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1.
mBio ; 12(1)2021 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-33402535

RESUMO

Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.IMPORTANCE Our study reveals the ecogenomic traits of microorganisms participating in the cellulose economy of soil. We identified three major categories of participants in this economy: (i) independent primary degraders, (ii) interdependent primary degraders, and (iii) secondary consumers (mutualists, opportunists, and parasites). Trade-offs between independent primary degraders, whose adaptations favor antagonism and competitive exclusion, and interdependent and secondary degraders, whose adaptations favor complex interspecies interactions, are expected to affect the fate of microbially processed carbon in soil. Our findings provide useful insights into the ecological relationships that govern one of the planet's most abundant resources of organic carbon. Furthermore, we demonstrate a novel gradient-resolved approach for stable isotope probing, which provides a cultivation-independent, genome-centric perspective into soil microbial processes.


Assuntos
Agricultura , Celulose/metabolismo , Metagenoma , Microbiologia do Solo , Solo/química , Actinobacteria/genética , Actinobacteria/metabolismo , Actinomycetales/genética , Actinomycetales/metabolismo , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biomassa , Caulobacteraceae/genética , Caulobacteraceae/metabolismo , Celulose/química , Chaetomium/genética , Chaetomium/metabolismo , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Metagenômica , Filogenia , Proteobactérias/genética , Proteobactérias/metabolismo , RNA Ribossômico 16S/genética , Simbiose
2.
Nat Commun ; 11(1): 5598, 2020 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-33154364

RESUMO

Pimelic acid, a seven carbon α,ω-dicarboxylic acid (heptanedioic acid), is known to provide seven of the ten biotin carbon atoms including all those of the valeryl side chain. Distinct pimelate synthesis pathways were recently elucidated in Escherichia coli and Bacillus subtilis where fatty acid synthesis plus dedicated biotin enzymes produce the pimelate moiety. In contrast, the α-proteobacteria which include important plant and mammalian pathogens plus plant symbionts, lack all of the known pimelate synthesis genes and instead encode bioZ genes. Here we report a pathway in which BioZ proteins catalyze a 3-ketoacyl-acyl carrier protein (ACP) synthase III-like reaction to produce pimeloyl-ACP with five of the seven pimelate carbon atoms being derived from glutaryl-CoA, an intermediate in lysine degradation. Agrobacterium tumefaciens strains either deleted for bioZ or which encode a BioZ active site mutant are biotin auxotrophs, as are strains defective in CaiB which catalyzes glutaryl-CoA synthesis from glutarate and succinyl-CoA.


Assuntos
3-Oxoacil-(Proteína de Transporte de Acila) Sintase/metabolismo , Alphaproteobacteria/metabolismo , Biotina/metabolismo , Lisina/metabolismo , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/genética , Proteína de Transporte de Acila/metabolismo , Acil Coenzima A/metabolismo , Adipatos/metabolismo , Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Vias Biossintéticas , Coenzima A-Transferases/genética , Coenzima A-Transferases/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Genes Bacterianos , Glutaratos/metabolismo , Mutação , Ácidos Pimélicos/metabolismo
3.
Nat Commun ; 11(1): 2642, 2020 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-32457313

RESUMO

Bacteria acquire phosphate (Pi) by maintaining a periplasmic concentration below environmental levels. We recently described an extracellular Pi buffer which appears to counteract the gradient required for Pi diffusion. Here, we demonstrate that various treatments to outer membrane (OM) constituents do not affect the buffered Pi because bacteria accumulate Pi in the periplasm, from which it can be removed hypo-osmotically. The periplasmic Pi can be gradually imported into the cytoplasm by ATP-powered transport, however, the proton motive force (PMF) is not required to keep Pi in the periplasm. In contrast, the accumulation of Pi into the periplasm across the OM is PMF-dependent and can be enhanced by light energy. Because the conventional mechanism of Pi-specific transport cannot explain Pi accumulation in the periplasm we propose that periplasmic Pi anions pair with chemiosmotic cations of the PMF and millions of accumulated Pi pairs could influence the periplasmic osmolarity of marine bacteria.


Assuntos
Bactérias/metabolismo , Fosfatos/metabolismo , Alphaproteobacteria/metabolismo , Alphaproteobacteria/efeitos da radiação , Oceano Atlântico , Bactérias/efeitos da radiação , Membrana Celular/metabolismo , Transporte de Íons/efeitos da radiação , Luz , Modelos Biológicos , Concentração Osmolar , Osmose , Periplasma/metabolismo , Fitoplâncton/metabolismo , Fitoplâncton/efeitos da radiação , Prochlorococcus/metabolismo , Prochlorococcus/efeitos da radiação , Força Próton-Motriz , Água do Mar/microbiologia , Synechococcus/metabolismo , Synechococcus/efeitos da radiação
4.
PLoS Genet ; 16(4): e1008724, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32324740

RESUMO

The Alphaproteobacteria show a remarkable diversity of cell cycle-dependent developmental patterns, which are governed by the conserved CtrA pathway. Its central component CtrA is a DNA-binding response regulator that is controlled by a complex two-component signaling network, mediating distinct transcriptional programs in the two offspring. The CtrA pathway has been studied intensively and was shown to consist of an upstream part that reads out the developmental state of the cell and a downstream part that integrates the upstream signals and mediates CtrA phosphorylation. However, the role of this circuitry in bacterial diversification remains incompletely understood. We have therefore investigated CtrA regulation in the morphologically complex stalked budding alphaproteobacterium Hyphomonas neptunium. Compared to relatives dividing by binary fission, H. neptunium shows distinct changes in the role and regulation of various pathway components. Most notably, the response regulator DivK, which normally links the upstream and downstream parts of the CtrA pathway, is dispensable, while downstream components such as the pseudokinase DivL, the histidine kinase CckA, the phosphotransferase ChpT and CtrA are essential. Moreover, CckA is compartmentalized to the nascent bud without forming distinct polar complexes and CtrA is not regulated at the level of protein abundance. We show that the downstream pathway controls critical functions such as replication initiation, cell division and motility. Quantification of the signal flow through different nodes of the regulatory cascade revealed that the CtrA pathway is a leaky pipeline and must involve thus-far unidentified factors. Collectively, the quantitative system-level analysis of CtrA regulation in H. neptunium points to a considerable evolutionary plasticity of cell cycle regulation in alphaproteobacteria and leads to hypotheses that may also hold in well-established model organisms such as Caulobacter crescentus.


Assuntos
Alphaproteobacteria/genética , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Redes Reguladoras de Genes , Fatores de Transcrição/genética , Alphaproteobacteria/metabolismo , Proteínas de Bactérias/metabolismo , Divisão Celular , Movimento Celular , Replicação do DNA , Evolução Molecular , Fatores de Transcrição/metabolismo
5.
PLoS One ; 15(4): e0231839, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32310978

RESUMO

Magnetotactic bacteria (MTB) are prokaryotes that sense the geomagnetic field lines to geolocate and navigate in aquatic sediments. They are polyphyletically distributed in several bacterial divisions but are mainly represented in the Proteobacteria. In this phylum, magnetotactic Deltaproteobacteria represent the most ancestral class of MTB. Like all MTB, they synthesize membrane-enclosed magnetic nanoparticles, called magnetosomes, for magnetic sensing. Magnetosome biogenesis is a complex process involving a specific set of genes that are conserved across MTB. Two of the most conserved genes are mamB and mamM, that encode for the magnetosome-associated proteins and are homologous to the cation diffusion facilitator (CDF) protein family. In magnetotactic Alphaproteobacteria MTB species, MamB and MamM proteins have been well characterized and play a central role in iron-transport required for biomineralization. However, their structural conservation and their role in more ancestral groups of MTB like the Deltaproteobacteria have not been established. Here we studied magnetite cluster MamB and MamM cytosolic C-terminal domain (CTD) structures from a phylogenetically distant magnetotactic Deltaproteobacteria species represented by BW-1 strain, which has the unique ability to biomineralize magnetite and greigite. We characterized them in solution, analyzed their crystal structures and compared them to those characterized in Alphaproteobacteria MTB species. We showed that despite the high phylogenetic distance, MamBBW-1 and MamMBW-1 CTDs share high structural similarity with known CDF-CTDs and will probably share a common function with the Alphaproteobacteria MamB and MamM.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Transporte/metabolismo , Cátions/metabolismo , Magnetossomos/metabolismo , Proteobactérias/metabolismo , Alphaproteobacteria/química , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Biomineralização , Proteínas de Transporte/química , Proteínas de Transporte/genética , Sequência Conservada , Deltaproteobacteria/química , Deltaproteobacteria/genética , Deltaproteobacteria/metabolismo , Transporte de Íons , Magnetossomos/química , Magnetossomos/genética , Modelos Moleculares , Filogenia , Conformação Proteica , Proteobactérias/química , Proteobactérias/genética , Alinhamento de Sequência
6.
FEMS Microbiol Lett ; 367(5)2020 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-32166327

RESUMO

Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.


Assuntos
Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Imidazóis/química , Metano/metabolismo , Oligopeptídeos/química , Oligopeptídeos/genética , Cobre/metabolismo , Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Oxirredução , Processamento de Proteína Pós-Traducional
7.
PLoS One ; 15(2): e0228936, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32084150

RESUMO

A total of fifteen potential methyl t-butyl ether (MtBE)-degrading bacterial strains were isolated from contaminated soil. They have been identified as belonging to the genera Bacillus, Pseudomonas, Kocuria, Janibacter, Starkeya, Bosea, Mycolicibacterium, and Rhodovarius. Bacillus aryabhattai R1B, S. novella R8b, and M. mucogenicum R8i were able to grow using MtBE as carbon source, exhibiting different growth behavior and contaminant degradation ability. Their biocontrol ability was tested against various fungal pathogens. Both S. novella R8b and B. aryabhattai were effective in reducing the development of necrotic areas on leaves within 48 hours from Botritys cinerea and Alternaria alternata inoculation. Whereas, M. mucogenicum effectively controlled B. cinerea after 72 hours. Similar results were achieved using Pythium ultimum, in which the application of isolated bacteria increased seed germination. Only M. mucogenicum elicited tomato plants resistance against B. cinerea. This is the first report describing the occurrence of bioremediation and biocontrol activities in M. mucogenicum, B. aryabhattai and S. novella species. The production of maculosin and its antibiotic activity against Rhizoctonia solani has been reported for first time from S. novella. Our results highlight the importance of multidisciplinary approaches to achieve a consistent selection of bacterial strains useful for plant protection and bioremediation purposes.


Assuntos
Bactérias/isolamento & purificação , Biodegradação Ambiental , Éteres Metílicos/toxicidade , Alphaproteobacteria/isolamento & purificação , Alphaproteobacteria/metabolismo , Bacillus/isolamento & purificação , Bacillus/metabolismo , Bactérias/metabolismo , Lycopersicon esculentum/microbiologia , Éteres Metílicos/química , Mycobacteriaceae/isolamento & purificação , Mycobacteriaceae/metabolismo , Doenças das Plantas/microbiologia , Rhizoctonia/crescimento & desenvolvimento , Solo , Microbiologia do Solo
8.
Appl Microbiol Biotechnol ; 104(5): 2067-2077, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31932896

RESUMO

Halohydrin dehalogenases (HHDHs) have attracted much attention due to their ability to synthesize enantiomerically enriched epoxides and ß-haloalcohols. However, most of the HHDHs exhibit low enantioselectivity. Here, a HHDH from the alphaproteobacteria isolate 46_93_T64 (AbHHDH), which shows only poor enantioselectivity in the catalytic resolution of rac-PGE (E = 9.9), has been subjected to protein engineering to enhance its enantioselectivity. Eight mutants (R89K, R89Y, V137I, P178A, N179Q, N179L, F187L, F187A) showed better enantioselectivity than the wild type. The best single mutant N179L (E = 93.0) showed a remarkable 9.4-fold increase in the enantioselectivity. Then, the single mutations were combined to produce the double, triple, quadruple, and quintuple mutants. Among the combinational mutants, the best variant (R89Y/N179L) showed an increased E value of up to 48. The E values of the variants N179L and R89Y/N179L for other epoxides 2-7 were 12.2 to > 200, which showed great improvement compared to 1.2 to 10.5 for the wild type. Using the variant N179L, enantiopure (R)-PGE with > 99% ee could be readily prepared, affording a high yield and a high concentration.


Assuntos
Proteínas de Bactérias/metabolismo , Compostos de Epóxi/química , Compostos de Epóxi/metabolismo , Hidrolases/metabolismo , Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Biocatálise , Hidrolases/química , Hidrolases/genética , Hidrolases/isolamento & purificação , Cinética , Modelos Moleculares , Mutação , Engenharia de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Estereoisomerismo , Especificidade por Substrato
9.
Antonie Van Leeuwenhoek ; 113(4): 477-489, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31741189

RESUMO

This study of lichens in the subarctic zone of the northern hemisphere has resulted in the detection of new representatives of the order Rhizobiales. The16S rRNA gene sequence phylogeny placed the strains as a separate branch inside the Rhizobiales clade. Strain RmlP001T exhibits 91.85% similarity to Roseiarcus fermentans strain Pf56T and 91.76% to Beijerinckia doebereinerae strain LMG 2819T, whilst strain RmlP026T is closely related to B. doebereinerae strain LMG 2819T (91.85%) and Microvirga pakistanensis strain NCCP-1258T (91.39%). A whole-genome phylogeny of the strains confirmed their taxonomic positions. The cells of both strains were observed to be Gram-negative, motile rods that multiplied by binary fission. The cells were found to contain poly-ß-hydroxybutyrate and polyphosphate, to grow at pH 3.5-8.0 and 10-30 °C, and could not fix atmospheric nitrogen. Their major cellular fatty acid identified was C18:1ω7c (68-71%) and their DNA G + C contents determined to be 70.5-70.8%. Beta-carotene was identified as their major carotenoid pigment; Q-10 was the only ubiquinone detected. Strains RmlP001T and RmlP026T are distinguishable from related species by the presence of ß-carotene, the absence of C1 metabolism and the ability to grow in the presence of 3.5% NaCl. Based on their phylogenetic, phenotypic and chemotaxonomic features, we propose a novel genus Lichenibacterium and two novel species, Lichenibacterium ramalinae (the type species of the genus) and Lichenibacterium minor, to accommodate these bacteria within the family Lichenibacteriaceae fam. nov. of the order Rhizobiales. The L. ramalinae type strain is RmlP001T (= KCTC 72076T = VKM B-3263T) and the L. minor type strain is RmlP026T (= KCTC 72077T = VKM B-3277T).


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/isolamento & purificação , Líquens/microbiologia , beta Caroteno/biossíntese , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , DNA Bacteriano/genética , Genoma Bacteriano , Filogenia , Reação em Cadeia da Polimerase , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Especificidade da Espécie
10.
Appl Biochem Biotechnol ; 190(2): 540-550, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31396886

RESUMO

Use of nanoparticles as carriers of anticancer drugs is a suitable way for targeted drug delivery and reduction of the side effects. This research focuses on a novel drug carrier for therapeutic goals by the bacterial magnetic nanoparticles (magnetosomes). The unique characteristics of magnetosomes make them ideal nanobiotechnological materials. In this study, magnetic nanoparticles of Alphaproteobacterium MTB-KTN90 were labeled with the radioisotope rhenium-188 and optimized the factors affecting the labeling efficiency. The results showed that the labeling efficiency of magnetosomes with rhenium-188 was more than 96%. The optimum concentration of bacterial nanoparticles was 133 mg/ml and the best time for maximum efficiency labeling was 60 min. The labeling stability showed that the 188Re-nanoparticle complexes have good stability in 29 h. The results of magnetic nanoparticles bacterial cytotoxicity on cancer cells AsPC1 did not show significant toxicity to concentration of 100 µg/µl. Finally, the biogenic magnetic nanoparticles labeled with rhenium-188 can be introduced as a valuable candidate for the targeted therapy of tumor with reducing radiation to surrounding healthy tissues.


Assuntos
Alphaproteobacteria/metabolismo , Magnetismo , Nanopartículas , Radioisótopos/química , Radioterapia/métodos , Rênio/química , Linhagem Celular Tumoral , Humanos
11.
N Biotechnol ; 56: 96-102, 2020 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-31881285

RESUMO

Marine sediments may represent a sink of persistent organic pollutants including polychlorinated biphenyls (PCBs), toxic compounds prone to reductive or oxidative biodegradation pathways depending on the degree of chlorination and the positions of the chlorine atoms on the biphenyl rings. Superficial marine sediments can be subjected to episodic sediment resuspension by boat traffic and wind action causing the exposure of the underlying anaerobic layer to oxygen. Under these dynamic conditions, a deeper knowledge of the adaptation capability of the autochthonous microbial communities towards severe changes of the reaction environment is required. Insights into the metabolic potential of sediment community members may contribute greatly to the definition of efficient and reliable in situ bioremediation strategies. In this study, an anaerobic PCB-dechlorinating microbial consortium, developed from the chronically polluted marine sediment of Mar Piccolo (Taranto, Italy), was used to evaluate the response of the sediment microbiome to the imposition of aerobic conditions after prolonged anaerobic incubation. Compared to the anaerobic control, a dramatic change in microbiome composition, with a marked increase of Alphaproteobacteria of up to 39.2 % of total operational taxonomic units (OTUs) was revealed by high-throughput 16S rRNA gene sequencing. Accordingly, a decrement of low chlorinated PCBs (up to 58.3 ±â€¯7.5 % for PCB 18) and the concomitant appearance of genes coding for PCB-degrading biphenyl dioxygenase (bph) were observed at the end of the aerobic incubation, suggesting the occurrence of oxidative PCB biodegradation processes.


Assuntos
Alphaproteobacteria/metabolismo , Oxigênio/metabolismo , Bifenilos Policlorados/metabolismo , Sedimentos Geológicos/microbiologia , Estresse Oxidativo , Microbiologia do Solo
12.
Sci Rep ; 9(1): 19401, 2019 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-31852991

RESUMO

The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.


Assuntos
Biodegradação Ambiental , Sedimentos Geológicos/microbiologia , Bactérias Fixadoras de Nitrogênio/metabolismo , Petróleo/toxicidade , Alphaproteobacteria/metabolismo , Praias , Florida , Gammaproteobacteria/metabolismo , Sedimentos Geológicos/química , Humanos , Louisiana , Nitrogênio/metabolismo , Fixação de Nitrogênio/efeitos dos fármacos , Poluição por Petróleo/efeitos adversos
13.
Appl Environ Microbiol ; 85(24)2019 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-31585988

RESUMO

A number of anaerobic ciliates, unicellular eukaryotes, intracellularly possess methanogenic archaea and bacteria as symbiotic partners. Although this tripartite relationship is of interest in terms of the fact that each participant is from a different domain, the difficulty in culture and maintenance of those host species with symbiotic partners has disturbed both ecological and functional studies so far. In this study, we obtained a stable culture of a small anaerobic scuticociliate, strain GW7. By transmission electron microscopic observation and fluorescent in situ hybridization with domain-specific probes, we demonstrate that GW7 possesses both archaeal and bacterial endosymbionts in its cytoplasm. These endosymbionts are in dependently associated with hydrogenosomes, which are organelle producing hydrogen and ATP under anaerobic conditions. Clone library analyses targeting prokaryotic 16S rRNA genes, fluorescent in situ hybridization with endosymbiont-specific probes, and molecular phylogenetic analyses revealed the phylogenetic affiliations and intracellular localizations of these endosymbionts. The endosymbiotic archaeon is a methanogen belonging to the genus Methanoregula (order Methanomicrobiales); a member of this genus has previously been described as the endosymbiont of an anaerobic ciliate from the genus Metopus (class Armophorea), which is only distantly related to strain GW7 (class Oligohymenophorea). The endosymbiotic bacterium belongs to the family Holosporaceae of the class Alphaproteobacteria, which also comprises several endosymbionts of various aerobic ciliates. For this endosymbiotic bacterium, we propose a novel candidate genus and species, "Candidatus Hydrogenosomobacter endosymbioticus."IMPORTANCE Tripartite symbioses between anaerobic ciliated protists and their intracellular archaeal and bacterial symbionts are not uncommon, but most reports have been based mainly on microscopic observations. Deeper insights into the function, ecology, and evolution of these fascinating symbioses involving partners from all three domains of life have been hampered by the difficulties of culturing anaerobic ciliates in the laboratory and the frequent loss of their prokaryotic partners during long-term cultivation. In the present study, we report the isolation of an anaerobic scuticociliate, strain GW7, which has been stably maintained in our laboratory for more than 3 years without losing either of its endosymbionts. Unexpectedly, molecular characterization of the endosymbionts revealed that the bacterial partner of GW7 is phylogenetically related to intranuclear endosymbionts of aerobic ciliates. This strain will enable future genomic, transcriptomic, and proteomic analyses of the interactions in this tripartite symbiosis and a comparison with endosymbioses in aerobic ciliates.


Assuntos
Alphaproteobacteria/metabolismo , Anaerobiose/fisiologia , Cilióforos/microbiologia , Euryarchaeota/metabolismo , Holosporaceae/fisiologia , Organelas/microbiologia , Simbiose , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Meios de Cultura/química , Euryarchaeota/classificação , Euryarchaeota/genética , Holosporaceae/classificação , Holosporaceae/genética , Hibridização in Situ Fluorescente , Filogenia , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação , Análise de Sequência de DNA
14.
J Mol Graph Model ; 92: 329-340, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31446203

RESUMO

Citrus greening (huanglongbing) is the most destructive disease of citrus worldwide caused by Candidatus Liberibacter asiaticus (CLA). Currently, no strategies have been developed to manage the Huanglongbing (HLB) disease and to stop the spreading of this disease to new citrus areas. Esbp is an extracellular solute-binding protein, involved in the uptake of iron in CLA. Thus, inhibiting this process may be a promising approach to design a drug against CLA. Thus, the present study focused on the identification of novel effective inhibitors which can inhibit the activity of CLas Esbp. A series of small molecules were screened against the CLas Esbp and the binding affinities were assessed using docking simulation studies. Top scored molecules were screened for different pharmacophore properties and Inhibitory Concentration 50 (IC50) values. Density functional theory was employed to check the chemical properties of the molecules. Further, Molecular Dynamics simulation analysis like RMSD, RMSF, Rg, SASA and MMPBSA results reveal that the identified molecules (ZINC03143779, ZINC05491830, ZINC19210425, ZINC08750867, and ZINC14671545) exhibit a good binding affinity for CLas Esbp and results in the formation of stable CLas Esbp-inhibitor(s) complex. The present study reported that these compounds appeared to be the suitable novel inhibitor of CLas Esbp and pave the way to further development of antimicrobial agents against CLA.


Assuntos
Alphaproteobacteria , Antibacterianos/química , Proteínas de Bactérias/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Alphaproteobacteria/metabolismo , Antibacterianos/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Sítios de Ligação , Conformação Molecular , Ligação Proteica , Eletricidade Estática
15.
Colloids Surf B Biointerfaces ; 183: 110435, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31430636

RESUMO

Recently, liposomes have been explored as a potential solution to improve the biocompatibility and the colloidal stability of magnetic nanoparticles. Protocols have been developed for producing magnetoliposomes of magnetite nanoparticles obtained inorganically (MNPs). However, the biomimetic synthesis of magnetite using heterologous proteins from magnetotactic bacteria has become a real alternative to produce novel biomimetic magnetic nanoparticles (BMNPs). Among these, the BMNPs obtained in presence of MamC protein from Magnetococcus marinus MC-1 have been proposed as excellent candidates to be potentially used as drug nanocarriers and as hyperthermia agents. However, their colloidal stability still needs to be improved while maintaining their magnetic properties intact. One possibility explored in this manuscript is to form magnetoliposomes that contain BMNPs. Indeed, the protocols developed for producing magnetoliposomes of MNPs need to be tested and modified to be able to include BMNPs. In this context, a protocol has been developed to produce both magnetoliposomes filled with MNPs and/or BMNPs and their potential as hyperthermia agents was tested. In fact, for the first time, these two types of nanoparticles were mixed in different proportions to test the composition that would optimize such as behaviour as hyperthermia agents. Interestingly, it was observed that the hyperthermia behaviour of the magnetoliposomes greatly improved if they were filled with a mixture of MNPs and BMNPs. These results indicate that these magnetoliposomes display optimal characteristics to become a potential agent for hyperthermia and that the opening of those liposomes could be externally controlled by applying an alternate magnetic field.


Assuntos
Materiais Biomiméticos/química , Hipertermia Induzida/métodos , Lipossomos/química , Magnetismo , Nanopartículas de Magnetita/química , Alphaproteobacteria/metabolismo , Proteínas de Bactérias/química , Materiais Biomiméticos/síntese química , Campos Magnéticos , Nanopartículas de Magnetita/ultraestrutura , Microscopia Eletrônica de Transmissão
16.
Environ Microbiol ; 21(11): 4092-4108, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31344308

RESUMO

The low temperature and elevated hydrostatic pressure in hadal trenches at water depths below 6000 m render sample collection difficult. Here, in situ hadal water microbial samples were collected from the Mariana Trench and analysed. The hadal microbial communities at different depths were revealed to be consistent and were dominated by heterotrophic Marinimicrobia. Thirty high-quality metagenome-assembled genomes (MAGs) were retrieved to represent the major hadal microbes affiliated with 12 prokaryotic phyla. Most of the MAGs were newly reported and probably derived from novel hadal inhabitants as exemplified by a potentially new candidate archaeal phylum in the DPANN superphylum. Metabolic reconstruction indicated that a great number of the MAGs participated in nitrogen and sulfur cycling, in which the nitrification process was driven sequentially by Thaumarchaeota and Nitrospirae and sulfur oxidization by Rhodospirillales in the Alphaproteobacteria class. Moreover, several groups of hadal microbes were revealed to be potential carbon monoxide oxidizers. Metatranscriptomic result highlighted the contribution of Chloroflexi in degrading recalcitrant dissolved organic matter and Marinimicrobia in extracellular protein decomposition. The present work provides an in-depth view on the hadal microbial communities regarding their endemism and element cycles.


Assuntos
Alphaproteobacteria/metabolismo , Archaea/metabolismo , Chloroflexi/metabolismo , Gammaproteobacteria/metabolismo , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Organismos Aquáticos/classificação , Organismos Aquáticos/genética , Organismos Aquáticos/metabolismo , Archaea/classificação , Archaea/genética , Chloroflexi/classificação , Chloroflexi/genética , Ecologia , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Processos Heterotróficos , Metagenoma , Microbiota/genética , Nitrificação/fisiologia , Oceano Pacífico
17.
Sci Total Environ ; 690: 739-747, 2019 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-31301512

RESUMO

The occurrence of pharmaceuticals in the environment is a topic of concern. Carbamazepine (CBZ) is a widespread antiepileptic drug and due to its physical-chemical characteristics minimal removal is achieved in conventional water treatments, and thus has been suggested as a molecular marker of wastewater contamination in surface water and groundwater. The present study reports the biotransformation of CBZ by the bacterial strain Labrys portucalensis F11. When supplied as a sole carbon source, a 95.4% biotransformation of 42.69 µM CBZ was achieved in 30 days. In co-metabolism with acetate, complete biotransformation was attained at a faster rate. Following a target approach, the detection and identification of 14 intermediary metabolites was achieved through UPLC-QTOF/MS/MS. Biotransformation of CBZ by the bacterial strain is mostly based on oxidation, loss of -CHNO group and ketone formation reactions; a biotransformation pathway with two routes is proposed. The toxicity of untreated and treated CBZ solutions was assessed using Vibrio Fischeri and Lepidium sativum acute toxicity tests and Toxi-Chromo Test. The presence of CBZ and/or its degradations products in solution resulted in moderate toxic effect on Vibrio Fischeri, whereas the other organisms were not affected. To the best of our knowledge this is the first report that proposes the metabolic degradation pathway of CBZ by a single bacterial strain.


Assuntos
Alphaproteobacteria/metabolismo , Biodegradação Ambiental , Carbamazepina/metabolismo , Poluentes Químicos da Água/metabolismo , Anticonvulsivantes/metabolismo
18.
Sci Rep ; 9(1): 8804, 2019 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-31217514

RESUMO

The role of magnetosome associated proteins on the in vitro synthesis of magnetite nanoparticles has gained interest, both to obtain a better understanding of the magnetosome biomineralization process and to be able to produce novel magnetosome-like biomimetic nanoparticles. Up to now, only one recombinant protein has been used at the time to in vitro form biomimetic magnetite precipitates, being that a scenario far enough from what probably occurs in the magnetosome. In the present study, both Mms6 and MamC from Magnetococcus marinus MC-1 have been used to in vitro form biomimetic magnetites. Our results show that MamC and Mms6 have different, but complementary, effects on in vitro magnetite nucleation and growth. MamC seems to control the kinetics of magnetite nucleation while Mms6 seems to preferably control the kinetics for crystal growth. Our results from the present study also indicate that it is possible to combine both proteins to tune the properties of the resulting biomimetic magnetites. In particular, by changing the relative ratio of these proteins, better faceted and/or larger magnetite crystals with, consequently, different magnetic moment per particle could be obtained. This study provides with tools to obtain new biomimetic nanoparticles with a potential utility for biotechnological applications.


Assuntos
Proteínas de Bactérias/metabolismo , Materiais Biomiméticos/química , Nanopartículas de Magnetita/química , Magnetossomos/química , Alphaproteobacteria/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Simulação por Computador , Nanopartículas de Magnetita/ultraestrutura , Magnetossomos/ultraestrutura
19.
Curr Issues Mol Biol ; 33: 117-132, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31166188

RESUMO

Paracoccus denitrificans Pd 1222 is a model methylotrophic bacterium. Its methylotrophy is based on autotrophic growth (enabled by the Calvin cycle) supported by energy from the oxidation of methanol or methylamine. The growing availability of genome sequence data has made it possible to investigate methylotrophy in other Paracoccus species. The examination of a large number of Paracoccus spp. genomes reveals great variability in C1 metabolism, which have been shaped by different evolutionary mechanisms. Surprisingly, the methylotrophy schemes of many Paracoccus strains appear to have quite different genetic and biochemical bases. Besides the expected 'autotrophic methylotrophs', many strains of this genus possess another C1 assimilatory pathway, the serine cycle, which seems to have at least three independent origins. Analysis of the co-occurrence of different methylotrophic pathways indicates, on the one hand, evolutionary linkage between the Calvin cycle and the serine cycle, and, on the other hand, that genes encoding some C1 substrate-oxidizing enzymes occur more frequently in association with one or the other. This suggests that some genetic module combinations form more harmonious enzymatic sets, which act with greater efficiency in the methylotrophic process and thus undergo positive selection.


Assuntos
Biodiversidade , Metanol/metabolismo , Paracoccus/genética , Paracoccus/metabolismo , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Evolução Biológica , Genoma Bacteriano , Redes e Vias Metabólicas/genética , Metilaminas/metabolismo , Oxirredução , Paracoccus/classificação
20.
Mol Microbiol ; 112(2): 438-441, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31120626

RESUMO

The general stress response (GSR) allows many bacterial species to react to myriad different stressors. In Alphaproteobacteria, this signaling pathway proceeds through the partner-switching PhyR-EcfG sigma-factor mechanism and is involved in multiple life processes, including virulence in Brucella abortus. To date, details of the alphaproteobacterial GSR signaling pathway have been determined using genetic and biochemical work on a diverse set of species distributed throughout the clade. Fiebig and co-workers establish Erythrobacter litoralis DSM 8509 as a genetically tractable lab strain and use it to both directly and indirectly delineate photoresponsive GSR pathways mediated by multiple HWE/HisKA_2 histidine kinases. The existence of a new phototrophic lab strain allows researchers to compare the GSR across different Alphaproteobacteria, as well as study the interplay between the GSR and phototrophy. Additionally, the discovery of new HWE/HisKA_2 kinases regulating the GSR poses new questions about how different stimuli feed into this widespread stress pathway.


Assuntos
Alphaproteobacteria/metabolismo , Alphaproteobacteria/efeitos da radiação , Proteínas de Bactérias/metabolismo , Fator sigma/metabolismo , Alphaproteobacteria/genética , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica/efeitos da radiação , Histidina Quinase/genética , Histidina Quinase/metabolismo , Luz , Fator sigma/genética , Transdução de Sinais/efeitos da radiação , Estresse Fisiológico
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