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1.
Nat Commun ; 12(1): 4774, 2021 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-34362886

RESUMO

Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.


Assuntos
Chromatiaceae/metabolismo , Molibdênio/metabolismo , Fixação de Nitrogênio , Nitrogênio/metabolismo , Biomassa , Ciclo do Carbono , Dióxido de Carbono , Tamanho Celular , Chromatiaceae/genética , Metagenoma , Modelos Teóricos , Nitrogenase/metabolismo , Oceanos e Mares , Análise de Célula Única
2.
J Phys Chem B ; 125(35): 9979-9989, 2021 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-34460261

RESUMO

The denaturation of globular proteins by high pressure is frequently associated with the release of internal voids and/or the exposure of the hydrophobic protein interior to a polar aqueous solvent. Similar evidence with respect to membrane proteins is not available. Here, we investigate the impact of hydrostatic pressures reaching 12 kbar on light-harvesting 2 integral membrane complexes of purple photosynthetic bacteria using two types of innate chromophores in separate strategic locations: bacteriochlorophyll-a in the hydrophobic interior and tryptophan at both protein-solvent interfacial gateways to internal voids. The complexes from mutant Rhodobacter sphaeroides with low resilience against pressure were considered in parallel with the naturally robust complexes of Thermochromatium tepidum. In the former case, a firm correlation was established between the abrupt blue shift of the bacteriochlorophyll-a exciton absorption, a known indicator of the breakage of tertiary structure pigment-protein hydrogen bonds, and the quenching of tryptophan fluorescence, a supposed result of further protein solvation. No such effects were observed in the reference complex. While these data may be naively taken as supporting evidence of the governing role of hydration, the analysis of atomistic model structures of the complexes confirmed the critical part of the structure in the pressure-induced denaturation of the membrane proteins studied.


Assuntos
Chromatiaceae , Rhodobacter sphaeroides , Proteínas de Bactérias , Pressão Hidrostática , Complexos de Proteínas Captadores de Luz , Proteínas de Membrana
3.
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
4.
Environ Sci Technol ; 55(12): 8410-8421, 2021 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-34078080

RESUMO

Although denitrification-dependent chemolithotrophic sulfur oxidizers proliferated in tsunami-deposited marine sediment with nitrate amendment, their ecophysiological roles in biogeochemical carbon transfer are not addressed. We employed time-resolved high-sensitivity 13C-bicarbonate probing of rRNA to unveil the carbon fixation and resulting trophic relationship of the nitrate-amended sediment microorganisms. Nitrate reduction and sulfur oxidation co-occurred along with significant decreases in the 13CO2 and dissolved bicarbonate concentrations for the first 4 days of the incubation, during which the denitrification-dependent sulfur-oxidizing chemolithotrophs, i.e., the Sulfurimonas sp. HDS01 and Thioalkalispira sp. HDS22 relatives, and the sulfate-reducing heterotrophs, i.e., the Desulfobulbus spp. and Desulfofustis glycolicus relatives, actively incorporated 13C. These indicated that the sulfur oxidizers and sulfate reducers were tightly associated with each other through the direct carbon transfer. Relatives of the fermentative Thalassomonas sediminis and the hydrolytic Pararheinheimera aquatica, in addition to various sulfur-cycling microorganisms, significantly assimilated 13C at day 14. Although the incorporation of 13C was not detected, a syntrophic volatile-fatty-acid oxidizer and hydrogenotrophic methanogens significantly expressed their 16S rRNA molecules at day 21, indicating the metabolic activation of these final decomposers under the latter nutrient-limited conditions. The results demonstrated the nitrate-driven trophic association of sulfur-cycling microorganisms and the subsequent microbial activation and diversification, triggering the restoration of the marine ecosystem function.


Assuntos
Bicarbonatos , Nitratos , Chromatiaceae , Deltaproteobacteria , Ecossistema , Gammaproteobacteria , Sedimentos Geológicos , Oxirredução , Filogenia , RNA Ribossômico 16S/genética , Enxofre , Tsunamis
5.
J Biosci Bioeng ; 132(2): 174-182, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34074597

RESUMO

Alcaligenaceae and Chromatiaceae were previously reported as the specific pollution bioindicators in the receiving river water contaminated by palm oil mill effluent (POME) final discharge. Considering the inevitable sensitivity of bacteria under environmental stresses, it is crucial to assess the survivability of both bacteria in the fluctuated environmental factors, proving their credibility as POME pollution bioindicators in the environment. In this study, the survivability of Alcaligenaceae and Chromatiaceae from facultative pond, algae (aerobic) pond and final discharge were evaluated under varying sets of temperature (25-40°C), pH (pH 7-9) and low/high total suspended solid (TSS) contents of POME collected during low/high crop seasons of oil palm, respectively. Following treatment, the viability status and compositions of the bacterial community were assessed using flow cytometry-based assay and high-throughput Illumina MiSeq, respectively, in correlation with the changes of physicochemical properties. The changes in temperature, pH and TSS indeed changed the physicochemical properties of POME. The functionality of bacterial cells was also shifted where the viable cells and high nucleic acid contents reduced at elevated levels of temperature and pH but increased at high TSS content. Interestingly, the Alcaligenaceae and Chromatiaceae continuously detected in the samples which accounted for more than 0.5% of relative abundance, with a positive correlation with biological oxygen demand (BOD5) concentration. Therefore, either Alcaligenaceae or Chromatiaceae or both could be regarded as the reliable and specific bacterial indicators to indicate the pollution in river water due to POME final discharge despite the fluctuations in temperature, pH and TSS.


Assuntos
Alcaligenaceae , Chromatiaceae , Biomarcadores Ambientais , Concentração de Íons de Hidrogênio , Resíduos Industriais , Óleo de Palmeira , Óleos Vegetais , Temperatura , Eliminação de Resíduos Líquidos
6.
Biosci Biotechnol Biochem ; 85(8): 1846-1852, 2021 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-34124760

RESUMO

Hydrogenophilus thermoluteolus, Thermochromatium tepidum, and Allochromatium vinosum, which grow optimally at 52, 49, and 25 °C, respectively, have homologous cytochromes c' (PHCP, TTCP, and AVCP, respectively) exhibiting at least 50% amino acid sequence identity. Here, the thermal stability of the recombinant TTCP protein was first confirmed to be between those of PHCP and AVCP. Structure comparison of the 3 proteins and a mutagenesis study on TTCP revealed that hydrogen bonds and hydrophobic interactions between the heme and amino acid residues were responsible for their stability differences. In addition, PHCP, TTCP, and AVCP and their variants with altered stability similarly bound nitric oxide and carbon oxide, but not oxygen. Therefore, the thermal stability of TTCP together with PHCP and AVCP can be tuned through specific interactions around the heme without affecting their gas-binding function. These cytochromes c' will be useful as specific gas sensor proteins exhibiting a wide thermal stability range.


Assuntos
Proteínas de Bactérias/metabolismo , Chromatiaceae/enzimologia , Citocromos c'/metabolismo , Gases/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Chromatiaceae/crescimento & desenvolvimento , Dicroísmo Circular , Cristalografia por Raios X , Citocromos c'/química , Ligação Proteica , Conformação Proteica , Desnaturação Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Homologia de Sequência de Aminoácidos , Temperatura
7.
J Phys Chem B ; 125(14): 3538-3545, 2021 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-33818091

RESUMO

The excitation energy transfer (EET) from the bacteriochlorophyll (BChl) Soret band to the second excited state(s) (S2) of carotenoids in pigment-protein complexes of purple bacteria was investigated. The efficiency of EET was determined, based on fluorescence excitation and absorption spectra of chromatophores, peripheral light-harvesting complexes (LH2), core complexes (LH1-RC), and pigments in solution. Carotenoid-containing and carotenoid-less samples were compared: LH1-RC and LH2 from Allochromatium minutissimum, Ectothiorhodospira haloalkaliphila, and chromatophores from Rhodobacter sphaeroides and Rhodospirillum rubrum wild type and carotenoid-free strains R-26 and G9. BChl-to-carotenoid EET was absent, or its efficiency was less than the accuracy of the measurements of ∼5%. Quantum chemical calculations support the experimental results: The transition dipole moments of spatially close carotenoid/BChl pairs were found to be nearly orthogonal. The structural arrangements suggest that Soret EET may be lacking for the studied systems, however, EET from carotenoids to Qx appears to be possible.


Assuntos
Complexo de Proteínas do Centro de Reação Fotossintética , Rhodobacter sphaeroides , Bacterioclorofilas , Carotenoides , Chromatiaceae , Ectothiorhodospira , Transferência de Energia , Complexos de Proteínas Captadores de Luz/metabolismo , Complexo de Proteínas do Centro de Reação Fotossintética/metabolismo , Proteobactérias/metabolismo , Rhodobacter sphaeroides/metabolismo , Espectrometria de Fluorescência
8.
Nat Commun ; 12(1): 1104, 2021 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-33597527

RESUMO

Photosynthetic electron transfers occur through multiple components ranging from small soluble proteins to large integral membrane protein complexes. Co-crystallization of a bacterial photosynthetic electron transfer complex that employs weak hydrophobic interactions was achieved by using high-molar-ratio mixtures of a soluble donor protein (high-potential iron-sulfur protein, HiPIP) with a membrane-embedded acceptor protein (reaction center, RC) at acidic pH. The structure of the co-complex offers a snapshot of a transient bioenergetic event and revealed a molecular basis for thermodynamically unfavorable interprotein electron tunneling. HiPIP binds to the surface of the tetraheme cytochrome subunit in the light-harvesting (LH1) complex-associated RC in close proximity to the low-potential heme-1 group. The binding interface between the two proteins is primarily formed by uncharged residues and is characterized by hydrophobic features. This co-crystal structure provides a model for the detailed study of long-range trans-protein electron tunneling pathways in biological systems.


Assuntos
Proteínas de Bactérias/química , Chromatiaceae/metabolismo , Proteínas Ferro-Enxofre/química , Complexos de Proteínas Captadores de Luz/química , Fotossíntese , Complexo de Proteínas do Centro de Reação Fotossintética/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Cristalização , Citocromos/química , Citocromos/metabolismo , Transporte de Elétrons , Heme/análogos & derivados , Heme/química , Heme/metabolismo , Proteínas Ferro-Enxofre/metabolismo , Complexos de Proteínas Captadores de Luz/metabolismo , Modelos Moleculares , Complexo de Proteínas do Centro de Reação Fotossintética/metabolismo , Conformação Proteica , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
9.
Carbohydr Polym ; 256: 117592, 2021 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-33483078

RESUMO

Historical monuments are increasingly being threatened by unexpected microbial colonizers, leading to their subsequent deterioration. Here, two tetraalkylphosphonium polyoxometalate ionic liquids (Q14-IL and Q16-IL) were successfully synthesized, which showed excellent antibacterial activity against four bacteria colonising wall paintings. Notably, Q14-IL exhibited superior antibacterial efficacy compared to longer alkyl Q16-IL. Additionally, polyvinyl alcohol/chitosan (PVA-CS) hydrogels containing two ILs were prepared, and the morphology, thermal stability, swelling ratio and antibacterial activity were systematically evaluated. The results suggest that higher CS content resulted in more uniform micropores and increased the swelling ratio. However, fewer antibacterial ILs were released and diffused over time from the matrix. Hydrogels with 5% CS content exhibited the highest antibacterial activity, which was mainly attributed to the synergetic antibacterial activity of positively charged ammonium (-NH3+) groups of CS and quaternary phosphonium cation of ILs. This study may provide an alternative strategy for fighting against bacterial communities colonising ancient artworks.


Assuntos
Antibacterianos/química , Bactérias/efeitos dos fármacos , Quitosana/química , Hidrogéis/química , Líquidos Iônicos/química , Pinturas , Álcool de Polivinil/química , Bacillus cereus/efeitos dos fármacos , Biofilmes/efeitos dos fármacos , Chromatiaceae/efeitos dos fármacos , Difusão , Micrococcus/efeitos dos fármacos , Microscopia Eletrônica de Transmissão , Espectroscopia de Infravermelho com Transformada de Fourier , Eletricidade Estática , Difração de Raios X
10.
Arch Microbiol ; 203(1): 97-105, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32757114

RESUMO

In a conserved culture of the purple sulfur bacterium Thiospirillum jenense DSM216T, cells of this species were easily recognized by cell morphology, large-size spirilla and visible flagellar tuft. The Tsp. jenense genome is 3.22 Mb in size and has a GC content of 48.7 mol%. It was readily identified as a member of the Chromatiaceae by the complement of proteins in its genome. A whole genome comparison clearly placed Tsp. jenense near Thiorhodovibrio and Rhabdochromatium species and somewhat more distant from Thiohalocapsa and Halochromatium species. This relationship was also found with the sequences of the photosynthetic reaction center protein PufM. The genome sequence supported important properties of this bacterium: the presence of ribulose-bisphosphate carboxylase and enzymes of the Calvin cycle of autotrophic carbon dioxide fixation but the absence of carboxysomes, an incomplete tricarboxylic acid cycle and the lack of malate dehydrogenase, the presence of a sulfur oxidation pathway including adenylylsulfate reductase (aprAB) but absence of assimilatory sulfate reduction, the presence of hydrogenase (hoxHMFYUFE), nitrogenase and a photosynthetic gene cluster (pufBALMC). The FixNOP type of cytochrome oxidase was notably lacking, which may be the reason that renders the cells highly sensitive to oxygen. Two minor phototrophic contaminants were found using metagenomic binning: one was identified as a strain of Rhodopseudomonas palustris and the second one has an average nucleotide identity of 82% to the nearest neighbor Rhodoferax antarcticus. It should be considered as a new species of this genus and Rhodoferax jenense is proposed as the name.


Assuntos
Chromatiaceae/classificação , Chromatiaceae/genética , Genoma Bacteriano/genética , Filogenia , Composição de Bases , Comamonadaceae/classificação , Comamonadaceae/genética , Nitrogenase/genética , Fotossíntese/genética , Complexo de Proteínas do Centro de Reação Fotossintética/genética , Rodopseudomonas/classificação , Rodopseudomonas/genética
11.
J Biomol Struct Dyn ; 39(8): 2771-2787, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-32276557

RESUMO

The gamma-proteobacteria Allochromatium vinosum DSM 180T (A. vinosum) encodes the sulfur oxidizing dsr operon comprising of 15 genes. Dsr proteins are involved in oxidation of sulfur globules produced as an obligatory intermediate during the sulfur oxidation process. The dsrA and dsrB gene products are known to function as a α2ß2 hetero-tetramer and the protein complex plays the catalytic role in sulfur oxidation process. DsrC has a highly conserved C-terminal domain that forms a flexible arm, where two strictly conserved cysteines were found to act as a substrate donating residue for DsrAB instead of being a subunit of this redox enzyme. Therefore, to elucidate the molecular mechanism of the sulfur oxidation process here an attempt was made to study the dynamics, stability and binding mechanisms of DsrAB and DsrC proteins through computational docking and molecular dynamics (MD) simulations. This structure function relationship investigation revealed that the C-terminal domain of DsrC interacts with DsrA of DsrAB protein complex for catalytic functions. Some basic amino acid residues of DsrC are found to form the catalytic pockets along with DsrAB protein complex where the sulfur anions bind to get oxidized. Structural dynamics and fluctuations as well as the secondary structural alterations study revealed the possible regions responsible for protein-protein interactions. Principal Component Analysis (PCA) of protein motions displayed that the collective motions of DsrAB-DsrC complex was higher and more anti-correlated than the unbound DsrAB form. The present molecular insight study would therefore help researchers to predict the plausible biochemical mechanism of sulfur oxidation process in sulfur metabolic pathways in near future. Communicated by Ramaswamy H. Sarma.


Assuntos
Proteínas de Bactérias , Proteobactérias , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Chromatiaceae , Oxirredução , Proteobactérias/metabolismo , Enxofre
12.
Biochim Biophys Acta Bioenerg ; 1862(1): 148307, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-32926863

RESUMO

Redox-active quinones play essential roles in efficient light energy conversion in type-II reaction centers of purple phototrophic bacteria. In the light-harvesting 1 reaction center (LH1-RC) complex of purple bacteria, QB is converted to QBH2 upon light-induced reduction and QBH2 is transported to the quinone pool in the membrane through the LH1 ring. In the purple bacterium Rhodobacter sphaeroides, the C-shaped LH1 ring contains a gap for quinone transport. In contrast, the thermophilic purple bacterium Thermochromatium (Tch.) tepidum has a closed O-shaped LH1 ring that lacks a gap, and hence the mechanism of photosynthetic quinone transport is unclear. Here we detected light-induced Fourier transform infrared (FTIR) signals responsible for changes of QB and its binding site that accompany photosynthetic quinone reduction in Tch. tepidum and characterized QB and QBH2 marker bands based on their 15N- and 13C-isotopic shifts. Quinone exchanges were monitored using reconstituted photosynthetic membranes comprised of solubilized photosynthetic proteins, membrane lipids, and exogenous ubiquinone (UQ) molecules. In combination with 13C-labeling of the LH1-RC and replacement of native UQ8 by ubiquinones of different tail lengths, we demonstrated that quinone exchanges occur efficiently within the hydrophobic environment of the lipid membrane and depend on the side chain length of UQ. These results strongly indicate that unlike the process in Rba. sphaeroides, quinone transport in Tch. tepidum occurs through the size-restricted hydrophobic channels in the closed LH1 ring and are consistent with structural studies that have revealed narrow hydrophobic channels in the Tch. tepidum LH1 transmembrane region.


Assuntos
Proteínas de Bactérias/química , Chromatiaceae/enzimologia , Complexos de Proteínas Captadores de Luz/química , Ubiquinona/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Transporte Biológico Ativo , Complexos de Proteínas Captadores de Luz/metabolismo , Oxirredução , Ubiquinona/metabolismo
13.
Biochemistry (Mosc) ; 85(7): 773-780, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33040721

RESUMO

Phytoene and phytofluene - uncolored C40 carotenoids with short chain of conjugated double bonds (3 and 5, respectively) - are known to be universal precursors in biosynthesis of colored carotenoids in photosynthesizing organisms. It is commonly recognized that C40 carotenoids are photoprotectors of cells and tissues. We have shown that phytofluene is an exception to this rule. By measuring photosensitized phosphorescence of singlet oxygen (1O2) we found out that phytofluene was very effective photosensitizer of 1O2 formation in aerated solutions under UVA irradiation (quantum yield of 85 ± 5%), whereas phytoene was almost inactive in this process. It was demonstrated that both carotenoids quench singlet oxygen in the dark. The obtained quenching rate constants [(4 ± 1) × 106 M-1·s-1 for phytoene and (2 ± 0.5) × 107 M-1·s-1 for phytofluene] were smaller than the rate constant of the diffusion-controlled reactions by 3-4 orders of magnitude. Thus, both carotenoids displayed rather weak protector properties. Moreover, phytofluene due to its high photosensitizing activity might be considered as a promoter of cell photodamage and a promising UVA photosensitizer for medical purposes.


Assuntos
Carotenoides/química , Carotenoides/metabolismo , Oxigênio Singlete/química , Chromatiaceae/metabolismo , Ectothiorhodospira/metabolismo , Oxigênio/metabolismo , Fotoquímica/métodos , Fármacos Fotossensibilizantes/química , Oxigênio Singlete/metabolismo
14.
Nat Commun ; 11(1): 4955, 2020 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-33009385

RESUMO

The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αß-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αß-polypeptides that are hydrogen-bonded to BChl a. The Ca2+-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and ß-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside.


Assuntos
Cálcio/metabolismo , Microscopia Crioeletrônica , Complexos de Proteínas Captadores de Luz/ultraestrutura , Peptídeos/metabolismo , Fotossíntese , Sequência de Aminoácidos , Bacterioclorofila A/metabolismo , Sítios de Ligação , Chromatiaceae/metabolismo , Detergentes/química , Dimerização , Complexos de Proteínas Captadores de Luz/química , Complexos de Proteínas Captadores de Luz/metabolismo , Lipídeos/química , Peptídeos/química , Quinonas/química
15.
Int J Syst Evol Microbiol ; 70(12): 6188-6194, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33052808

RESUMO

A Gram-stain-negative, rod-shaped, motile and strictly aerobic bacterium, designated LHK132T, was isolated from a mangrove sediment sample collected in Haikou, Hainan Province, PR China. Strain LHK132T was able to grow at temperatures of 10-45 °C, at salinities of 0-7.0 % (w/v) and at pH 6.0-9.0. Catalase and oxidase activities, H2S production, urease and methyl red reaction were positive. Indole, nitrate reduction, hydrolysis of gelatin, starch, casein and Tweens 20, 40, 60 and 80 were negative. The major cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. According to 16S rRNA gene sequence analysis, strain LHK132T had 98.3, 97.5, 97.4, 97.2 and 97.1% similarities to Rheinheimera soli BD-d46T, Rheinheimera sediminis YQF-1T, Rheinheimera tangshanensis JA3-B52T, Rheinheimera mesophila IITR-13T and Rheinheimera arenilitoris J-MS1T, respectively. Phylogenetic analyses indicated that strain LHK132T formed a distinct lineage with R. soli BD-d46T within the genus Rheinheimera. The average nucleotide identity and digital DNA-DNA hybridization values between strain LHK132T and related species of the genus Rheinheimera were well below the thresholds for species delineation. The DNA G+C content was 46.7 mol%. On the basis of its phenotypic, chemotaxonomic and genotypic data, strain LHK132T is considered a representative of a novel species in the genus Rheinheimera, for which the name Rheinheimera mangrovi sp. nov. is proposed. The type strain is LHK132T (=KCTC 62580T=MCCC 1K03529T).


Assuntos
Chromatiaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Áreas Alagadas , Técnicas de Tipagem Bacteriana , Composição de Bases , China , Chromatiaceae/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
16.
Int J Syst Evol Microbiol ; 70(11): 5701-5710, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32931408

RESUMO

A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were the major pigments. Dense liquid cultures were red in colour. Strain No.7T was able to grow photoautotrophically using sulfide, thiosulfate, sulfite and hydrogen (in the presence of sulfide) as electron donors and bicarbonate as the sole carbon source. Optimum growth occurred under anaerobic conditions in the light at 50 °C (range, 40-56 °C) and pH 7.2 (range, pH 7-8). Major fatty acids were C16 : 0 (46.8 %), C16 : 1 ω7c (19.9 %), C18 : 1 ω7c (21.1 %), C14 : 0 (4.6 %) and C18 : 0 (2.4 %). The polar lipid profile showed phosphatidylglycerol and unidentified aminophospholipids to be the major lipids. The only quinone detected was ubiquinone-8. 16S rRNA gene sequence comparisons indicated that the novel bacterium is only distantly related to Thermochromatium tepidum with a nucleotide identity of 90.4 %. The phylogenetic analysis supported the high novelty of strain No.7T with a long-branching phylogenetic position within the Chromatiaceae next to Thermochromatium tepidum. The genome comprised a circular chromosome of 2.99 Mbp (2 989 870 bp), included no plasmids and had a DNA G+C content of 61.2 mol%. Polyphasic taxonomic analyses of the isolate suggested strain No.7T is a novel genus within the Chromatiaceae. The proposed genus name of the second truly thermophilic purple sulphur bacterium is Caldichromatium gen. nov. with the type species Caldichromatium japonicum sp. nov. (DSM 110881=JCM 39101).


Assuntos
Chromatiaceae/classificação , Fontes Termais/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Chromatiaceae/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Japão , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sulfetos , Enxofre , Tiossulfatos , Ubiquinona/química
17.
Curr Protein Pept Sci ; 21(10): 993-1010, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32778023

RESUMO

Ligand-linked changes in the aggregation state of biological macromolecules occur and have importance in several physiological processes, e.g., the response of hormone receptors, cooperative ligand binding, and others. The mathematical formalisms that express the thermodynamics governing these processes are complex, as they are required to describe observations made under experimental conditions in which many parameters may be simultaneously varied. The description of the functional behaviour of proteins that present ligand-linked association-dissociation events must accommodate cases where both the binding stoichiometries and reaction mechanisms are variable. In this paper, we review some paradigmatic cases that cover different structural arrangements and binding modes, with special attention to the case of dissociating homodimeric transport proteins and receptors. Even though we cannot pretend to be comprehensive on the proteins presenting this behaviour, we believe that we can attempt to be comprehensive on the structural arrangements and thermodynamic properties of these systems, which fall into a limited set of possible types.


Assuntos
Monóxido de Carbono/química , Citocromos c/química , Fator de Crescimento Epidérmico/química , Hemoglobinas/química , Fator de Crescimento Derivado de Plaquetas/química , Animais , Sítios de Ligação , Monóxido de Carbono/metabolismo , Chromatiaceae/metabolismo , Citocromos c/genética , Citocromos c/metabolismo , Fator de Crescimento Epidérmico/genética , Fator de Crescimento Epidérmico/metabolismo , Receptores ErbB/química , Receptores ErbB/genética , Receptores ErbB/metabolismo , Hemoglobinas/genética , Hemoglobinas/metabolismo , Humanos , Cinética , Ligantes , Fator de Crescimento Derivado de Plaquetas/genética , Fator de Crescimento Derivado de Plaquetas/metabolismo , Ligação Proteica , Multimerização Proteica , Scapharca/metabolismo , Estereoisomerismo , Termodinâmica
18.
Sci Rep ; 10(1): 10870, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32616837

RESUMO

Ophidiomycosis (snake fungal disease) is caused by the fungus Ophidiomyces ophiodiicola and threatens snake health worldwide. It has been documented throughout the eastern United States and severe cases have recently been reported in Georgia, USA. To evaluate disease distribution and prevalence in this state, 786 free-ranging snakes were examined for skin lesions consistent with ophidiomycosis and swabbed to detect O. ophiodiicola DNA using qPCR. Sampled snakes represented 34 species and 4 families; 27.5% had skin lesions, 13.3% were positive for O. ophiodiicola DNA, and 77.8% of the qPCR positive individuals had skin lesions. This is the first report of O. ophiodiicola in five of the 22 species that were qPCR positive. Multinomial logistic regression modeling indicated that Drymarchon couperi had a higher relative risk of apparent ophidiomycosis (lesions present and qPCR positive), and the best models predicting qPCR result and ophidiomycosis category included individual factors and excluded temporal and spatial factors. Phylogeny-based bipartite network analysis showed that Nerodia erythrogaster, Nerodia taxispilota, and D. couperi had the highest prevalence of apparent ophidiomycosis; this category was more prevalent in the subfamily Colubrinae and less prevalent in Natricinae. These results provide important information about ophidiomycosis epidemiology, which has implications for snake conservation.


Assuntos
Doenças dos Animais/epidemiologia , Doenças dos Animais/microbiologia , Chromatiaceae/fisiologia , Especificidade de Hospedeiro , Filogenia , Serpentes/classificação , Serpentes/microbiologia , Animais , Feminino , Georgia/epidemiologia , Masculino
19.
J Biosci Bioeng ; 130(2): 179-186, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32381439

RESUMO

The sediment-water interface is not only an important location for substrate conversion in a mariculture system, but also a major source of eutrophication. This study aimed to clarify the characteristics of inorganic nitrogen (ammonia, nitrite and nitrate) removal by Marichromatium gracile YL28 in the presence of both organic nitrogen and inorganic nitrogen. The results showed that, in the presence of peptone or urea, seaweed oligosaccharides (SOS) effectively enhanced the ammonia removal capacity of YL28 (6.42 mmol/L) and decreased the residual rate by 54.04% or 8.17%, respectively. With increasing peptone or urea concentrations, the removal of both ammonia and nitrate was gradually inhibited, and the residual rates of ammonia and nitrate reached 22.56-34.36% and 12.03-15.64% in the peptone system and 20.65-24.03% and 12.20-13.21% in the urea system, respectively. However, in the control group the residual rates of ammonia and nitrate reached 11.97% and 5.12%, respectively. In addition, the concentrations of peptone and urea did not affect nitrite removal, and YL28 displayed better cell growth and nitrogen removal activity in the presence of bait and SOS. Overall, the ability of YL28 to remove inorganic nitrogen was enhanced in the presence of organic nitrogen.


Assuntos
Aquicultura , Chromatiaceae/metabolismo , Nitrogênio/química , Nitrogênio/isolamento & purificação , Peptonas/farmacologia , Ureia/farmacologia , Água/química , Amônia/isolamento & purificação , Amônia/metabolismo , Desnitrificação/efeitos dos fármacos , Nitratos/isolamento & purificação , Nitratos/metabolismo , Nitritos/isolamento & purificação , Nitritos/metabolismo
20.
Photosynth Res ; 145(2): 83-96, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32430765

RESUMO

All purple photosynthetic bacteria contain RC-LH1 'Core' complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC-LH1 'Core' complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC-LH1 'Core' complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.


Assuntos
Chromatiaceae/metabolismo , Complexos de Proteínas Captadores de Luz/metabolismo , Fotossíntese , Complexo de Proteínas do Centro de Reação Fotossintética/metabolismo , Rhodobacter sphaeroides/metabolismo , Rodopseudomonas/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Benzoquinonas/metabolismo , Chromatiaceae/genética , Transferência de Energia , Variação Genética , Complexos de Proteínas Captadores de Luz/química , Complexos de Proteínas Captadores de Luz/genética , Modelos Moleculares , Complexo de Proteínas do Centro de Reação Fotossintética/química , Complexo de Proteínas do Centro de Reação Fotossintética/genética , Conformação Proteica , Rhodobacter sphaeroides/genética , Rodopseudomonas/genética , Relação Estrutura-Atividade
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