in Sinui island at Shinan, Korea. The isolates were aerobic, non-motile, short rods and grew at 15-45 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 8.0) and with 3-25 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains ECH52T and KHM46 belonged to the genus Aliifodinibius in the family Balneolaceae with sequence similarities of 94.3-98.6 % and showed the highest sequence similarity to Aliifodinibius halophilus 2W32T (98.6 %), A. sediminis YIM J21T (94.7%), A. salicampi KHM44T (94.6 %) and A. roseus YIM D15T (94.3 %). The DNA G+C content of the genomic DNA of strain ECH52T was 40.8 mol%. The predominant isoprenoid quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and four unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic data, strains ECH52T and KHM46 are considered to represent a novel species of the genus Aliifodinibius , for which the name Aliifodinibius saliphilus sp. nov. is proposed. The type strain is ECH52T (=KACC 19126T=NBRC 112664T).


Assuntos
Bacteroides/classificação , Chlorobi/classificação , Filogenia , Lagoas/microbiologia , Salinidade , Técnicas de Tipagem Bacteriana , Bacteroides/isolamento & purificação , Composição de Bases , Chlorobi/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química , Microbiologia da Água
19.
J Chem Theory Comput ; 16(2): 1175-1187, 2020 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-31841349

RESUMO

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.


Assuntos
Proteínas de Bactérias/química , Complexos de Proteínas Captadores de Luz/química , Modelos Moleculares , Teoria Quântica , Proteínas de Bactérias/metabolismo , Bacterioclorofila A/química , Bacterioclorofila A/metabolismo , Chlorobi/metabolismo , Transferência Ressonante de Energia de Fluorescência , Complexos de Proteínas Captadores de Luz/metabolismo
20.
Biochemistry (Mosc) ; 84(11): 1403-1410, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31760926

RESUMO

Genomes of photoautotrophic organisms containing type I photosynthetic reaction center were searched for the rnf genes encoding Na+-translocating ferredoxin:NAD+ oxidoreductase (RNF). These genes were absent in heliobacteria, cyanobacteria, algae, and plants; however, genomes of many green sulfur bacteria (especially marine ones) were found to contain the full rnf operon. Analysis of RNA isolated from the marine green sulfur bacterium Chlorobium phaeovibrioides revealed a high level of rnf expression. It was found that the activity of Na+-dependent flavodoxin:NAD+ oxidoreductase detected in the membrane fraction of Chl. phaeovibrioides was absent in the membrane fraction of the freshwater green sulfur bacterium Chlorobaculum limnaeum, which is closely related to Chl. phaeovibrioides but whose genome lacks the rnf genes. Illumination of the membrane fraction of Chl. phaeovibrioides but not of Cba. limnaeum resulted in the light-induced NAD+ reduction. Based on the obtained data, we concluded that in some green sulfur bacteria, RNF may be involved in the NADH formation that should increase the efficiency of light energy conservation in these microorganisms and can serve as the first example of the use of Na+ energetics in photosynthetic electron transport chains.


Assuntos
Proteínas de Bactérias/metabolismo , Chlorobi/metabolismo , Oxirredutases/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Transporte de Elétrons , Luz , NAD/química , NAD/metabolismo , Oxirredutases/química , Oxirredutases/genética , Fotossíntese , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...