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1.
Glia ; 2020 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-33217041

RESUMO

The most frequent variant of multiple sclerosis (MS) is the relapsing-remitting form, characterized by symptomatic phases followed by periods of total/partial recovery. Hence, it is possible that these patients can benefit from endogenous agents that control the inflammatory process and favor spontaneous remyelination. In this context, there is increasing interest in the role of myeloid-derived suppressor cells (MDSCs) during the clinical course of experimental autoimmune encephalomyelitis (EAE). MDSCs speed up infiltrated T-cell anergy and apoptosis. In different animal models of MS, a milder disease course is related to higher presence/density of MDSCs in the periphery, and smaller demyelinated lesions in the central nervous system (CNS). These observations lead us to wonder whether MDSCs might not only exert an anti-inflammatory effect but might also have direct influence on oligodendrocyte precursor cells (OPCs) and remyelination. In the present work, we reveal for the first time the relationship between OPCs and MDSCs in EAE, relationship that is guided by the distance from the inflammatory core. We describe the effects of MDSCs on survival, proliferation, as well as potent promoters of OPC differentiation toward mature phenotypes. We show for the first time that osteopontin is remarkably present in the analyzed secretome of MDSCs. The ablation of this cue from MDSCs-secretome demonstrates that osteopontin is the main MDSC effector on these oligodendroglial cells. These data highlight a crucial pathogenic interaction between innate immunity and the CNS, opening ways to develop MDSC- and/or osteopontin-based therapies to promote effective myelin preservation and repair in MS patients.

2.
Foods ; 8(10)2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31557849

RESUMO

This work aimed to evaluate the contribution of isoflavones and melatonin to the aqueous extract obtained from the coffee silverskin (CSE) antiglycative properties, which has not been previously studied. To achieve this goal, two model systems constituted by bovine serum albumin (BSA) and reactive carbonyls (glucose or methylglyoxal) in the presence or absence of pure phytochemicals (chlorogenic acid (CGA), genistein, and melatonin) and CSE were employed. Glucose was used to evaluate the effect on the formation of glycation products formed mainly in the early stage of the reaction, while methylglyoxal was employed for looking at the formation of advanced products of the reaction, also called methylglyoxal-derivative advanced glycation end products (AGE) or glycoxidation products. CGA inhibited the formation of fructosamine, while genistein and melatonin inhibited the formation of advanced glycation end products and protein glycoxidation. It was also observed that phenolic compounds from CSE inhibited protein glycation and glycoxidation by forming BSA-phytochemical complexes. CSE showed a significant antiglycative effect (p < 0.05). Variations in the UV-Vis spectrum and the antioxidant capacity of protein fractions suggested the formation of protein-phytochemical complexes. Fluorescence quenching and in silico analysis supported the formation of antioxidant-protein complexes. For the first time, we illustrate that isoflavones and melatonin may contribute to the antiglycative/antiglycoxidative properties associated with CSE. CGA, isoflavones, and melatonin composing CSE seem to act simultaneously by different mechanisms of action.

3.
Nutrients ; 11(6)2019 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-31234581

RESUMO

The bioaccessibility, metabolism, and excretion of lipids composing spent coffee grounds (SCGs) were investigated. An analysis of mycotoxins and an acute toxicity study in rats were performed for safety evaluation. Total fat, fatty acids, and diterpenes (cafestol and kahweol) were determined in SCGs and their digests obtained in vitro. A pilot repeated intake study was carried out in Wistar rats using a dose of 1 g SCGs/kg b.w. for 28 days. Fat metabolism was evaluated by analysis of total fat, cholesterol, and histology in liver. The dietary fiber effect of SCGs was measured radiographically. The absence of mycotoxins and toxicity was reported in SCGs. A total of 77% of unsaturated fatty acids and low amounts of kahweol (7.09 µg/g) and cafestol (414.39 µg/g) were bioaccessible after in vitro digestion. A significantly lower (p < 0.1) accumulation of lipids in the liver and a higher excretion of these in feces was found in rats treated with SCGs for 28 days. No lipid droplets or liver damage were observed by histology. SCGs acutely accelerated intestinal motility in rats. SCGs might be considered a sustainable, safe, and healthy food ingredient with potential for preventing hepatic steatosis due to their effect as dietary fiber with a high fat-holding capacity.


Assuntos
Coffea/metabolismo , Diterpenos/metabolismo , Ácidos Graxos/metabolismo , Sementes/metabolismo , Animais , Disponibilidade Biológica , Biotransformação , Coffea/toxicidade , Diterpenos/administração & dosagem , Ácidos Graxos/administração & dosagem , Fezes/química , Feminino , Motilidade Gastrointestinal/efeitos dos fármacos , Eliminação Intestinal , Fígado/metabolismo , Masculino , Projetos Piloto , Ratos Wistar , Sementes/toxicidade , Fatores de Tempo
4.
Food Res Int ; 118: 72-80, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30898355

RESUMO

The aim of the present research was to study the formation of Maillard reaction products (MRPs) during digestive process of meal-resembling systems. An average meal (protein, starch and oil) and sugar-containing meals (protein and glucose or fructose or high fructose corn syrup (HCFS)) were tested. Intestinal simple amino acid systems were also analyzed to gain insight into their contribution to the Maillard reaction (MR). Decrease of lysine (11.7-34%), arginine (24-35%) and other amino acids occurred after digestion of the meals. Fructosamine (42.6±4.7 and 332.9±10.4µg/ml) and fluorescent adducts (22,270±119.6 and 9283±188.3 RFU) were detected in digests of those meals containing HCFS and starch, respectively. Carboxymethyllysine (CML) (5.03±1.09µg/ml) and MGO-derivative AGEs (12.2±1.5µg/ml) were found in the meals composed of fructose and only MGO-derivative AGEs (12.2±1.6µg/ml) in presence of glucose. Physiological intestinal concentrations (43mM) of sugars in simplified systems composed by single amino acids caused formation of MRPs under digestive conditions. Arginine and fructose (314mM) showed formation of fructosamine and different AGEs. Fructose (43mM) gave rise to CML by interaction with lysine, which was observed within 1h of incubation at intestinal conditions. These conditions are possible in the intestine during fructose malabsorption. The results suggest the importance of using meal systems for better understanding of complex chemical events taking place during digestion such as MR. This is the first study proposing the formation of non-fluorescent AGEs associated to the pathogenesis of diabetes during digestion of sugar containing and average meals. This formation may be possible in conditions where sugar absorption is delayed such as fructose malabsorption or intake of a fatty meal. The occurrence of the MR during the digestion process may reduce the bioavailability of essential amino acids and increase the production of MRPs causing health disorders.


Assuntos
Digestão , Reação de Maillard , Refeições , Aminoácidos/análise , Arginina/química , Disponibilidade Biológica , Carboidratos/química , Frutosamina/química , Frutose/química , Glucose/química , Intestinos/fisiologia , Lisina/análogos & derivados , Lisina/química , Síndromes de Malabsorção , Proteínas/química , Amido/química , Açúcares/química
5.
Sci Rep ; 9(1): 1042, 2019 01 31.
Artigo em Inglês | MEDLINE | ID: mdl-30705356

RESUMO

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.


Assuntos
Bactérias/genética , Pradaria , Microbiota/genética , Plantas/microbiologia , Solo , Bactérias/classificação , Chile , Geografia , Filogenia , Rizosfera , Microbiologia do Solo
6.
ISME J ; 13(2): 316-333, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30228379

RESUMO

Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.


Assuntos
Bactérias/isolamento & purificação , Aquecimento Global , Camada de Gelo/microbiologia , Actinobacteria/isolamento & purificação , Alphaproteobacteria/isolamento & purificação , Regiões Antárticas , Regiões Árticas , Bactérias/classificação , Ecossistema , Flavobacteriaceae/isolamento & purificação , Gammaproteobacteria/isolamento & purificação , Salinidade , Estações do Ano , Água do Mar/microbiologia
7.
Sci Rep ; 8(1): 5875, 2018 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-29651160

RESUMO

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.


Assuntos
Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos/genética , Ecologia , Microbiota/fisiologia , Archaea/crescimento & desenvolvimento , Microbiota/genética , RNA Ribossômico 16S , Microbiologia do Solo , Estresse Fisiológico/genética , Estresse Fisiológico/fisiologia
8.
Sci Data ; 4: 170093, 2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28763055

RESUMO

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.


Assuntos
Plâncton , Vírus , Ecossistema , Genômica , Nucleotídeos , Oceanos e Mares
9.
Food Chem ; 197(Pt A): 14-23, 2016 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-26616919

RESUMO

The antiglycoxidative properties of theanine (TEF) and polyphenols enriched fractions (PEF) prepared from tea dust were tested in a model system composed of bovine serum albumin (BSA) and methylglyoxal (MGO). PEF caused a decrease in available free amino groups of BSA in presence and absence of MGO, suggesting the simultaneous occurrence of glycoxidation reaction and phenols-protein interaction. The presence of PEF and TEF inhibited formation of fluorescent advanced glycation end-products (AGEs). Moreover, theanine (TB) and polyphenol-enriched bread (PB) were formulated. A significant increase in free amino groups was observed in TBs with a dose-response effect, while addition of PEF in bread produced a significant decrease (p<0.05). PEF efficiently reduced fluorescent AGE formation in breads compared with TEF. The results are in line with the simplified model systems. PEF used as food ingredient allows obtaining a tasty food possessing health promoting properties and lower content of potential harmful compounds (AGEs).


Assuntos
Pão/análise , Poeira , Glutamatos/química , Produtos Finais de Glicação Avançada/análise , Polifenóis/química , Chá/química , Cafeína , Glutamatos/isolamento & purificação , Humanos , Reação de Maillard , Fenóis , Polifenóis/isolamento & purificação , Aldeído Pirúvico/química , Soroalbumina Bovina/química
10.
Food Funct ; 6(7): 2405, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26065645

RESUMO

Correction for 'New knowledge on the antiglycoxidative mechanism of chlorogenic acid' by Beatriz Fernandez-Gomez et al., Food Funct., 2015, DOI: 10.1039/c5fo00194c.

11.
Food Funct ; 6(6): 2081-90, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-26037734

RESUMO

The role of chlorogenic acid (CGA) in the formation of advanced glycation end-products (AGEs) (glycoxidation reaction) was studied. Model systems composed of bovine serum albumin (BSA) (1 mg mL(-1)) and methylglyoxal (5 mM) under mimicked physiological conditions (pH 7.4, 37 °C) were used to evaluate the antiglycoxidative effect of CGA (10 mM). The stability of CGA under reaction conditions was assayed by HPLC and MALDI-TOF MS. The glycoxidation reaction was estimated by analysis of free amino groups by the OPA assay, spectral analysis of fluorescent AGEs and total AGEs by ELISA, and colour formation by absorbance at 420 nm. Structural changes in protein were evaluated by analysis of phenol bound to the protein backbone using the Folin reaction, UV-Vis spectral analysis and MALDI-TOF-MS, while changes in protein function were measured by determining the antioxidant capacity using the ABTS radical cation decolourisation assay. CGA was isomerised and oxidised under our experimental conditions. Evidence of binding between BSA and multiple CGA and/or its derivative molecules (isomers and oxidation products) was found. CGA inhibited (p < 0.05) the formation of fluorescent and total AGEs at 72 h of reaction by 91.2 and 69.7%, respectively. The binding of phenols to BSA significantly increased (p < 0.001) its antioxidant capacity. Correlations between free amino group content, phenol bound to protein and antioxidant capacity were found. Results indicate that CGA simultaneously inhibits the formation of potentially harmful compounds (AGEs) and promotes the generation of neoantioxidant structures.


Assuntos
Ácido Clorogênico/metabolismo , Alimento Funcional/análise , Produtos Finais de Glicação Avançada/antagonistas & inibidores , Modelos Biológicos , Animais , Antioxidantes/química , Antioxidantes/metabolismo , Ácido Clorogênico/análogos & derivados , Ácido Clorogênico/química , Cromatografia Líquida de Alta Pressão , Produtos Finais de Glicação Avançada/química , Produtos Finais de Glicação Avançada/metabolismo , Glicosilação , Humanos , Indicadores e Reagentes/química , Indicadores e Reagentes/metabolismo , Cinética , Estrutura Molecular , Oxirredução , Conformação Proteica , Aldeído Pirúvico/química , Aldeído Pirúvico/metabolismo , Soroalbumina Bovina/química , Soroalbumina Bovina/metabolismo , Espectrometria de Fluorescência , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
12.
Microbiologyopen ; 2(4): 541-52, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23723056

RESUMO

Free-living (FL) and particle-attached (PA) bacterial assemblages in the Northwest Mediterranean Sea were studied using pyrosequencing data of the 16S rRNA. We have described and compared the richness, the distribution of Operational Taxonomic Units (OTUs) within the two fractions, the spatial distribution, and the taxonomic composition of FL and PA bacterial assemblages. The number of OTUs in the present work was two orders of magnitude higher than in previous studies. Only 25% of the total OTUs were common to both fractions, whereas 49% OTUs were exclusive to the PA fraction and 26% to the FL fraction. The OTUs exclusively present in PA or FL assemblages were very low in abundance (6% of total abundance). Detection of the rare OTUs revealed the larger richness of PA bacteria that was hidden in previous studies. Alpha-Proteobacteria dominated the FL bacterial assemblage and gamma-Proteobacteria dominated the PA fraction. Bacteroidetes were important in the PA fraction mainly at the coast. The high number of sequences in this study detected additional phyla from the PA fraction, such as Actinobacteria, Firmicutes, and Verrucomicrobia.


Assuntos
Bactérias/classificação , Bactérias/genética , Biota , Água do Mar/microbiologia , Aderência Bacteriana , Fenômenos Fisiológicos Bacterianos , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Mar Mediterrâneo , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
13.
ISME J ; 7(5): 1026-37, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23303374

RESUMO

Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.


Assuntos
Bacteroidetes/classificação , Bacteroidetes/fisiologia , Genômica/métodos , Água do Mar/microbiologia , Aderência Bacteriana , Bacteroidetes/enzimologia , Bacteroidetes/genética , Ecologia , Genoma Bacteriano , Glicosiltransferases/genética , Glicosiltransferases/metabolismo , Locomoção , Dados de Sequência Molecular
14.
Gen Comp Endocrinol ; 182: 24-40, 2013 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-23220040

RESUMO

In mammals, downstream function of the nuclear progestin receptor (PGR) can be differentially regulated in each target tissue by altering the expression levels of PGR mRNA variants. Such PGR isoforms have also been identified in birds and reptiles, but not in non-amniote vertebrates. Based upon extensive phylogenetic, syntenic and functional analyses, here we show that higher orders of Teleostei retain a single pgr gene, and that four different pgr transcript variants of the extant gene are expressed in the ovary of an evolutionary advanced perciform teleost, the gilthead seabream (Sparus aurata). Three of the isoforms (pgr_tv2, pgr_tv3 and pgr_tv4) arise from alternative pre-mRNA splicing resulting in different N-terminally truncated receptors, whereas one isoform (pgr_tv1) is a deletion variant. Seabream wild-type Pgr shows the highest transactivational response to native euteleostean progestins, 17α,20ß-dihydroxy-4-pregnen-3-one and 17α,20ß,21-trihydroxy-4-pregnen-3-one, whereas the Pgr_tv3 and Pgr_tv4 isoforms independently regulate novel nuclear and cytosolic mechanisms of dominant-negative repression of Pgr-mediated transcription. In the seabream ovary, the wild-type Pgr protein is localized in oogonia, in the nuclei of primary (previtellogenic) oocytes, as well as in follicular (granulosa) cells and the oocyte cytoplasm of early and late vitellogenic ovarian follicles. Expression of wild-type pgr, pgr_tv3 and pgr_tv4 was the highest in seabream primary ovaries, while expression of both inhibitory receptor isoforms, but not of pgr, decreased during vitellogenesis. Stimulation of primary ovarian explants in vitro with recombinant piscine follicle-stimulating hormone and estrogen differentially regulated the temporal expression of pgr, pgr_tv3 and pgr_tv4. These findings suggest that, as in mammals, ovarian progestin responsiveness in the seabream, particularly during early oogenesis, may be regulated through alternative splicing of the nuclear pgr mRNA. Thus, the dominant-negative mechanism of PGR transcriptional regulation likely evolved prior to the separation of Actinopterygii (ray-finned fishes) from Sarcopterygii (lobe-finned fishes).


Assuntos
Processamento Alternativo/fisiologia , Isoformas de Proteínas/metabolismo , Receptores de Progesterona/metabolismo , Dourada/metabolismo , Processamento Alternativo/genética , Animais , Estradiol/metabolismo , Feminino , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Hormônio Foliculoestimulante/metabolismo , Regulação da Expressão Gênica/genética , Regulação da Expressão Gênica/fisiologia , Ovário/metabolismo , Isoformas de Proteínas/genética , Receptores de Progesterona/genética , Dourada/genética
15.
BMC Genomics ; 13: 347, 2012 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-22839777

RESUMO

BACKGROUND: Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance. RESULTS: We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the ß-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome. CONCLUSIONS: Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction.


Assuntos
Bactérias/genética , Transferência Genética Horizontal , Genoma Bacteriano , Ilhas Genômicas , Organismos Aquáticos/genética , Bases de Dados Genéticas , Anotação de Sequência Molecular , Filogenia , Microbiologia da Água
16.
Appl Environ Microbiol ; 77(24): 8676-86, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22003006

RESUMO

Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. strain MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases, suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia sp. MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyle.


Assuntos
Flavobacteriaceae/crescimento & desenvolvimento , Flavobacteriaceae/genética , Genoma Bacteriano , Processos Fototróficos , Rodopsina/metabolismo , Carbono/metabolismo , Flavobacteriaceae/metabolismo , Luz , Compostos Orgânicos/metabolismo , Regiões Promotoras Genéticas , Rodopsinas Microbianas
17.
Stand Genomic Sci ; 5(3): 269-78, 2011 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-22675578

RESUMO

Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain is of interest because it is one of the first known isolates from a globally ubiquitous clade of marine bacteria known as SAR116 within the family Rhodospirillaceae. Here we describe preliminary features of the organism, together with the draft genome sequence and annotation. This is the second genome sequence of a member of the SAR116 clade. The 2,458,945 bp genome contains 2,334 protein-coding and 42 RNA genes.

18.
Proc Natl Acad Sci U S A ; 105(25): 8724-9, 2008 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-18552178

RESUMO

Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO(2) fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.


Assuntos
Flavobacteriaceae/genética , Genoma Bacteriano , Rodopsina/genética , Água do Mar/microbiologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Dióxido de Carbono/metabolismo , Flavobacteriaceae/metabolismo , Genes Bacterianos , Modelos Biológicos , Rodopsina/metabolismo , Rodopsinas Microbianas
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